Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008748.1 Hibiscus syriacus cultivar Beakdansim tig00111838_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: 286141
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6059 original size:36 final size:36
Alignment explanation
Indices: 6006--6190 Score: 273
Period size: 36 Copynumber: 5.1 Consensus size: 36
5996 TGAATAAGAA
* * **
6006 GAACGAAAGAAAGCATCGGTACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* *
6042 GAACAGAAGAAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
6078 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTT
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
6114 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* *
6150 GAACGGAAGGAGGCATCTG-TACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATC-GACACTTCCGATTCAAGTC
6186 GAACG
1 GAACG
6191 AAAAGATGTA
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
36 137 0.99
37 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
Found at i:6330 original size:11 final size:11
Alignment explanation
Indices: 6298--6349 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
6288 TTAGTTAGTA
6298 TTTGTTATTAG
1 TTTGTTATTAG
* *
6309 TTAG-GACTTAG
1 TTTGTTA-TTAG
6320 TTTGTTATTAG
1 TTTGTTATTAG
6331 TTTGTTATTAG
1 TTTGTTATTAG
6342 TTTGTTAT
1 TTTGTTAT
6350 GATTTGTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 1 0.03
11 33 0.94
12 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (11 bp):
TTTGTTATTAG
Found at i:12047 original size:18 final size:18
Alignment explanation
Indices: 12020--12054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12010 GAACGAGGAA
*
12020 GAGGAGGAGGATGACGAT
1 GAGGAGGAGGACGACGAT
*
12038 GAGGATGAGGACGACGA
1 GAGGAGGAGGACGACGA
12055 GGAACAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.49, T:0.09
Consensus pattern (18 bp):
GAGGAGGAGGACGACGAT
Found at i:12862 original size:31 final size:32
Alignment explanation
Indices: 12821--12897 Score: 120
Period size: 31 Copynumber: 2.4 Consensus size: 32
12811 AAAAAAGTTC
12821 ATTTTAGGTGTATGTGTATGCTTTTATTTACT
1 ATTTTAGGTGTATGTGTATGCTTTTATTTACT
12853 ATTTT-GGTGTATGTGTATGCTTTTATTTACT
1 ATTTTAGGTGTATGTGTATGCTTTTATTTACT
* * *
12884 GTTTAAGGTCTATG
1 ATTTTAGGTGTATG
12898 AAAGATGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 29 0.71
32 12 0.29
ACGTcount: A:0.18, C:0.06, G:0.21, T:0.55
Consensus pattern (32 bp):
ATTTTAGGTGTATGTGTATGCTTTTATTTACT
Found at i:12970 original size:27 final size:26
Alignment explanation
Indices: 12934--12991 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
12924 TGGTTTGATA
* *
12934 TGTTTCATGTCATGTTTAATAGTTTGT
1 TGTTTAATGTAATGTTT-ATAGTTTGT
*
12961 TGTTTAATGTAATGTTTATGGTTTGT
1 TGTTTAATGTAATGTTTATAGTTTGT
12987 TGTTT
1 TGTTT
12992 TTATAGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.17, C:0.03, G:0.21, T:0.59
Consensus pattern (26 bp):
TGTTTAATGTAATGTTTATAGTTTGT
Found at i:14487 original size:83 final size:83
Alignment explanation
Indices: 13871--14476 Score: 563
Period size: 83 Copynumber: 7.3 Consensus size: 83
13861 TTTCATAGTG
* * * * *
13871 TTTTCCATTATTATTTAGAGAATCTC-ACCATATCATATTGTTCAATCCCATCCGAAATGAAATG
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
* * * *
13935 CGCGTTCTAGGGTAAGCG
66 CGCGTTCCAGGGGAAACA
* * * *
13953 TTTTCCATTATTATTCAAAGAATCTCTACCATGTCATAGGGTTCTATCTCAT-TCGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCT-GAAATGAAAG
** * *
14017 GCGTATTCTAGGGGAATCA
65 GCGCGTTCCAGGGGAAACA
* * *
14036 TTCTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCCGAAATGAAAGA
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
* * * *
14101 CACATCCCAGGGGAAGCA
66 CGCGTTCCAGGGGAAACA
* * * * **
14119 TTTTTCATTATTATTCAGAGAATCTATGCCATGTCATAGTGTTCCATCCCATAAGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
* * ** *
14184 CTCATTATAGGGGAAGCA
66 CGCGTTCCAGGGGAAACA
* * * * * *
14202 TTTTCCACTATTATTCAGAGAATCTCTATCATGTTAGAGTGTTCAATCCTATTTGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
* * * **
14267 AGTGTTCCAGAGGAAATG
66 CGCGTTCCAGGGGAAACA
* * * * * *
14285 TTTTTCATTAATATTTAGAGAATCTCTACCATATCATAGTGTTCAATCTCATCTGAAATGAAATG
1 TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
* *** *
14350 CACGTTCCA-ATAAAATA
66 CGCGTTCCAGGGGAAACA
* * ** * ** *
14367 TTTTCCATTATTATTCAAATAATCGT-TGTCATGTCATAATGTGAAATCTCATCTGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATC-TCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAG
* *
14431 GTGCGTTCCAGGGAAAACA
65 GCGCGTTCCAGGGGAAACA
14450 TTTTCCATTATTATTCAGAGAATCTCT
1 TTTTCCATTATTATTCAGAGAATCTCT
14477 GTCATTTCAT
Statistics
Matches: 422, Mismatches: 96, Indels: 11
0.80 0.18 0.02
Matches are distributed among these distances:
82 88 0.21
83 334 0.79
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (83 bp):
TTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCTGAAATGAAAGG
CGCGTTCCAGGGGAAACA
Found at i:14599 original size:24 final size:23
Alignment explanation
Indices: 14562--14607 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
14552 CTTTGAAATA
*
14562 TCAAACTCTCAAATGTTCAAACTT
1 TCAAACTCTCAAAT-CTCAAACTT
* *
14586 TCAAACTTTGAAATCTCAAACT
1 TCAAACTCTCAAATCTCAAACT
14608 AAGAAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (23 bp):
TCAAACTCTCAAATCTCAAACTT
Found at i:17729 original size:20 final size:20
Alignment explanation
Indices: 17704--17752 Score: 91
Period size: 19 Copynumber: 2.5 Consensus size: 20
17694 CAAATATAAC
17704 ACCCTAAAACCAATTACAAA
1 ACCCTAAAACCAATTACAAA
17724 ACCCT-AAACCAATTACAAA
1 ACCCTAAAACCAATTACAAA
17743 ACCCTAAAAC
1 ACCCTAAAAC
17753 TACTTTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (20 bp):
ACCCTAAAACCAATTACAAA
Found at i:31263 original size:19 final size:18
Alignment explanation
Indices: 31221--31263 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
31211 ATTTGTTTTT
*
31221 AATAAATTTTTATATGAA
1 AATAAATTTTTATATCAA
* *
31239 ATTAAATTTTTATTTTCAA
1 AATAAATTTTTA-TATCAA
31258 AATAAA
1 AATAAA
31264 ATATTAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
AATAAATTTTTATATCAA
Found at i:48170 original size:23 final size:23
Alignment explanation
Indices: 48119--48164 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
48109 CGATTCCCCT
*
48119 AAGGGGGAATCAGTTCTCATTCA
1 AAGGGGGAATCAGTTCCCATTCA
* *
48142 AAGGGGGAATCGGTTCCCCTTCA
1 AAGGGGGAATCAGTTCCCATTCA
48165 TGGGGGTATT
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:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (23 bp):
AAGGGGGAATCAGTTCCCATTCA
Found at i:57507 original size:14 final size:14
Alignment explanation
