Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001025.1 Hibiscus syriacus cultivar Beakdansim tig00002042_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: 318342
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:275 original size:13 final size:13
Alignment explanation
Indices: 253--282 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
243 ACTAAACACC
253 TTTC-ACATACCT
1 TTTCAACATACCT
265 TTTCAACATACCT
1 TTTCAACATACCT
278 TTTCA
1 TTTCA
283 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:3293 original size:20 final size:21
Alignment explanation
Indices: 3270--3313 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
3260 TTCTTTTCTT
*
3270 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
3290 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
3309 TGCTT
1 TGCTT
3314 CTTTTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:4678 original size:22 final size:20
Alignment explanation
Indices: 4653--4692 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4643 ATGTTTGTTT
4653 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
4675 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
4693 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:5664 original size:36 final size:36
Alignment explanation
Indices: 5584--5664 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
5574 TGGCATGAAA
*
5584 GTGATGGAATATGGTGATGATATAGACGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
*
5620 GTGATGGACTATGGTGATGATATAGGCGTGATAATG
1 GTGATGGACTATGGTGATGATATAGACGTGATAATG
5656 GTGATGGAC
1 GTGATGGAC
5665 AGATTGTATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
GTGATGGACTATGGTGATGATATAGACGTGATAATG
Found at i:6053 original size:19 final size:20
Alignment explanation
Indices: 6006--6056 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5996 GAAACCCCTT
**
6006 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
6026 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
6045 TGAAGATACATG
1 TGAAAATACATG
6057 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:14279 original size:28 final size:26
Alignment explanation
Indices: 14231--14296 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
14221 TTTCTTTTCT
*
14231 TTTC-TTCTTTTTTTAAGTGCTGGAA
1 TTTCTTTCTTTTTTTAAGTGCTGCAA
* *
14256 TTTCTTTCTTTATTTTGGAGTGCTTCAA
1 TTTCTTTCTTT-TTTT-AAGTGCTGCAA
14284 TTTCTTT-TTTTTT
1 TTTCTTTCTTTTTT
14297 CTGATTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 4 0.11
26 9 0.26
27 7 0.20
28 15 0.43
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (26 bp):
TTTCTTTCTTTTTTTAAGTGCTGCAA
Found at i:33727 original size:18 final size:19
Alignment explanation
Indices: 33689--33727 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
33679 AAGGAAAAAG
*
33689 AAGCACTCAAAAAGATTGA
1 AAGCACTCAAAAAGATAGA
33708 AAGCACTCAAAAAGA-AGA
1 AAGCACTCAAAAAGATAGA
33726 AA
1 AA
33728 AAAGCAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGCACTCAAAAAGATAGA
Found at i:46601 original size:8 final size:8
Alignment explanation
Indices: 46590--46614 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
46580 TCTTTTTCTT
46590 TTCTTTTC
1 TTCTTTTC
46598 TTCTTTTC
1 TTCTTTTC
46606 TTCTTTTC
1 TTCTTTTC
46614 T
1 T
46615 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:47375 original size:19 final size:21
Alignment explanation
Indices: 47332--47383 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
47322 GAAACCCCTT
47332 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
47353 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
47372 TGAAGATACATG
1 TGAAAATACATG
47384 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:52584 original size:22 final size:21
Alignment explanation
Indices: 52558--52599 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
52548 GGCTGTGGAA
52558 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
52580 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
52600 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:54010 original size:35 final size:36
Alignment explanation
Indices: 53971--54055 Score: 138
Period size: 35 Copynumber: 2.4 Consensus size: 36
53961 AAATGGAATT
**
53971 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
54006 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
54042 TGGTGATGA-ATAGG
1 TGGTGATGATATAGG
54056 TTGTATCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 26 0.55
36 21 0.45
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAAA
Found at i:54284 original size:19 final size:19
Alignment explanation
Indices: 54262--54308 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
54252 TAAAGAGAGA
*
54262 ATAATATTACAAAGGATTT
1 ATAATATCACAAAGGATTT
54281 ATAATATCACAAAGGATTT
1 ATAATATCACAAAGGATTT
54300 ATAATATCA
1 ATAATATCA
54309 AAGGGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (19 bp):
ATAATATCACAAAGGATTT
Found at i:57010 original size:17 final size:17
Alignment explanation
Indices: 56988--57033 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
56978 AGAAAAGACA
56988 AAAAGAAGAAAATTCAG
1 AAAAGAAGAAAATTCAG
57005 AAAAGAAGAAAATTCAG
1 AAAAGAAGAAAATTCAG
57022 AAAAGAAGAAAA
1 AAAAGAAGAAAA
57034 AGAAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (17 bp):
AAAAGAAGAAAATTCAG
Found at i:57034 original size:26 final size:25
Alignment explanation
Indices: 57005--57058 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
56995 GAAAATTCAG
57005 AAAAGAAGAAA-A-TTCAGAAAAGAAGA
1 AAAAGAA-AAAGATTTCA-AAAAG-AGA
57031 AAAAGAAAAAGATTTCAAAAAGAGA
1 AAAAGAAAAAGATTTCAAAAAGAGA
57056 AAA
1 AAA
57059 GCAAGCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 9 0.35
26 13 0.50
27 4 0.15
ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09
Consensus pattern (25 bp):
AAAAGAAAAAGATTTCAAAAAGAGA
Found at i:64333 original size:20 final size:20
Alignment explanation
Indices: 64308--64352 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
64298 TGATGTATGA
*
64308 TTTTTTTTCTTTTCTTTTTG-
1 TTTTTTTTC-TTTCTTGTTGC
64328 TTTTTTTTCTTTCTTGTTGC
1 TTTTTTTTCTTTCTTGTTGC
64348 TTTTT
1 TTTTT
64353 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (20 bp):
TTTTTTTTCTTTCTTGTTGC
Found at i:64335 original size:15 final size:15
Alignment explanation
Indices: 64308--64351 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
64298 TGATGTATGA
64308 TTTTT-TTTCTTTTC
1 TTTTTGTTTCTTTTC
*
64322 TTTTTGTTTTTTTTC
1 TTTTTGTTTCTTTTC
*
64337 TTTCTTGTTGCTTTT
1 TTT-TTGTTTCTTTT
64352 TGTTGTAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.20
15 11 0.44
16 9 0.36
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (15 bp):
TTTTTGTTTCTTTTC
Found at i:67076 original size:23 final size:24
Alignment explanation
Indices: 67048--67101 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
67038 AAAATCAGCA
67048 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
67071 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
67095 AAGAAAA
1 AAGAAAA
67102 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:67106 original size:24 final size:23
Alignment explanation
Indices: 67048--67107 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
67038 AAAATCAGCA
67048 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
67071 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
67095 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
67108 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:69887 original size:11 final size:13
Alignment explanation
Indices: 69855--69884 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
69845 TGGCCAAAGA
69855 TGAAAAGGTATGT
1 TGAAAAGGTATGT
69868 TGAAAAGGTATG-
1 TGAAAAGGTATGT
69880 TGAAA
1 TGAAA
69885 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:71418 original size:27 final size:27
Alignment explanation
Indices: 71378--71429 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
71368 CCTTGGCTTG
* *
71378 CTTTCTTTTTTACTTTTATTTTTTTTT
1 CTTTCTTTTTTACTCTAATTTTTTTTT
71405 CTTT-TTTTTGTACTCTAATTTTTTT
1 CTTTCTTTTT-TACTCTAATTTTTTT
71430 GAAGGAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.77
Consensus pattern (27 bp):
CTTTCTTTTTTACTCTAATTTTTTTTT
Found at i:72085 original size:19 final size:20
Alignment explanation
Indices: 72038--72088 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
72028 GAAACCCCTT
**
72038 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
72058 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
72077 TGAAGATACATG
1 TGAAAATACATG
72089 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:81562 original size:21 final size:20
Alignment explanation
Indices: 81523--81560 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
81513 AAATTTTGGC
81523 TTTTTTGGCTTTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGT
81543 TTTTTTGGCTTTTTTTTT
1 TTTTTTGGCTTTTTTTTT
81561 TGAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (20 bp):
TTTTTTGGCTTTTTTTTTGT
Found at i:98448 original size:13 final size:12
Alignment explanation
Indices: 98426--98473 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
98416 TCAACATCAA
98426 TCATCATCAACT
1 TCATCATCAACT
**
98438 TCATCCATCAAGA
1 TCAT-CATCAACT
*
98451 CCATCATCAACT
1 TCATCATCAACT
98463 TCATCCATCAA
1 TCAT-CATCAA
98474 GACCATCATC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.27
Consensus pattern (12 bp):
TCATCATCAACT
Found at i:98460 original size:25 final size:25
Alignment explanation
Indices: 98427--98489 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
98417 CAACATCAAT
98427 CATCATCAACTTCATCCATCAAGAC
1 CATCATCAACTTCATCCATCAAGAC
98452 CATCATCAACTTCATCCATCAAGAC
1 CATCATCAACTTCATCCATCAAGAC
*
98477 CATCATCATCTTC
1 CATCATCAACTTC