Indices: 57488--57543 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
57478 CTACTCTAAC
57488 CGAGTCAACTCGTT
1 CGAGTCAACTCGTT
*
57502 CGAGTCAACTTG-T
1 CGAGTCAACTCGTT
57515 CTGAG-CTAACTCGTT
1 C-GAGTC-AACTCGTT
* *
57530 CGAATTAACTCGTT
1 CGAGTCAACTCGTT
57544 AACTTTGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.09
14 29 0.85
15 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (14 bp):
CGAGTCAACTCGTT
Found at i:64369 original size:2 final size:2
Alignment explanation
Indices: 64364--64403 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
64354 ATTAACAAGA
64364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64404 CATTATGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64604 original size:23 final size:23
Alignment explanation
Indices: 64578--64621 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
64568 TACGTAGAAA
64578 TGTCCCGAAGGACCACATAGTAT
1 TGTCCCGAAGGACCACATAGTAT
*
64601 TGTCCTGAAGGACCACATAGT
1 TGTCCCGAAGGACCACATAGT
64622 CTAATTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGTAT
Found at i:70392 original size:2 final size:2
Alignment explanation
Indices: 70387--70419 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
70377 ATGATATATA
*
70387 TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
70420 ATTCTTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:76890 original size:39 final size:39
Alignment explanation
Indices: 76846--76920 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
76836 CCCTCCATCC
*
76846 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAATTCCAGCAGCTTCCAGCG
* * *
76885 AGCAGCCCCTCCACGCATCAATTGCAGTAGCTTCCA
1 AGCAGCCCCTCCACACATCAATTCCAGCAGCTTCCA
76921 ACACTACCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAATTCCAGCAGCTTCCAGCG
Found at i:80688 original size:15 final size:14
Alignment explanation
Indices: 80647--80687 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
80637 ATTTTAAATA
80647 ATTTACATTTTTGC
1 ATTTACATTTTTGC
80661 ATTTATGCA-TTTTGC
1 ATTTA--CATTTTTGC
80676 ATTTACATTTTT
1 ATTTACATTTTT
80688 TATTTGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 9 0.38
15 11 0.46
16 2 0.08
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTACATTTTTGC
Found at i:82835 original size:91 final size:84
Alignment explanation
Indices: 82722--82881 Score: 203
Period size: 85 Copynumber: 1.8 Consensus size: 84
82712 GATACCCATG
*
82722 TTATATTATTATATACAATAAAGCTTGAGTTGTCCCACTAGAGCAAATGGTTAATCGCCCCGGCT
1 TTATATTATTATATACAATAAAGC-T-A----TCCCACTAGAGCAAATGGTTAATAGCCCCGGCT
82787 TTATAGATAATATTCAGCCAACCCA
60 TTATAGATAATATTCAGCCAACCCA
** * * *
82812 TTATATTATTTATATGTAATAAAGCTATCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATG
1 TTATATTA-TTATATACAATAAAGCTATCCCACTAGAGCAAATGGTTAATAGCCCCGGCTTTATA
82877 GATAA
65 GATAA
82882 GTTTCAATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 39 0.62
89 1 0.02
90 9 0.14
91 14 0.22
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (84 bp):
TTATATTATTATATACAATAAAGCTATCCCACTAGAGCAAATGGTTAATAGCCCCGGCTTTATAG
ATAATATTCAGCCAACCCA
Found at i:86980 original size:54 final size:54
Alignment explanation
Indices: 86839--86995 Score: 161
Period size: 55 Copynumber: 2.9 Consensus size: 54
86829 ATAAATTTGT
* * * * **
86839 GCATAAGCCACAGGAAAAGATGAATGTGTTATTAAATGTTTTATGAACATCTGG
1 GCATAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAA
* * * * * * *
86893 GCAGAAACCGCATGAGAATGATGAACGTGTTGTCAAATGTTTTACGAGCCTCTAA
1 GCATAAGCCACAGGA-AATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAA
** *
86948 GCATAAGCCACAGGAAATGATGAATGCATTGTCAAGTGTTTTACGAAC
1 GCATAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
86996 CAGTAATTAT
Statistics
Matches: 80, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
54 39 0.49
55 41 0.51
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (54 bp):
GCATAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAA
Found at i:87396 original size:20 final size:22
Alignment explanation
Indices: 87350--87407 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
87340 TACATCTACA
87350 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
87372 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
87394 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
87408 AAGCTTTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:88154 original size:77 final size:73
Alignment explanation
Indices: 88068--88385 Score: 439
Period size: 73 Copynumber: 4.4 Consensus size: 73
88058 CTATTTCCAA
* * * * *
88068 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA--TCTT--A
*
88133 AACCCTCAGGGT
62 AAGCCTCAGGGT
*
88145 CATCTGTAAGACCTATAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
*
88210 CTCAGAGT
66 CTCAGGGT
* * * *
88218 CATCTGTAAGACCTACAGTGCATGATGTTATCAAAAAGCCTTCAGAAGCTTTTT-ATCTTATAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
88282 CTCAGGG-
66 CTCAGGGT
88289 --TCTGTAAGACCTACAGTGCATGATGTTTTCAAAAA-CCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
88351 CTCAGGGT
66 CTCAGGGT
* *
88359 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
88386 ATAAGACCTC
Statistics
Matches: 217, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
68 14 0.06
69 50 0.23
72 38 0.18
73 61 0.28
75 3 0.01
77 51 0.24
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:89136 original size:39 final size:39
Alignment explanation
Indices: 89087--89163 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
89077 CCCTCCATCC
*
89087 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
* * *
89126 AGCATCCCCTCCACGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGC
89164 ACTGCCAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.18
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
Found at i:91152 original size:165 final size:165
Alignment explanation
Indices: 90880--91213 Score: 602
Period size: 165 Copynumber: 2.0 Consensus size: 165
90870 TAAAAAATCA
90880 TTTATTCACATTATTTTTCCCAGCGAGTAAAAAATGTGCCCGGACGAAAGCAGTTACGACAGAGG
1 TTTATTCACATTATTTTTCCCA-CGAGTAAAAAATGTGCCCGGACGAAAGCAGTTACGACAGAGG
*
90945 TGATGGAAGATCCTCGTCTTGTATGTTTGCGTAGTGGTGCGGGGTTGGAATCTGAAGATGTAGAA
65 TGATGGAAGATCCTCGTCTTGTACGTTTGCGTAGTGGTGCGGGGTTGGAATCTGAAGATGTAGAA
91010 TAATAATT-GAGATGTTTATGCATCCAGCCGATGTT
130 TAATAATTCGAGATGTTTATGCATCCAGCCGATGTT
91045 TTTATTCACATTATTTTTCCGC-CGAGTAAAAAACTGTGCCCGGACGAAAGCCAGTTACGACAGA
1 TTTATTCACATTATTTTTCC-CACGAGTAAAAAA-TGTGCCCGGACGAAAG-CAGTTACGACAGA
91109 GGTGATGGAAGATCCTCGTC-TGTACGTTTGCGTAGTGGTGCGGGGTTGGAATCTGAAGATGTAG
63 GGTGATGGAAGATCCTCGTCTTGTACGTTTGCGTAGTGGTGCGGGGTTGGAATCTGAAGATGTAG
91173 AATAATAATTCGAGATGTTTATGCATCCAGCCGATGTT
128 AATAATAATTCGAGATGTTTATGCATCCAGCCGATGTT