98490 CTAATTCCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (25 bp):
CATCATCAACTTCATCCATCAAGAC
Found at i:115356 original size:33 final size:33
Alignment explanation
Indices: 115314--115382 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
115304 GTTGATGAAT
*
115314 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
115347 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
115380 GAA
1 GAA
115383 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:115423 original size:36 final size:36
Alignment explanation
Indices: 115353--115454 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
115343 AATGGAAGGA
* * *
115353 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
*
115388 TGATGATATAGGCGTGATAATGGTGACGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
115424 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
115455 AGATTGTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 16 0.26
36 45 0.74
ACGTcount: A:0.26, C:0.06, G:0.36, T:0.31
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:122377 original size:22 final size:23
Alignment explanation
Indices: 122352--122408 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
122342 AACAAGCATT
*
122352 ATTCGGCCAAT-CATAATGGAAC
1 ATTCGGCCAATGCACAATGGAAC
*
122374 ATTCGGCC-ATGCACAATGTAAC
1 ATTCGGCCAATGCACAATGGAAC
*
122396 ATACGGCC-ATGCA
1 ATTCGGCCAATGCA
122409 TGTTCAAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
ATTCGGCCAATGCACAATGGAAC
Found at i:125399 original size:19 final size:21
Alignment explanation
Indices: 125375--125426 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
125365 TCGCCAAGAG
*
125375 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
125394 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
*
125415 TATGTATTTTCA
1 CATGTATTTTCA
125427 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 6 0.21
21 12 0.41
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:126166 original size:19 final size:19
Alignment explanation
Indices: 126133--126195 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
126123 AAATTGGAGT
126133 ACAAAAAG-A-AAGAAAAG
1 ACAAAAAGAAGAAGAAAAG
126150 ACAAAAAGAAGAAGAAAAG
1 ACAAAAAGAAGAAGAAAAG
*
126169 AAGAAAAAGAAAAGAAGAAAAG
1 -ACAAAAAG--AAGAAGAAAAG
126191 A-AAAA
1 ACAAAA
126196 GAAATTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 1 0.03
19 8 0.20
20 11 0.28
21 1 0.03
22 11 0.28
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
ACAAAAAGAAGAAGAAAAG
Found at i:126167 original size:11 final size:11
Alignment explanation
Indices: 126153--126199 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
126143 AGAAAAGACA
126153 AAAAGAAGAAG
1 AAAAGAAGAAG
126164 AAAAGAAGAA-
1 AAAAGAAGAAG
*
126174 AAAGAAAAGAAG
1 AAA-AGAAGAAG
*
126186 AAAAGAAAAAG
1 AAAAGAAGAAG
126197 AAA
1 AAA
126200 TTCAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 3 0.10
11 25 0.81
12 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:126169 original size:8 final size:8
Alignment explanation
Indices: 126158--126192 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
126148 AGACAAAAAG
126158 AAGAAGAA
1 AAGAAGAA
126166 AAGAAG-A
1 AAGAAGAA
126173 AA-AAGAA
1 AAGAAGAA
126180 AAGAAGAA
1 AAGAAGAA
126188 AAGAA
1 AAGAA
126193 AAAGAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 6 0.24
8 16 0.64
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:126172 original size:14 final size:13
Alignment explanation
Indices: 126136--126194 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 13
126126 TTGGAGTACA
126136 AAAAGAAAGAAAAG
1 AAAAG-AAGAAAAG
126150 ACAAA-AAGAAGAAG
1 A-AAAGAAGAA-AAG
126164 AAAAGAAGAAAAAG
1 AAAAGAAG-AAAAG
126178 AAAAGAAGAAAAG
1 AAAAGAAGAAAAG
126191 AAAA
1 AAAA
126195 AGAAATTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
13 17 0.41
14 19 0.46
15 5 0.12
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAG
Found at i:126195 original size:28 final size:29
Alignment explanation
Indices: 126135--126199 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
126125 ATTGGAGTAC
126135 AAAAAGAAAGAAAAGACAAAAAGAAGAAG
1 AAAAAGAAAGAAAAGACAAAAAGAAGAAG
126164 -AAAAG-AAGAAAAAGA-AAAGAAGAA-AAG
1 AAAAAGAAAG-AAAAGACAAA-AAGAAGAAG
126191 AAAAAGAAA
1 AAAAAGAAA
126200 TTCAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
27 9 0.28
28 21 0.66
29 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGACAAAAAGAAGAAG
Found at i:126196 original size:19 final size:19
Alignment explanation
Indices: 126136--126199 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
126126 TTGGAGTACA
126136 AAAAGAAAGAAAAGACAAAAAG
1 AAAAG-AAGAAAAG--AAAAAG
126158 AAGAAGAA-AAGAAGAAAAAG
1 AA-AAGAAGAA-AAGAAAAAG
126178 AAAAGAAGAAAAGAAAAAG
1 AAAAGAAGAAAAGAAAAAG
126197 AAA
1 AAA
126200 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.44
20 10 0.26