91211 TTT
1 TTT
91214 GAAGTATTCT
Statistics
Matches: 164, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
164 11 0.07
165 89 0.54
166 64 0.39
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (165 bp):
TTTATTCACATTATTTTTCCCACGAGTAAAAAATGTGCCCGGACGAAAGCAGTTACGACAGAGGT
GATGGAAGATCCTCGTCTTGTACGTTTGCGTAGTGGTGCGGGGTTGGAATCTGAAGATGTAGAAT
AATAATTCGAGATGTTTATGCATCCAGCCGATGTT
Found at i:99786 original size:35 final size:34
Alignment explanation
Indices: 99745--99825 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
99735 AAACCCAAAC
*
99745 TTTTATTTTATTTATTCATACTAACGTACTAACTT
1 TTTTATTTTATTTATTCATACTAACGTACTAA-TA
* * *
99780 TTTTATTTT-TATTGTTCTTACTAACTTACTAATA
1 TTTTATTTTAT-TTATTCATACTAACGTACTAATA
99814 TTTTATTTTATT
1 TTTTATTTTATT
99826 GCAAAAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 12 0.30
35 28 0.70
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.60
Consensus pattern (34 bp):
TTTTATTTTATTTATTCATACTAACGTACTAATA
Found at i:99977 original size:5 final size:5
Alignment explanation
Indices: 99967--99995 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
99957 TATTTCTGTT
99967 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
99996 CTAGCACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:102511 original size:158 final size:156
Alignment explanation
Indices: 102208--102521 Score: 594
Period size: 158 Copynumber: 2.0 Consensus size: 156
102198 TACTGACACA
102208 TTTTCTTTGTTTGATTTTATTGTCTGGTATTGCAGATCATCATAAATAAAAGAAAGGTGTTGATT
1 TTTTCTTTGTTTGATTTTATTGTCTGGTATTGCAGATCATCATAAATAAAAGAAAGGTGTTGATT
102273 AACCAAGTAATTCATCAGAGTAGAAGAGTGATCATTAAGATGGAAAAGAGTTTTCATAACAAGGA
66 AACCAAGTAATTCATCAGAGTAGAAGAGTGATCATTAAGATGGAAAAGAGTTTTCATAACAAGGA
102338 AGAACCTAATTCAGTTGCTCGAGTTT
131 AGAACCTAATTCAGTTGCTCGAGTTT
102364 TTTTCTTTGTTTGATTATTTATTGTCTGGTATTGCATGATCATCATAAATAAAAGAAAGGTGTTG
1 TTTTCTTTGTTTGA-T-TTTATTGTCTGGTATTGCA-GATCATCATAAATAAAAGAAAGGTGTTG
102429 ATTAACCAAGTAA-TCATCAGAGTAGAAGAGTGATCATTAAGATGGAAAAGAGTTTTCATAACAA
63 ATTAACCAAGTAATTCATCAGAGTAGAAGAGTGATCATTAAGATGGAAAAGAGTTTTCATAACAA
102493 GGAAGAACCTAATTCAGTTGCTCGAGTTT
128 GGAAGAACCTAATTCAGTTGCTCGAGTTT
102522 GGTCTGAAGA
Statistics
Matches: 155, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
156 14 0.09
157 1 0.01
158 99 0.64
159 41 0.26
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (156 bp):
TTTTCTTTGTTTGATTTTATTGTCTGGTATTGCAGATCATCATAAATAAAAGAAAGGTGTTGATT
AACCAAGTAATTCATCAGAGTAGAAGAGTGATCATTAAGATGGAAAAGAGTTTTCATAACAAGGA
AGAACCTAATTCAGTTGCTCGAGTTT
Found at i:116894 original size:7 final size:7
Alignment explanation
Indices: 116884--116948 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 7
116874 AGATCAAATC
116884 AAAGCAA
1 AAAGCAA
*
116891 AAAGAAA
1 AAAGCAA
116898 AAAG-AA
1 AAAGCAA
*
116904 AATA-AAA
1 AA-AGCAA
116911 AAAGCAA
1 AAAGCAA
116918 AAAGCAA
1 AAAGCAA
116925 AAAGCAA
1 AAAGCAA
*
116932 AAAGAAA
1 AAAGCAA
116939 CAAAG-AA
1 -AAAGCAA
116946 AAA
1 AAA
116949 AAAAGAAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
6 8 0.16
7 39 0.76
8 4 0.08
ACGTcount: A:0.78, C:0.08, G:0.12, T:0.02
Consensus pattern (7 bp):
AAAGCAA
Found at i:116919 original size:14 final size:14
Alignment explanation
Indices: 116884--116952 Score: 83
Period size: 14 Copynumber: 5.1 Consensus size: 14
116874 AGATCAAATC
116884 AAAGCAAAAAGAAA
1 AAAGCAAAAAGAAA
116898 AAAG-AAAATA-AAA
1 AAAGCAAAA-AGAAA
*
116911 AAAGCAAAAAGCAA
1 AAAGCAAAAAGAAA
116925 AAAGCAAAAAGAAA
1 AAAGCAAAAAGAAA
116939 CAAAG-AAAAA-AAA
1 -AAAGCAAAAAGAAA
116952 A
1 A
116953 GAAATAGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
12 1 0.02
13 15 0.31
14 29 0.59
15 4 0.08
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (14 bp):
AAAGCAAAAAGAAA
Found at i:116965 original size:17 final size:18
Alignment explanation
Indices: 116930--116966 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
116920 AGCAAAAAGC
116930 AAAAAGAAACAAAGAAAA
1 AAAAAGAAACAAAGAAAA
* *
116948 AAAAAGAAATAGAGAAAA
1 AAAAAGAAACAAAGAAAA
116966 A
1 A
116967 TAAGACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAGAAACAAAGAAAA
Found at i:117863 original size:24 final size:23
Alignment explanation
Indices: 117832--117894 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
117822 GGGCAATATT
*
117832 TTTTTCAAAATTTTTGATTAAACA
1 TTTTTCAAAATTTTTAATT-AACA
* *
117856 TTTTTCAAAATTCTTTTAATTGATA
1 TTTTTCAAAA-T-TTTTAATTAACA
117881 TTTTTCAAAATTTT
1 TTTTTCAAAATTTT
117895 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 3 0.09
24 11 0.32
25 13 0.38
26 7 0.21
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (23 bp):
TTTTTCAAAATTTTTAATTAACA
Found at i:120257 original size:139 final size:138
Alignment explanation
Indices: 120071--120556 Score: 562
Period size: 139 Copynumber: 3.5 Consensus size: 138
120061 ACTGACTAGG
** * * * *
120071 TCTCCTCAACGCGAAGGAGTAGCGTCACCCTTAGACAACCAGACTTCCTCACCACGTAGAAACTG
1 TCTCCTCAACGCGAAGGAACAACGTCATCCTTAGACAACCAGACTTCCTCATCACGTAGGAACTG
120136 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCAA
66 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCATC-A
120201 TCGACCAGA
130 TCGACCAGA
* *
120210 TCTCCTCAACGCGAAGGAGCAACGTCATCCTTAGACAACCAGACTTCCTCATCATGTAGGAA-TC
1 TCTCCTCAACGCGAAGGAACAACGTCATCCTTAGACAACCAGACTTCCTCATCACGTAGGAACT-
* ** * *
120274 GTGTTGTCTCCAAATTATCTCTAAAGAAAGTTAGACGTCCTCATCACGTAGGAACAATGTCGTCC
65 GTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCAT-C
*
120339 ATCGACAAGA
129 ATCGACCAGA
* * * * * * * *
120349 TCTCCTTAACACGAATGAACAATGTCATCTTTAGACAACCAGACTTCCTCATAACGCAGGAACCG
1 TCTCCTCAACGCGAAGGAACAACGTCATCCTTAGACAACCAGACTTCCTCATCACGTAGGAACTG
* * * * * * *
120414 TGTTGTCTCCAACTTATCCCTAAAGACGACTAGACATCCTTATCACATAGGAACAATTTCGTTCA
66 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTC-ATCA
* *
120479 CCGACCATA
130 TCGACCAGA
* * ** * * * *
120488 TCTCTTCAACGCGAAAGAACAGTGTTAT-CTTCAGACAATCAGACTTCCTCAACACGAAGGAACT
1 TCTCCTCAACGCGAAGGAACAACGTCATCCTT-AGACAACCAGACTTCCTCATCACGTAGGAACT
120552 GTGTT
65 GTGTT
120557 ACCTCTGAAT
Statistics
Matches: 294, Mismatches: 48, Indels: 10
0.84 0.14 0.03
Matches are distributed among these distances:
138 3 0.01
139 289 0.98
140 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (138 bp):
TCTCCTCAACGCGAAGGAACAACGTCATCCTTAGACAACCAGACTTCCTCATCACGTAGGAACTG
TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCAT
CGACCAGA
Found at i:120836 original size:122 final size:122
Alignment explanation
Indices: 120564--120840 Score: 340
Period size: 122 Copynumber: 2.3 Consensus size: 122
120554 GTTACCTCTG
* ** * * *
120564 AATTATCTCCATATTGACCAGATTTCCTCAACGAGAAGGAATAGTGTCATCTTCAACAAACAATT
1 AATTATCTCCAAATTGACCAGAACTCCTCAACGAGAAGGAAGACTGTCATATTCAACAAACAATT
*** * * * *
120629 TATCTAAAAGCGGTCATATCTCTTCAACATGGATGAGCAGTGTCGTTTTCAACACCA
66 TATCTAAAAGCAACCAGATCTCTTCAACACGGATGAGCAGAGTCGTCTTCAACACCA
* * * * *
120686 AATTATATCTAAATTAACCTGAAGTCCTCAACGAGAAGGAACGACT-TCATATTCAACAAACAAT
1 AATTATCTCCAAATTGACCAGAACTCCTCAACGAGAAGGAA-GACTGTCATATTCAACAAACAAT
*
120750 TTATCTGAAAGCAACCAGATCTCTTCAACACGGATGAGCAGAGTCGTCTTCAACACCA
65 TTATCTAAAAGCAACCAGATCTCTTCAACACGGATGAGCAGAGTCGTCTTCAACACCA
* * *
120808 AATTATCTCCAGATTGACCCGACCTCCTCAACG
1 AATTATCTCCAAATTGACCAGAACTCCTCAACG
120841 TGAATGAGCA
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
122 127 0.98
123 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (122 bp):
AATTATCTCCAAATTGACCAGAACTCCTCAACGAGAAGGAAGACTGTCATATTCAACAAACAATT
TATCTAAAAGCAACCAGATCTCTTCAACACGGATGAGCAGAGTCGTCTTCAACACCA
Found at i:121142 original size:122 final size:121
Alignment explanation
Indices: 120905--121186 Score: 314
Period size: 122 Copynumber: 2.3 Consensus size: 121
120895 TGTTGTCTCC
* * * ** *
120905 AAATTATCTCCAGATTGACTCGACTTCCTTAACGAGAAGGAACAATTTCATCTTCAATAAACAAT
1 AAATTATCTCCAGATTGAC-CCAATTCCTCAACGAGAAGGAACAACGTCATCTTCAACAAACAAT
*
120970 TTATCTAAAAGCTACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACAAA
65 TTATCTAAAAGCGACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACAAA
* * * *
121027 AAATTATCTCCAAATTGACCCAATTTCCTCAACGAGAAGGAACAACGTCATTTTTAGCAAACAAT
1 AAATTATCTCCAGATTGACCCAA-TTCCTCAACGAGAAGGAACAACGTCATCTTCAACAAACAAT
*** * * * **
121092 TTATCTAAAAGCGGTTAGGTCTCTTCAACATGGATGAGCA-ATTTCGTCTTCAACACC
65 TTATCTAAAAGCGACCAGATCTCTTCAACATGGATGAGCAGA-GTCATCTTCAACAAA
* * * *
121149 AAGTTATATCCAGATTGACCCGAAGTCCTCAACAAGAA
1 AAATTATCTCCAGATTGACCC-AATTCCTCAACGAGAA
121187 AGAGCAGTGT
Statistics
Matches: 133, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
121 3 0.02
122 128 0.96
123 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (121 bp):
AAATTATCTCCAGATTGACCCAATTCCTCAACGAGAAGGAACAACGTCATCTTCAACAAACAATT
TATCTAAAAGCGACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACAAA
Found at i:121145 original size:342 final size:342
Alignment explanation
Indices: 120520--121200 Score: 873
Period size: 342 Copynumber: 2.0 Consensus size: 342
120510 TGTTATCTTC
** *
120520 AGACAATCAGACTTCCTCAACACGAAGGAACTGTGTTACCTCTGAATTATCTCCATATTGACCAG
1 AGACAATCAGACTTCCTCAACACGAAGGAACTGTGTTACCTCCAAATTATCTCCAGATTGACCAG
* * * ** *
120585 ATTTCCTCAACGAGAAGGAATAGTGTCATCTTCAACAAACAATTTATCTAAAAGCGGTCATATCT
66 ACTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCTAAAAGCGACCAGATCT
* * * ** * *
120650 CTTCAACATGGATGAGCAGTGTCGTTTTCAACACCAAATTATATCTAAATTAACCTGAAGTCCTC
131 CTTCAACATGGATGAGCAGAGTCATCTTCAACAAAAAATTATATCCAAATTAACCTCAAGTCCTC
* * *
120715 AACGAGAAGGAACGACTTCATATTCAACAAACAATTTATCTGAAAGCAACCAGATCTCTTCAACA
196 AACGAGAAGGAACAACGTCATATTCAACAAACAATTTATCTAAAAGCAACCAGATCTCTTCAACA
* * **
120780 CGGATGAGCAGAGTCGTCTTCAACACCAAATTATCTCCAGATTGACCCGACCTCCTCAACGTGAA
261 CGGATGAGCAGAGTCGTCTTCAACACCAAATTATATCCAGATTGACCCGAACTCCTCAACAAGAA
*
120845 TGAGCAATGTCATCCTT
326 AGAGCAATGTCATCCTT
* * * **
120862 AGACAATCAGACTTCTTTAACGCGAAGGAACTGTGTTGTCTCCAAATTATCTCCAGATTGACTC-
1 AGACAATCAGACTTCCTCAACACGAAGGAACTGTGTTACCTCCAAATTATCTCCAGATTGAC-CA
* * * *
120926 GACTTCCTTAACGAGAAGGAACAATTTCATCTTCAATAAACAATTTATCTAAAAGCTACCAGATC
65 GACTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCTAAAAGCGACCAGATC
* * *
120991 TCTTCAACATGGATGAGCAGAGTCATCTTCAACAAAAAATTATCTCCAAATTGACC-CAATTTCC
130 TCTTCAACATGGATGAGCAGAGTCATCTTCAACAAAAAATTATATCCAAATTAACCTCAA-GTCC
* * * **** *
121055 TCAACGAGAAGGAACAACGTCATTTTTAGCAAACAATTTATCTAAAAGCGGTTAGGTCTCTTCAA
194 TCAACGAGAAGGAACAACGTCATATTCAACAAACAATTTATCTAAAAGCAACCAGATCTCTTCAA
* * * *
121120 CATGGATGAGCA-ATTTCGTCTTCAACACCAAGTTATATCCAGATTGACCCGAAGTCCTCAACAA
259 CACGGATGAGCAGA-GTCGTCTTCAACACCAAATTATATCCAGATTGACCCGAACTCCTCAACAA
*
121184 GAAAGAGCAGTGTCATC
323 GAAAGAGCAATGTCATC
121201 TCTGAATCAT
Statistics
Matches: 287, Mismatches: 49, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
341 3 0.01
342 283 0.99
343 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (342 bp):
AGACAATCAGACTTCCTCAACACGAAGGAACTGTGTTACCTCCAAATTATCTCCAGATTGACCAG
ACTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCTAAAAGCGACCAGATCT
CTTCAACATGGATGAGCAGAGTCATCTTCAACAAAAAATTATATCCAAATTAACCTCAAGTCCTC
AACGAGAAGGAACAACGTCATATTCAACAAACAATTTATCTAAAAGCAACCAGATCTCTTCAACA
CGGATGAGCAGAGTCGTCTTCAACACCAAATTATATCCAGATTGACCCGAACTCCTCAACAAGAA
AGAGCAATGTCATCCTT
Found at i:123880 original size:32 final size:30
Alignment explanation
Indices: 123844--123928 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 30
123834 TTTAACTTAC
123844 TAACATTCTAACTTTTATTTTATTGTTTAT
1 TAACATTCTAACTTTTATTTTATTGTTTAT
123874 AATAACATTCTAACTTTT-TTTT-TTG-TTAT
1 --TAACATTCTAACTTTTATTTTATTGTTTAT
*
123903 T--CATACTAACTTTTATTTTTATTGTT
1 TAACATTCTAACTTTTA-TTTTATTGTT
123929 CTTACTAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
25 12 0.25
27 5 0.10
28 3 0.06
29 5 0.10
30 3 0.06
31 4 0.08
32 16 0.33
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (30 bp):
TAACATTCTAACTTTTATTTTATTGTTTAT
Found at i:123911 original size:25 final size:25
Alignment explanation
Indices: 123883--123944 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
123873 TAATAACATT
*
123883 CTAACTTTTTTTTTTGTTATTCATA
1 CTAACTTTTTTTTTTATTATTCATA
* * *
123908 CTAACTTTTATTTTTATTGTTCTTA
1 CTAACTTTTTTTTTTATTATTCATA
*
123933 CTAACATTTTTT
1 CTAACTTTTTTT
123945 ATTGCGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.63
Consensus pattern (25 bp):
CTAACTTTTTTTTTTATTATTCATA
Found at i:124111 original size:34 final size:33
Alignment explanation
Indices: 124064--124149 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
124054 AAAACACCCC
124064 CTAACTTTTATTTTGT-TTGTTCATACTAA-TATA
1 CTAACTTTTATTTT-TATTGTTCATACTAACT-TA
*
124097 CTAACTTTTTATTTTTATTGTTCTTACTAACTTA
1 CTAAC-TTTTATTTTTATTGTTCATACTAACTTA
124131 CTAACATTTTA-TTTTATTG
1 CTAAC-TTTTATTTTTATTG
124150 CACAAATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 14 0.29
34 33 0.69
35 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.57
Consensus pattern (33 bp):
CTAACTTTTATTTTTATTGTTCATACTAACTTA
Found at i:126804 original size:20 final size:19
Alignment explanation
Indices: 126781--126827 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
126771 TTGTAAATCG
126781 CAACACATAAGTCAAATTCA
1 CAACACAT-AGTCAAATTCA
* *
126801 CAACGCGATAGTCAAATTCG
1 CAACAC-ATAGTCAAATTCA
126821 CAACACA
1 CAACACA
126828 GAATTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.45, C:0.28, G:0.11, T:0.17