21 2 0.05
22 7 0.18
23 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAAGAAAAAG
Found at i:126425 original size:17 final size:18
Alignment explanation
Indices: 126403--126437 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
126393 ACCTTTAAAT
*
126403 CATTTCTTTTA-TCTTTC
1 CATTTCTTATATTCTTTC
126420 CATTTCTTATATTCTTTC
1 CATTTCTTATATTCTTTC
126438 TACCCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (18 bp):
CATTTCTTATATTCTTTC
Found at i:129338 original size:19 final size:21
Alignment explanation
Indices: 129314--129365 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
129304 CGTCCAAGAG
*
129314 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
129333 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
129354 CATGTATTTTCA
1 CATGTATTTTCA
129366 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:130755 original size:19 final size:21
Alignment explanation
Indices: 130712--130763 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
130702 GAAACCCCTT
130712 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
130733 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
130752 TGAATATACATG
1 TGAAAATACATG
130764 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:131686 original size:30 final size:31
Alignment explanation
Indices: 131647--131706 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
131637 ACATTCTGCC
131647 ATGATATCTAAATG-ATATGTAAACATAATAA
1 ATGATATCTAAA-GCATATGTAAACATAATAA
131678 ATGA-ATCTAAAGCATATGTAAACATAATA
1 ATGATATCTAAAGCATATGTAAACATAATA
131707 TAAAGCAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 1 0.04
30 23 0.82
31 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAAGCATATGTAAACATAATAA
Found at i:131693 original size:20 final size:20
Alignment explanation
Indices: 131655--131693 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
131645 CCATGATATC
*
131655 TAAATGATATGTAAACATAA
1 TAAATGATATCTAAACATAA
131675 TAAATGA-ATCTAAAGCATA
1 TAAATGATATCTAAA-CATA
131694 TGTAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (20 bp):
TAAATGATATCTAAACATAA
Found at i:134477 original size:19 final size:20
Alignment explanation
Indices: 134441--134480 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
134431 GAATAATAAT
134441 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
134461 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
134480 A
1 A
134481 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:135860 original size:30 final size:31
Alignment explanation
Indices: 135821--135880 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
135811 ACATGCTGCC
**
135821 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
135852 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
135881 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:151816 original size:15 final size:15
Alignment explanation
Indices: 151796--151828 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
151786 GTAAAAACAG
151796 TAAATAA-AAGATAAA
1 TAAATAAGAAGA-AAA
151811 TAAATAAGAAGAAAA
1 TAAATAAGAAGAAAA
151826 TAA
1 TAA
151829 TCCTCACGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAATAAGAAGAAAA
Found at i:153869 original size:28 final size:27
Alignment explanation
Indices: 153825--153889 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
153815 TTTCTTTGCT
* *
153825 TTTCTTTTTTTTAAGTG-TTGGAATTTC
1 TTTCTTTTTTTGAAGTGCTT-CAATTTC
*
153852 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTCTTT-TTTTGAAGTGCTTCAATTTC
153880 TTT-TTTTTTT
1 TTTCTTTTTTT
153890 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 4 0.12
27 10 0.30
28 17 0.52
29 2 0.06
ACGTcount: A:0.11, C:0.11, G:0.12, T:0.66
Consensus pattern (27 bp):
TTTCTTTTTTTGAAGTGCTTCAATTTC
Found at i:153892 original size:11 final size:12
Alignment explanation
Indices: 153876--153905 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
153866 AGTGCTTCAA
153876 TTTCTTTTT-TT
1 TTTCTTTTTCTT
153887 TTTCTTTTTCTT
1 TTTCTTTTTCTT
153899 TTTCTTT
1 TTTCTTT
153906 GACTTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:153894 original size:6 final size:6
Alignment explanation
Indices: 153876--153905 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
153866 AGTGCTTCAA
153876 TTTCTT TTT-TT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
153906 GACTTTGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTCTT
Found at i:158051 original size:23 final size:24
Alignment explanation
Indices: 158005--158051 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
157995 AGAAAAAAGG
***
158005 CACTCAAAAAGAAGAAATTGAAAA
1 CACTCAAAAAGAAGAAAAAAAAAA
158029 CACTC-AAAAGAAGAAAAAAAAAA
1 CACTCAAAAAGAAGAAAAAAAAAA
158052 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.09
Consensus pattern (24 bp):
CACTCAAAAAGAAGAAAAAAAAAA
Found at i:160831 original size:11 final size:13