Consensus pattern (19 bp):
CAACACATAGTCAAATTCA
Found at i:126852 original size:19 final size:19
Alignment explanation
Indices: 126812--126884 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
126802 AACGCGATAG
*
126812 TCAAATTCGCAACACAGAATT
1 TCAAATTCGC-A-ACTGAATT
126833 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
126852 TCAAATTCGTAACT-ATATTT
1 TCAAATTCGCAACTGA-A-TT
*
126872 TCGAATTCGCAAC
1 TCAAATTCGCAAC
126885 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 1 0.02
19 21 0.46
20 14 0.30
21 10 0.22
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:126963 original size:14 final size:14
Alignment explanation
Indices: 126944--126974 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
126934 GGTATATAAT
126944 AACGCAGCAACAGC
1 AACGCAGCAACAGC
*
126958 AACGCAGCAGCAGC
1 AACGCAGCAACAGC
126972 AAC
1 AAC
126975 AACATGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.35, G:0.23, T:0.00
Consensus pattern (14 bp):
AACGCAGCAACAGC
Found at i:130499 original size:18 final size:18
Alignment explanation
Indices: 130478--130514 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
130468 GTAATTGGAG
130478 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
130496 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
130514 T
1 T
130515 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:130521 original size:24 final size:24
Alignment explanation
Indices: 130470--130522 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
130460 TTTCATATGT
* * *
130470 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
130494 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
130518 AATTT
1 AATTT
130523 CGGTTCCACT
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:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:131392 original size:26 final size:26
Alignment explanation
Indices: 131363--131420 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
131353 GGTTGCTATG
131363 AGAGATGGAGATAGACGGATTTCGCC
1 AGAGATGGAGATAGACGGATTTCGCC
131389 AGAGATGGAGATAGACGGATTTCGCC
1 AGAGATGGAGATAGACGGATTTCGCC
131415 AGAGAT
1 AGAGAT
131421 TGGGACATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (26 bp):
AGAGATGGAGATAGACGGATTTCGCC
Found at i:131433 original size:22 final size:22
Alignment explanation
Indices: 131407--131448 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
131397 AGATAGACGG
*
131407 ATTTCGCCAGAGATTGGGACAT
1 ATTTCGCCAGAGATGGGGACAT
* *
131429 ATTTCGTCGGAGATGGGGAC
1 ATTTCGCCAGAGATGGGGAC
131449 GGATGTCGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (22 bp):
ATTTCGCCAGAGATGGGGACAT
Found at i:131593 original size:20 final size:20
Alignment explanation
Indices: 131568--131694 Score: 139
Period size: 20 Copynumber: 6.3 Consensus size: 20
131558 TGTGTTTCGC
131568 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
131588 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTTTTGT
131608 GTTGCGAATTTGA-TTTATGT
1 GTTGCGAATTTGACTTT-TGT
* * ***
131628 GTTGTGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTTGT
*
131648 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
131668 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
131688 GTTGCGA
1 GTTGCGA
131695 TTTACAAATT
Statistics
Matches: 86, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
19 2 0.02
20 82 0.95
21 2 0.02
ACGTcount: A:0.17, C:0.12, G:0.26, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:131608 original size:40 final size:40
Alignment explanation
Indices: 131564--131682 Score: 186
Period size: 40 Copynumber: 3.0 Consensus size: 40
131554 ATATTGTGTT
*
131564 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGGCTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
*
131604 TCGCGTTGCGAATTTGA-TTTATGTGTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTT-TGTGTTGCGAATTTGACTA
* *
131644 TCACGTTGTGAATTTGACTTTTGTGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACT
131683 TCTGTGTTGC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.04
40 66 0.92
41 3 0.04
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.45
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
Found at i:131765 original size:20 final size:20
Alignment explanation
Indices: 131564--131755 Score: 136
Period size: 20 Copynumber: 9.9 Consensus size: 20
131554 ATATTGTGTT
*
131564 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
131584 TTGTGTTGCGAATTTGGCTA
1 TCGCGTTGCGAATTTGACTA
*
131604 TCGCGTTGCGAATTTGATTTA
1 TCGCGTTGCGAATTTGA-CTA
* *
131625 T-GTGTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* * *
131644 TCACGTTGTGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* *
131664 TTGTGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
131683 TCTGTGTTGCG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
131703 TTCGCGTTGTGAATTTG--TA
1 -TCGCGTTGCGAATTTGACTA
131722 -----TTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
131737 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
131756 TCTGTGTTGC
Statistics
Matches: 133, Mismatches: 24, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
13 10 0.08
15 2 0.02
18 2 0.02
19 9 0.07
20 101 0.76
21 9 0.07
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:131790 original size:73 final size:73
Alignment explanation
Indices: 131653--131791 Score: 224
Period size: 73 Copynumber: 1.9 Consensus size: 73
131643 ATCACGTTGT
* * * **
131653 GAATTTGACTTTTGTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGTGAATT
1 GAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTACGAATT
131718 TGTATTGC
66 TGTATTGC
*
131726 GAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGATTCGCGTTACGAATT
1 GAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTACGAATT
131791 T
66 T
131792 AGAAAATCGC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (73 bp):
GAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTACGAATT
TGTATTGC
Found at i:131831 original size:20 final size:20
Alignment explanation
Indices: 131786--131833 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
131776 TTCGCGTTAC
131786 GAATTTAGAAAATCGCAACGT
1 GAATTTAGAAAATCGCAAC-T
131807 GAATTT-GAAAATTCGCAA-T
1 GAATTTAGAAAA-TCGCAACT
131826 GCAATTTA
1 G-AATTTA
131834 CATATTCGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (20 bp):
GAATTTAGAAAATCGCAACT
Found at i:139268 original size:15 final size:15
Alignment explanation
Indices: 139223--139270 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
139213 ATATTTAACT
*
139223 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
*
139238 AGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