Alignment explanation
Indices: 160799--160828 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
160789 TGGCCAAAGA
160799 TGAAAAGGTATGT
1 TGAAAAGGTATGT
160812 TGAAAAGGTATG-
1 TGAAAAGGTATGT
160824 TGAAA
1 TGAAA
160829 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:165712 original size:19 final size:21
Alignment explanation
Indices: 165669--165720 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
165659 GAAACCCCTT
165669 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
165690 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
165709 TGAATATACATG
1 TGAAAATACATG
165721 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:169914 original size:21 final size:20
Alignment explanation
Indices: 169875--169946 Score: 110
Period size: 21 Copynumber: 3.6 Consensus size: 20
169865 GAAACCCCTT
*
169875 TGAAAATAGATGATTTTAAA
1 TGAAAATACATGATTTTAAA
169895 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
169916 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
169935 TGAAGATACATG
1 TGAAAATACATG
169947 CTCTTGGCCG
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 13 0.27
20 16 0.33
21 20 0.41
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:176692 original size:91 final size:91
Alignment explanation
Indices: 176537--176710 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
176527 GGTAGTTGAT
*
176537 GCTTGGCCAAATAGGGAGAAAACTCTTCATCTTGGTGCCTAAATGAACCACATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAAAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
*
176602 GGGGCTGATCACATGCAAAACACTTG
66 GAGGCTGATCACATGCAAAACACTTG
* * *
176628 GCTTGGCCGAATAGGGAGAGAAA-TCTTCATCTTGGCGCCTAAATGATCTACATGCAAGGCACAT
1 GCTTGGCCAAATAGGGAGA-AAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACAT
* *
176692 GGAGGCTGGTCATATGCAA
65 GGAGGCTGATCACATGCAA
176711 GGCACATGGG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
91 72 0.96
92 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAAAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATG
GAGGCTGATCACATGCAAAACACTTG
Found at i:185541 original size:15 final size:15
Alignment explanation
Indices: 185506--185534 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
185496 GTGCTTCAAC
185506 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
185520 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
185535 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:185579 original size:24 final size:24
Alignment explanation
Indices: 185527--185579 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
185517 CTTTTCTTTG
*
185527 CTTTTCTTCTTTTTGAGTGCTGGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
* *
185551 TTTTTCTTCTTTTGGAGTGCTTGA
1 CTTTTCTTCTTTTGGAGTGCTGGA
185575 CTTTT
1 CTTTT
185580 ATTTGCTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (24 bp):
CTTTTCTTCTTTTGGAGTGCTGGA
Found at i:186514 original size:91 final size:91
Alignment explanation
Indices: 186359--186532 Score: 258
Period size: 91 Copynumber: 1.9 Consensus size: 91
186349 GGTAGTTGAT
* * * * *
186359 GCTTGGTCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATTAACCACTTGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGAAAGGCACATG
*
186424 GGGGCTGATCACATGCAAAACACTTG
66 GAGGCTGATCACATGCAAAACACTTG
* *
186450 GCTTGGCCGAATGGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGAAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGAAAGGCACATG
* *
186515 GAGGCTGGTCATATGCAA
66 GAGGCTGATCACATGCAA
186533 GGCACATGGG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 73 1.00
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGAAAGGCACATG
GAGGCTGATCACATGCAAAACACTTG
Found at i:190509 original size:31 final size:31
Alignment explanation
Indices: 190446--190506 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
190436 TATCCTATCC
*
190446 TTATTTCATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCATTTCTAATCTTTA
*
190477 TTATTTCATTT-ATTTTCCTTTACTAATCTT
1 TTATTTCATTTCA-TTTCATTT-CTAATCTT
190507 ATTTCTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 18 0.69
32 7 0.27
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (31 bp):
TTATTTCATTTCATTTCATTTCTAATCTTTA
Found at i:190745 original size:19 final size:20
Alignment explanation
Indices: 190723--190778 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
190713 AATTGGAGTG
190723 CAAAAAGAAAAGAAAA-AGA
1 CAAAAAGAAAAGAAAACAGA
190742 CAAAAAGAAGAA-AAAATCAGA
1 CAAAAAGAA-AAGAAAA-CAGA
190763 -AAATAAGAAAAGAAAA
1 CAAA-AAGAAAAGAAAA
190779 GAAATTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 13 0.41
20 7 0.22
21 12 0.38
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (20 bp):
CAAAAAGAAAAGAAAACAGA
Found at i:193202 original size:22 final size:22
Alignment explanation
Indices: 193177--193228 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