139253 GGGCGGGCAGATGCG
1 GGGCGGGCGGATGCG
139268 GGG
1 GGG
139271 TGGGTAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.10, C:0.17, G:0.65, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:140412 original size:18 final size:18
Alignment explanation
Indices: 140389--140423 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
140379 GTAAACTTTA
140389 ACTACTAATTTAATTTTT
1 ACTACTAATTTAATTTTT
140407 ACTACTAATTTAATTTT
1 ACTACTAATTTAATTTT
140424 AACTTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (18 bp):
ACTACTAATTTAATTTTT
Found at i:141311 original size:177 final size:177
Alignment explanation
Indices: 141015--141369 Score: 710
Period size: 177 Copynumber: 2.0 Consensus size: 177
141005 CGAACTTTAT
141015 TTAAAACCATGATGGAAACAATACAAAAAGAGAGAAGAAACCACGTACGATCAAGATTTGAATTA
1 TTAAAACCATGATGGAAACAATACAAAAAGAGAGAAGAAACCACGTACGATCAAGATTTGAATTA
141080 ACAGTGTTCAGTTTTTTAAACGGCTGAAGGTCAGAAGATGATAAATATAGATCCTACTGGCAATT
66 ACAGTGTTCAGTTTTTTAAACGGCTGAAGGTCAGAAGATGATAAATATAGATCCTACTGGCAATT
141145 GTGAGGCTCATCCAACGATGCAAATCGCTACAAAAAAATTTTGTTGA
131 GTGAGGCTCATCCAACGATGCAAATCGCTACAAAAAAATTTTGTTGA
141192 TTAAAACCATGATGGAAACAATACAAAAAGAGAGAAGAAACCACGTACGATCAAGATTTGAATTA
1 TTAAAACCATGATGGAAACAATACAAAAAGAGAGAAGAAACCACGTACGATCAAGATTTGAATTA
141257 ACAGTGTTCAGTTTTTTAAACGGCTGAAGGTCAGAAGATGATAAATATAGATCCTACTGGCAATT
66 ACAGTGTTCAGTTTTTTAAACGGCTGAAGGTCAGAAGATGATAAATATAGATCCTACTGGCAATT
141322 GTGAGGCTCATCCAACGATGCAAATCGCTACAAAAAAATTTTGTTGA
131 GTGAGGCTCATCCAACGATGCAAATCGCTACAAAAAAATTTTGTTGA
141369 T
1 T
141370 AGGTTTTTGT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 178 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (177 bp):
TTAAAACCATGATGGAAACAATACAAAAAGAGAGAAGAAACCACGTACGATCAAGATTTGAATTA
ACAGTGTTCAGTTTTTTAAACGGCTGAAGGTCAGAAGATGATAAATATAGATCCTACTGGCAATT
GTGAGGCTCATCCAACGATGCAAATCGCTACAAAAAAATTTTGTTGA
Found at i:144408 original size:29 final size:30
Alignment explanation
Indices: 144363--144419 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
144353 AGCCCTCCGA
144363 CTATTAATAGTTACAAAA-TAATTATTTAT
1 CTATTAATAGTTACAAAACTAATTATTTAT
* *
144392 CTATTTATATGTT-CAAAACTTATTATTT
1 CTATTAATA-GTTACAAAACTAATTATTT
144420 TTCGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (30 bp):
CTATTAATAGTTACAAAACTAATTATTTAT
Found at i:144755 original size:17 final size:16
Alignment explanation
Indices: 144735--144781 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
144725 ATAATCTTGT
144735 AAAACAAATAAAATAAC
1 AAAA-AAATAAAATAAC
144752 -AAAAAATCATAAATAAC
1 AAAAAAAT-A-AAATAAC
*
144769 AAAAAATTAAAAT
1 AAAAAAATAAAAT
144782 TCAGTCAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 8 0.31
18 6 0.23
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAAATAAAATAAC
Found at i:146693 original size:21 final size:21
Alignment explanation
Indices: 146637--146695 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
146627 CCGCGTAGAA
** *
146637 ATGTCCCGAAGGATAACATAT
1 ATGTCCCGAAGGACCACATAG
*
146658 ATGTCCCGAAGGACCGCATAG
1 ATGTCCCGAAGGACCACATAG
146679 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
146696 TCCTTAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAG
Found at i:146797 original size:42 final size:42
Alignment explanation
Indices: 146701--146798 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
146691 ACCACTCCTT
* * * *
146701 AAGGATCACATATATATTCCAAATGACCAAATATGTGTCCCG
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
* ** * ** *
146743 AAGAACTGCATATATGTTCCAAAGGATTACATATATATCCCG
1 AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
146785 AAGGACCACATATA
1 AAGGACCACATATA
146799 ACCCGCGACT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (42 bp):
AAGGACCACATATATATTCCAAAGGACCAAATATATATCCCG
Found at i:151375 original size:15 final size:15
Alignment explanation
Indices: 151352--151395 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
151342 TGATCATGTA
151352 ATCATATAATTTATT
1 ATCATATAATTTATT
* *
151367 ATCACATAAATTA-T
1 ATCATATAATTTATT
151381 AGTCATATAATTTAT
1 A-TCATATAATTTAT
151396 CACACATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (15 bp):
ATCATATAATTTATT
Found at i:154490 original size:17 final size:17
Alignment explanation
Indices: 154452--154490 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
154442 TAAAATGAAT
*
154452 AAAATAGCAGAAAATCA
1 AAAATAACAGAAAATCA
* *
154469 CAAATAACAGAAAATTA
1 AAAATAACAGAAAATCA
154486 AAAAT
1 AAAAT
154491 TCAGTCAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAATAACAGAAAATCA
Found at i:162404 original size:25 final size:24
Alignment explanation
Indices: 162361--162409 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
162351 CACCTCTGAG
**
162361 AATTTTAAATTATCGCCCCTACCAA
1 AATTTTAAAAGATCGCCCCT-CCAA
*
162386 AATTTTAAAAGATCTCCCCTCCAA
1 AATTTTAAAAGATCGCCCCTCCAA
162410 CATAATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (24 bp):
AATTTTAAAAGATCGCCCCTCCAA
Found at i:168350 original size:18 final size:18
Alignment explanation
Indices: 168314--168347 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
168304 GTACATGCCC
168314 AAACCTAGATACTAACCT
1 AAACCTAGATACTAACCT
*
168332 AAACCTA-ATCCTAACC
1 AAACCTAGATACTAACC
168348 CTAGAGATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.32, G:0.03, T:0.21
Consensus pattern (18 bp):
AAACCTAGATACTAACCT
Found at i:181078 original size:7 final size:7
Alignment explanation
Indices: 181066--181204 Score: 52
Period size: 7 Copynumber: 19.1 Consensus size: 7
181056 AATATGCTTG
181066 AAGAAAA
1 AAGAAAA
181073 AAGAAATA
1 AAGAAA-A
* **
181081 ATGAATG
1 AAGAAAA
181088 AA-AAAA
1 AAGAAAA
*
181094 ATG-AAA
1 AAGAAAA
181100 AAGTAAAA
1 AAG-AAAA
181108 AAGAAAA
1 AAGAAAA
*
181115 ATGAAAA
1 AAGAAAA
181122 AA-AGAAA
1 AAGA-AAA
* *
181129 GAGAAAG
1 AAGAAAA
*
181136 ATGAAAA
1 AAGAAAA
*
181143 AAAAAAA
1 AAGAAAA
181150 AATG-AAA
1 AA-GAAAA
*
181157 ATGAAAA
1 AAGAAAA
**
181164 TGGAAAAA
1 AAG-AAAA
181172 ATAGAAAA
1 A-AGAAAA
181180 AAGAAATA
1 AAGAAA-A
*
181188 AAAAATGAA
1 AAGAA--AA
181197 AAGAAAA
1 AAGAAAA
181204 A
1 A
181205 GAGGGTTCGA
Statistics
Matches: 94, Mismatches: 25, Indels: 26
0.65 0.17 0.18
Matches are distributed among these distances:
6 10 0.11
7 51 0.54
8 26 0.28
9 6 0.06
10 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
AAGAAAA
Found at i:181113 original size:42 final size:42
Alignment explanation
Indices: 181066--181157 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
181056 AATATGCTTG
* * * **
181066 AAGAAAAAAGAAATAATGAATGAAAAAAATGAAAAAGTAAAA
1 AAGAAAAAAGAAAAAAAGAAAGAAAAAAATGAAAAAAAAAAA
* * *
181108 AAGAAAAATGAAAAAAAGAAAGAGAAAGATGAAAAAAAAAAA