193167 CTATTGAAAA
193177 CCAAAGGGAAATGATTTTTCAT
1 CCAAAGGGAAATGATTTTTCAT
193199 CCAAAGGGAAATGATTTTTCAT
1 CCAAAGGGAAATGATTTTTCAT
193221 CCAAAGGG
1 CCAAAGGG
193229 CGTGACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (22 bp):
CCAAAGGGAAATGATTTTTCAT
Found at i:194698 original size:11 final size:11
Alignment explanation
Indices: 194674--194718 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
194664 TTGGTGCAAG
194674 AAACAAGATAA
1 AAACAAGATAA
* *
194685 AAATAAGATTA
1 AAACAAGATAA
194696 AAACAAGATAA
1 AAACAAGATAA
194707 ATAA-AAGATAA
1 A-AACAAGATAA
194718 A
1 A
194719 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:194702 original size:22 final size:22
Alignment explanation
Indices: 194674--194715 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
194664 TTGGTGCAAG
194674 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAATAA-AAGATTA
194696 AAACAAGATAAATAAAAGAT
1 AAACAAGATAAATAAAAGAT
194716 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAATAAAAGATTA
Found at i:204419 original size:43 final size:45
Alignment explanation
Indices: 204343--204444 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 45
204333 TAGGATCAGA
* * *
204343 ATTATTATTTTATTAGGAATTAAGGTTGGGTTAAAAATATTTTTAG-TT
1 ATTATTATTTTATTAGGAATTAA-G--GAGTT-AAAACATGTTTAGTTT
204391 ATTATTATTTTATTAGGAATT-A-GAGTTAAAACATGTTTAGTTT
1 ATTATTATTTTATTAGGAATTAAGGAGTTAAAACATGTTTAGTTT
*
204434 ATTAATATTTT
1 ATTATTATTTT
204445 TTCTTTAGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
42 11 0.22
43 16 0.33
47 1 0.02
48 21 0.43
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (45 bp):
ATTATTATTTTATTAGGAATTAAGGAGTTAAAACATGTTTAGTTT
Found at i:213628 original size:13 final size:13
Alignment explanation
Indices: 213606--213635 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
213596 ACTAAACACC
213606 TTTC-ACATACCT
1 TTTCAACATACCT
213618 TTTCAACATACCT
1 TTTCAACATACCT
213631 TTTCA
1 TTTCA
213636 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:219319 original size:26 final size:29
Alignment explanation
Indices: 219290--219348 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 29
219280 TCTTTCTTTG
* *
219290 CTTTTC-TTCTTTTTGAGTG-TT-GATTT
1 CTTTTCTTTCTTTTGGAGTGCTTCAATTT
219316 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTCTTTCTTTTGGAGTGCTTCAATTT
219344 CTTTT
1 CTTTT
219349 ATGATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.15
26 13 0.48
27 2 0.07
28 5 0.19
29 3 0.11
ACGTcount: A:0.08, C:0.15, G:0.14, T:0.63
Consensus pattern (29 bp):
CTTTTCTTTCTTTTGGAGTGCTTCAATTT
Found at i:221982 original size:23 final size:23
Alignment explanation
Indices: 221939--221984 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
221929 TTTCAAAGAT
*
221939 AATGCCGTTTGAAGTTACAAAAG
1 AATGCCGTTTGAAGTGACAAAAG
* *
221962 AATGTCGTTTGAAGTGCCAAAAG
1 AATGCCGTTTGAAGTGACAAAAG
221985 TTTTGTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (23 bp):
AATGCCGTTTGAAGTGACAAAAG
Found at i:227244 original size:324 final size:317
Alignment explanation
Indices: 226765--227406 Score: 1148
Period size: 323 Copynumber: 2.0 Consensus size: 317
226755 GCCAAAGATG
226765 AAATAGTGCTAAGGAACACAATCCCGGTCTTCACAACTTGCTTGAGGGTGGTGATAGTGTCTTCA
1 AAATAGTGCTAAGGAACACAATCCCGGTCTTCACAACTTGCTTGAGGGTGGTGATAGTGTCTTCA
226830 ACCCAATAGATATAATCTAGGAATTTTGGAATCAAATGAAGGAATGACGCCACAATAGGAACTAT
66 ACCCAATAGATATAATCTAGGAATTTTGGAATCAAATGAAGGAATGACGCCACAATAGGAACTAT
226895 ACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAAAGAAAT-ACTCACAAGAGTA-ATTTTT
131 ACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAAAGAAATAACTCACAAGAGTATATTTTT
226958 ATAAGAGATGAGATCCTAACAAATGAAATGAAAAAGCCTATTTATAGTTTTCAAAGGGTTTAGG-
196 ATAAGAGATGAGA---TAACAAATGAAATG-AAAAGCCTATTTATAGTTTTCAAAGGGTTTAGGC
227022 CGAATAGGTACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGACTTTTAA
257 CGAATAGGTACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGACTTTTAA
227083 AAATAGTGCTAAGGAACACAATCCCGGTCTTCACAAACTTGCTTGAGGGGTGGTGATAGTGTCTT
1 AAATAGTGCTAAGGAACACAATCCCGGTCTTCAC-AACTTGCTTGA-GGGTGGTGATAGTGTCTT
*
227148 CAACCCACTAGATATCAATCTAGGAA-TTTGGAATCAAAATGAAGGAATGACGCCACAAGTATAG
64 CAACCCAATAGATAT-AATCTAGGAATTTTGGAATC-AAATGAAGGAATGACGCCAC-A--ATAG
227212 GAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAAAGAAATAACTCACAAGAGTA
124 GAACTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAAAGAAATAACTCACAAGAGTA
227277 TATTTTTATAAGAGATGAGATAACAAATGAAATGAAAAGCCTATTTATAGTTTTCAAAGGGTTTA
189 TATTTTTATAAGAGATGAGATAACAAATGAAATGAAAAGCCTATTTATAGTTTTCAAAGGGTTTA
227342 GGCCGAATAGGTACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGACTTTTAA
254 GGCCGAATAGGTACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGACTTTTAA
227406 A
1 A
227407 TGAAAATACA
Statistics
Matches: 313, Mismatches: 1, Indels: 15
0.95 0.00 0.05
Matches are distributed among these distances:
318 34 0.11
319 11 0.04
320 41 0.13
321 30 0.10
322 34 0.11
323 76 0.24
324 55 0.18
325 13 0.04
326 19 0.06
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (317 bp):
AAATAGTGCTAAGGAACACAATCCCGGTCTTCACAACTTGCTTGAGGGTGGTGATAGTGTCTTCA
ACCCAATAGATATAATCTAGGAATTTTGGAATCAAATGAAGGAATGACGCCACAATAGGAACTAT
ACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAAAGAAATAACTCACAAGAGTATATTTTT
ATAAGAGATGAGATAACAAATGAAATGAAAAGCCTATTTATAGTTTTCAAAGGGTTTAGGCCGAA
TAGGTACATGATGGTTCGGCTATGGATGAAACCCCTTTGAAAATACATGACTTTTAA
Found at i:227429 original size:19 final size:21
Alignment explanation
Indices: 227386--227437 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
227376 GAAACCCCTT
227386 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
227407 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
227426 TGAAGATACATG
1 TGAAAATACATG
227438 CTTGACCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:230524 original size:19 final size:20
Alignment explanation
Indices: 230496--230535 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
230486 AGGGGATAAT
230496 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
230516 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
230535 A
1 A
230536 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:230991 original size:19 final size:21
Alignment explanation
Indices: 230948--230999 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
230938 GAAACCCCTT
*
230948 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGAATTTTAAA
230969 TGAAAATACAT-AATTTT-AA
1 TGAAAATACATGAATTTTAAA
*
230988 TGAAGATACATG
1 TGAAAATACATG
231000 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGAATTTTAAA
Found at i:233529 original size:20 final size:22
Alignment explanation
Indices: 233500--233539 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
233490 GGGAGAGCTT
233500 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
233520 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
233540 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Found at i:238209 original size:17 final size:18
Alignment explanation
Indices: 238187--238220 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
238177 CCTTTAAATC
238187 ATTTCTTCTA-TCTTTCA
1 ATTTCTTCTATTCTTTCA
238204 ATTTCTTCTATTCTTTC
1 ATTTCTTCTATTCTTTC
238221 TACCCTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTCTTCTATTCTTTCA
Found at i:241344 original size:26 final size:25
Alignment explanation
Indices: 241315--241363 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
241305 CATAATATCG
*
241315 CTAAGTATATGAATTATTATAAAGTA
1 CTAAGAATATGAA-TATTATAAAGTA
* *
241341 CTAAGAATGTGCATATTATAAAG
1 CTAAGAATATGAATATTATAAAG
241364 ATGTGAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
CTAAGAATATGAATATTATAAAGTA
Found at i:243715 original size:21 final size:22
Alignment explanation
Indices: 243663--243721 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
243653 CTTGGCTTGC
243663 TTTCTCTTTTTCTTT-TCTTCT
1 TTTCTCTTTTTCTTTCTCTTCT
**
243684 TTTCTGATTTT-TTTCTCTTCT
1 TTTCTCTTTTTCTTTCTCTTCT
*
243705 TTTGTCTTTTTCTTTCT
1 TTTCTCTTTTTCTTTCT
243722 TTTTGCACTC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 23 0.74
22 5 0.16
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTCTCTTTTTCTTTCTCTTCT
Found at i:244457 original size:17 final size:19
Alignment explanation
Indices: 244416--244465 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
244406 GAAACCCCTT
244416 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA--TTTAAA
244437 TGAAAATACATGA-TT-AA
1 TGAAAATACATGATTTAAA
*
244454 TGAAGATACATG
1 TGAAAATACATG
244466 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.46
18 2 0.07
21 13 0.46
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:246285 original size:28 final size:28
Alignment explanation
Indices: 246245--246298 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
246235 CTCACATTCT
246245 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
246273 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
246299 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:247878 original size:24 final size:24
Alignment explanation
Indices: 247831--247886 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 24
247821 TTCATCCTGG
247831 AAAAAAAATTCCGAAAATTAAAAA
1 AAAAAAAATTCCGAAAATTAAAAA
*
247855 AAAAACAAATTCGGAAAATTAAAAA
1 AAAAA-AAATTCCGAAAATTAAAAA
*
247880 AAGAAAA
1 AAAAAAA
247887 GAAAGTTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (24 bp):
AAAAAAAATTCCGAAAATTAAAAA
Found at i:250614 original size:28 final size:28
Alignment explanation
Indices: 250574--250627 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
250564 CTCACATTCA
250574 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
250602 CATAACAGCATGTTCATCATTTGTTT