1 AAGAAAAAAGAAAAAAAGAAAGAAAAAAATGAAAAAAAAAAA
181150 AATGAAAA
1 AA-GAAAA
181158 TGAAAATGGA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 36 0.88
43 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (42 bp):
AAGAAAAAAGAAAAAAAGAAAGAAAAAAATGAAAAAAAAAAA
Found at i:181114 original size:21 final size:20
Alignment explanation
Indices: 181090--181204 Score: 73
Period size: 18 Copynumber: 5.9 Consensus size: 20
181080 AATGAATGAA
181090 AAAAATGAAAAAGTAAAAAAG
1 AAAAATGAAAAAG-AAAAAAG
*
181111 AAAAATGAAAAA-AAGAAAG
1 AAAAATGAAAAAGAAAAAAG
* **
181130 AGAAA-GATGAA-AAAAAA-
1 AAAAATGAAAAAGAAAAAAG
* **
181147 AAAAATGAAAATGAAAATGG
1 AAAAATGAAAAAGAAAAAAG
*
181167 AAAAAATAGAAAAA-AGAAATA-
1 -AAAAAT-GAAAAAGA-AAAAAG
181188 AAAAATG-AAAAGAAAAA
1 AAAAATGAAAAAGAAAAA
181205 GAGGGTTCGA
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
17 4 0.05
18 19 0.26
19 16 0.22
20 6 0.08
21 19 0.26
22 9 0.12
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (20 bp):
AAAAATGAAAAAGAAAAAAG
Found at i:181134 original size:14 final size:14
Alignment explanation
Indices: 181087--181163 Score: 66
Period size: 15 Copynumber: 5.4 Consensus size: 14
181077 AATAATGAAT
181087 GAAAAAAATGAAAAA
1 GAAAAAAA-GAAAAA
*
181102 GTAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
*
181116 TGAAAAAAAGAAAGA
1 -GAAAAAAAGAAAAA
* *
181131 G-AAAGATGAAAAA
1 GAAAAAAAGAAAAA
* *
181144 AAAAAAAATGAAAAT
1 GAAAAAAA-GAAAAA
181159 GAAAA
1 GAAAA
181164 TGGAAAAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
13 9 0.19
14 11 0.23
15 28 0.58
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.08
Consensus pattern (14 bp):
GAAAAAAAGAAAAA
Found at i:181141 original size:28 final size:28
Alignment explanation
Indices: 181084--181198 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 28
181074 AGAAATAATG
*
181084 AATGAAAAAAATGAAAAAGTAAAAAAGAAA
1 AATGAAAAAAATG-AAAAG-AAAAATGAAA
*
181114 AATGAAAAAAA-GAAAGAGAAAGATGAAA
1 AATGAAAAAAATGAAA-AGAAAAATGAAA
*
181142 AA-AAAAAAAATGAAAATG-AAAATGGAAAA
1 AATGAAAAAAATGAAAA-GAAAAAT-G-AAA
181171 AAT-AGAAAAAA-GAAATA-AAAAATGAAA
1 AATGA-AAAAAATGAAA-AGAAAAATGAAA
181198 A
1 A
181199 GAAAAAGAGG
Statistics
Matches: 72, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
27 16 0.22
28 20 0.28
29 18 0.25
30 18 0.25
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (28 bp):
AATGAAAAAAATGAAAAGAAAAATGAAA
Found at i:181143 original size:35 final size:33
Alignment explanation
Indices: 181068--181205 Score: 95
Period size: 36 Copynumber: 4.0 Consensus size: 33
181058 TATGCTTGAA
*
181068 GAAAAAAGAAATAATGAATGAAAAAAATGAAAAAGT
1 GAAAAAAGAAA-AATGAA--AAAAAAAAGAAAAAGT
*
181104 -AAAAAAGAAAAATGAAAAAAAGAAAGAGAAAGAT
1 GAAAAAAGAAAAATGAAAAAAA-AAAGAAAAAG-T
* ** *
181138 GAAAAAAAAAAAAATGAAAATGAAAATGGAAAAAAT
1 G-AAAAAAGAAAAATGAAAA--AAAAAAGAAAAAGT
181174 AGAAAAAAG--AAAT-AAAAAATGAAAAGAAAAAG
1 -GAAAAAAGAAAAATGAAAAAA--AAAAGAAAAAG
181206 AGGGTTCGAG
Statistics
Matches: 82, Mismatches: 11, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
31 2 0.02
32 5 0.06
33 20 0.24
34 11 0.13
35 10 0.12
36 24 0.29
37 7 0.09
38 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (33 bp):
GAAAAAAGAAAAATGAAAAAAAAAAGAAAAAGT
Found at i:181204 original size:57 final size:57
Alignment explanation
Indices: 181088--181204 Score: 141
Period size: 57 Copynumber: 2.1 Consensus size: 57
181078 ATAATGAATG
*
181088 AAAAAAATGAAAAAGTAAAAAAGAAAAATGAAAAAAAGAAAGAGAAAGATGAAAAAA
1 AAAAAAATGAAAAAGTAAAAAAGAAAAATGAAAAAAAGAAAGAGAAAAATGAAAAAA
* ** * *
181145 AAAAAAATGAAAATG-AAAATGGAAAAAAT-AGAAAAAAGAAATA-AAAAATGAAAAGA
1 AAAAAAATGAAAAAGTAAAAAAG-AAAAATGA-AAAAAAGAAAGAGAAAAATGAAAAAA
181201 AAAA
1 AAAA
181205 GAGGGTTCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
56 21 0.40
57 31 0.60
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (57 bp):
AAAAAAATGAAAAAGTAAAAAAGAAAAATGAAAAAAAGAAAGAGAAAAATGAAAAAA
Found at i:182267 original size:105 final size:105
Alignment explanation
Indices: 182137--182544 Score: 602
Period size: 105 Copynumber: 3.9 Consensus size: 105
182127 AACAACTATG
* ***
182137 ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTTTTCTTA
1 ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
* * *
182202 AAGGAGAAAGTTCAAAATAAGATGAACTTGTTCCTTTTAA
66 AAGGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
* *
182242 ATCCACCGTATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAATAACTCGCCTTA
1 ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
** * *
182307 AAGGAGAAAGTTTGTAATGAGAAGAACATGTTCCTTTCAA
66 AAGGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
* * *
182347 ATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCTTA
1 ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
182412 AAGGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
66 AAGGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
* * *
182452 ATCCATCGTATAA-GAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAATAACTCGCCTTA
1 ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
* * * *
182516 AAGGAGGAAGTTCGTCATGAGAAGAACTT
66 AAGGAGAAAGTTCATAATAAGAAGAACTT
182545 ACTCAACTTT
Statistics
Matches: 271, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
104 74 0.27
105 197 0.73
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (105 bp):
ATCCACCGCATAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGCCTTA
AAGGAGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCAA
Found at i:184399 original size:11 final size:11
Alignment explanation
Indices: 184377--184409 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
184367 TTATATATTT
184377 ATAAAG-TAAA
1 ATAAAGTTAAA
184387 ATAAAGTTAAA
1 ATAAAGTTAAA
*
184398 ATAAATTTAAA
1 ATAAAGTTAAA
184409 A
1 A
184410 ATGTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (11 bp):
ATAAAGTTAAA
Found at i:185551 original size:2 final size:2
Alignment explanation
Indices: 185544--185621 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
185534 TTTTACAAGA
185544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185622 GATTAGACTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:186611 original size:29 final size:29
Alignment explanation
Indices: 186555--186611 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
186545 GAAATATACT
* * *
186555 AAATTATCAGTTTTATACATAATGTTTTA
1 AAATTATCAATTTCATACATAATATTTTA
*
186584 AAATTATCAATTTCATACATAGTATTTT
1 AAATTATCAATTTCATACATAATATTTT
186612 CTGTCATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATTATCAATTTCATACATAATATTTTA
Found at i:189582 original size:15 final size:15
Alignment explanation
Indices: 189537--189596 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