1 CATAACAGCATGTTCATCATTTGTTT
250628 AGTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:264035 original size:13 final size:13
Alignment explanation
Indices: 264013--264042 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
264003 ACTAAACACC
264013 TTTC-ACATACCT
1 TTTCAACATACCT
264025 TTTCAACATACCT
1 TTTCAACATACCT
264038 TTTCA
1 TTTCA
264043 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:272448 original size:23 final size:24
Alignment explanation
Indices: 272422--272478 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
272412 CCAACTTTTC
272422 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
***
272445 TTTCCAATTTCTTCTTTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
* *
272469 CTTATTTTTT
1 TTTCTTTTTT
272479 GATTTTTTCT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:275202 original size:13 final size:13
Alignment explanation
Indices: 275180--275209 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
275170 ACTAAACACC
275180 TTTC-ACATACCT
1 TTTCAACATACCT
275192 TTTCAACATACCT
1 TTTCAACATACCT
275205 TTTCA
1 TTTCA
275210 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:285927 original size:13 final size:13
Alignment explanation
Indices: 285905--285934 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
285895 ACTAAACACC
285905 TTTC-ACATACCT
1 TTTCAACATACCT
285917 TTTCAACATACCT
1 TTTCAACATACCT
285930 TTTCA
1 TTTCA
285935 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:294377 original size:36 final size:35
Alignment explanation
Indices: 294304--294408 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 35
294294 ATTTATAAGT
* * * *
294304 TGGTGATAATATAGGCGTGATATGGTGGTGGAATA
1 TGGTGATGATATAGGCATGATATGGTGATGGACTA
294339 TGGTGATGATATAGGCATGATGATGGTGATGGACTA
1 TGGTGATGATATAGGCATGAT-ATGGTGATGGACTA
294375 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCATGAT-ATGGTGATGGAC
294409 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (35 bp):
TGGTGATGATATAGGCATGATATGGTGATGGACTA
Found at i:295843 original size:9 final size:10
Alignment explanation
Indices: 295823--295859 Score: 60
Period size: 9 Copynumber: 3.9 Consensus size: 10
295813 AGTGCTTCAA
295823 CTTTCTTTTT
1 CTTTCTTTTT
295833 CTTTC-TTTT
1 CTTTCTTTTT
295842 CTTTCTTTTT
1 CTTTCTTTTT
295852 CTTT-TTTT
1 CTTTCTTTT
295860 GAGTGCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:295844 original size:15 final size:15
Alignment explanation
Indices: 295824--295856 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
295814 GTGCTTCAAC
295824 TTTCTTT-TTCTTTCT
1 TTTCTTTCTT-TTTCT
295839 TTTCTTTCTTTTTCT
1 TTTCTTTCTTTTTCT
295854 TTT
1 TTT
295857 TTTGAGTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTTTCTTTTTCT
Found at i:295847 original size:19 final size:18
Alignment explanation
Indices: 295823--295859 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
295813 AGTGCTTCAA
295823 CTTTCTTTTTCTTTCTTTT
1 CTTTCTTTTTCTTT-TTTT
295842 CTTTCTTTTTCTTTTTTT
1 CTTTCTTTTTCTTTTTTT
295860 GAGTGCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
CTTTCTTTTTCTTTTTTT
Found at i:295868 original size:23 final size:23
Alignment explanation
Indices: 295842--295901 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
295832 TCTTTCTTTT
*
295842 CTTTCTTTTTCTTTTTTTGAGTG
1 CTTTCATTTTCTTTTTTTGAGTG
* *
295865 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTTTTTTTGAGTG
*
295888 CTTTGATTTTCTTT
1 CTTTCATTTTCTTT
295902 GCTGGATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.08, C:0.15, G:0.12, T:0.65
Consensus pattern (23 bp):
CTTTCATTTTCTTTTTTTGAGTG
Found at i:306642 original size:18 final size:18
Alignment explanation
Indices: 306596--306642 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
306586 ATCAGCAAAG
306596 AAAAA-AAG-AAGCACTC
1 AAAAAGAAGAAAGCACTC
* *
306612 AAAAAGATTGAAAGTACTC
1 AAAAAGA-AGAAAGCACTC
306631 AAAAAGAAGAAA
1 AAAAAGAAGAAA
306643 AAGAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 5 0.20
17 1 0.04
18 5 0.20
19 14 0.56
ACGTcount: A:0.64, C:0.11, G:0.15, T:0.11
Consensus pattern (18 bp):
AAAAAGAAGAAAGCACTC
Found at i:309419 original size:11 final size:13
Alignment explanation
Indices: 309387--309416 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
309377 TGGCCAAAGA
309387 TGAAAAGGTATGT
1 TGAAAAGGTATGT
309400 TGAAAAGGTATG-
1 TGAAAAGGTATGT
309412 TGAAA
1 TGAAA
309417 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:313399 original size:20 final size:22
Alignment explanation
Indices: 313370--313409 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
313360 GGGAGAGCTT
313370 TGGACCAAA-GT-GCTGAAAAG
1 TGGACCAAAGGTAGCTGAAAAG
*
313390 TGGACTAAAGGTAGCTGAAA
1 TGGACCAAAGGTAGCTGAAA
313410 GTAGCTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.17
Consensus pattern (22 bp):
TGGACCAAAGGTAGCTGAAAAG
Done.