189527 AATAGATTTC
189537 TTTTTATTTATTT-T
1 TTTTTATTTATTTAT
189551 GTTTCTTAATGTT-TTTAT
1 -TTT-TT-AT-TTATTTAT
189569 TATTTTA-TTATTTAT
1 T-TTTTATTTATTTAT
189584 TTTTTATTTATTT
1 TTTTTATTTATTT
189597 TGTTTCTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.18
15 15 0.39
16 3 0.08
17 8 0.21
18 5 0.13
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTATTTATTTAT
Found at i:189590 original size:11 final size:11
Alignment explanation
Indices: 189537--189597 Score: 63
Period size: 11 Copynumber: 5.3 Consensus size: 11
189527 AATAGATTTC
189537 TTTTTATTTAT
1 TTTTTATTTAT
189548 TTTGTT-TCTTAAT
1 TTT-TTAT-TT-AT
189561 GTTTTTA-TTAT
1 -TTTTTATTTAT
189572 TTTATTATTTAT
1 TTT-TTATTTAT
189584 TTTTTATTTAT
1 TTTTTATTTAT
189595 TTT
1 TTT
189598 GTTTCTAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
10 3 0.07
11 20 0.47
12 13 0.30
13 4 0.09
14 3 0.07
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:189611 original size:23 final size:23
Alignment explanation
Indices: 189537--189619 Score: 98
Period size: 23 Copynumber: 3.5 Consensus size: 23
189527 AATAGATTTC
189537 TTTTTATTTATTTTGTTTCTTAATG
1 TTTTTA-TTATTTTGTTTC-TAATG
* *
189562 TTTTTATTATTTTATTAT-TTAT-
1 TTTTTATTATTTTGTT-TCTAATG
189584 TTTTTATTTATTTTGTTTCTAATG
1 TTTTTA-TTATTTTGTTTCTAATG
189608 TTTTTATTATTT
1 TTTTTATTATTT
189620 AATTGTTTGA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
22 7 0.14
23 21 0.42
24 15 0.30
25 7 0.14
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (23 bp):
TTTTTATTATTTTGTTTCTAATG
Found at i:194014 original size:17 final size:17
Alignment explanation
Indices: 193988--194025 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
193978 TATTTTTAAT
193988 ATTT-TGTATTTAATTA
1 ATTTATGTATTTAATTA
*
194004 ATTTATGTATTTAATTT
1 ATTTATGTATTTAATTA
194021 ATTTA
1 ATTTA
194026 ATATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTATGTATTTAATTA
Found at i:194049 original size:17 final size:17
Alignment explanation
Indices: 193983--194047 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
193973 TATTATATTT
193983 TTAATATTTTGTATTTAA
1 TTAAT-TTTTGTATTTAA
*
194001 TTAATTTATGTATTTAA
1 TTAATTTTTGTATTTAA
* *
194018 TTTATTTAATATTTTATTTAA
1 -TTAATT--T-TTGTATTTAA
194039 TTAATTTTT
1 TTAATTTTT
194048 TTGCAGATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
17 13 0.34
18 11 0.29
20 6 0.16
21 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTAATTTTTGTATTTAA
Found at i:195824 original size:33 final size:33
Alignment explanation
Indices: 195764--195828 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
195754 CCTGATGCCA
* *
195764 CCGCCGCCACCATCACCTGGTTTTATGACTCCG
1 CCGCCGCCACCATCACCAGGTTATATGACTCCG
*
195797 CCGCCGCCACCTTCA-CAGAGTTATATGACTCC
1 CCGCCGCCACCATCACCAG-GTTATATGACTCC
195829 TCCTGGAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.18, C:0.42, G:0.17, T:0.23
Consensus pattern (33 bp):
CCGCCGCCACCATCACCAGGTTATATGACTCCG
Found at i:196291 original size:25 final size:26
Alignment explanation
Indices: 196222--196294 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
196212 TAGATTTTGT
* *
196222 TTTTTTATTAT-ATTTATATTTAGTAC
1 TTTTTTATTATAATTTTTA-TTAGGAC
* *
196248 -TTTTTATTGTAGTTGTTTATT-GGAC
1 TTTTTTATTATAATT-TTTATTAGGAC
196273 TTTTTTATTATAATTTTTATTA
1 TTTTTTATTATAATTTTTATTA
196295 TTATTTATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
25 18 0.49
26 16 0.43
27 3 0.08
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.66
Consensus pattern (26 bp):
TTTTTTATTATAATTTTTATTAGGAC
Found at i:204570 original size:3 final size:3
Alignment explanation
Indices: 204564--204590 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
204554 CTGCTGCTGC
204564 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
204591 CATACCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:212610 original size:23 final size:24
Alignment explanation
Indices: 212583--212633 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
212573 AAAGTTTCAT
*
212583 AAAATCAAATT-TTTATCATTTT-A
1 AAAATAAAATTATTT-TCATTTTGA
*
212606 AAAATAAAATTATTTTCGTTTTGA
1 AAAATAAAATTATTTTCATTTTGA
212630 AAAA
1 AAAA
212634 AACGTTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATAAAATTATTTTCATTTTGA
Found at i:222016 original size:2 final size:2
Alignment explanation
Indices: 221966--221997 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
221956 CATATAACAC
221966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
221998 TACACATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:230899 original size:196 final size:198
Alignment explanation
Indices: 230565--230959 Score: 703
Period size: 196 Copynumber: 2.0 Consensus size: 198
230555 ATAACAAATA
230565 TCTATAAACTCAACATACCCATTAATCATATAAACTTACACATATAACATATATTAAATATATAT
1 TCTATAAACTCAACATACCCATTAATCATATAAACTTACACATATAACATATATTAAATATATAT
230630 TTACGCATATCTATATATTAACAATCAATATTAATATATATAATATATTTAGTGACAAATATTAA
66 TTACGCATATCTATATATTAACAATCAATATTAATATATATAATATATTTAGTGACAAATATTAA
230695 TTAACTAATTAAAACATTA-TGATTTAAAGAGTAAAACAATAA-TATGTAAAAACTTGAATAAAA
131 TTAACTAATTAAAACATTATTGATTTAAAGAGTAAAACAATAAGTATGTAAAAACTTGAATAAAA
230758 ACC
196 ACC
230761 TCTATAAACTCAACATACCCATTAATCATAT-AACTTACACATAT-ACATATATTAAATATATAT
1 TCTATAAACTCAACATACCCATTAATCATATAAACTTACACATATAACATATATTAAATATATAT
230824 TTACGCATATAACCTATATATTTAACAATCAATATT-A-ATATATAATATATTTAGTGACAAATA
66 TTACGCATAT---CTATATA-TTAACAATCAATATTAATATATATAATATATTTAGTGACAAATA
230887 TTAATTAACTAATTAAAACATTATTGATTTAAAGAGTAAAACAATAATGTATGTAAAAACTTGAA
127 TTAATTAACTAATTAAAACATTATTGATTTAAAGAGTAAAACAATAA-GTATGTAAAAACTTGAA
230952 TAAAAACC
191 TAAAAACC
230960 CCGGACAAAA
Statistics
Matches: 192, Mismatches: 0, Indels: 11
0.95 0.00 0.05
Matches are distributed among these distances:
194 29 0.15
195 13 0.07
196 80 0.42
197 31 0.16
198 15 0.08
199 24 0.12
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.34
Consensus pattern (198 bp):
TCTATAAACTCAACATACCCATTAATCATATAAACTTACACATATAACATATATTAAATATATAT
TTACGCATATCTATATATTAACAATCAATATTAATATATATAATATATTTAGTGACAAATATTAA
TTAACTAATTAAAACATTATTGATTTAAAGAGTAAAACAATAAGTATGTAAAAACTTGAATAAAA
ACC
Found at i:237542 original size:280 final size:275
Alignment explanation
Indices: 237003--237552 Score: 741
Period size: 280 Copynumber: 2.0 Consensus size: 275
236993 AGTTATTAAG
* * * * *
237003 ATTTTTGTCTAACGCTTTGATCCTAGTGGCATCGATCCTTGATAGACCGATAATTTCTACCTGAC
1 ATTTCTGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGATAATCTCTACCTGAC
* * *
237068 GGTCTTTGAGATTCAATGGATATGTGCTGGGACAACATGATGAATCTGAAAAAATGAAAAGTCAT
66 GGTCTTTGAAATTCAATGGA-ATGTGCTGGGACAACAAGATGAATCTGAAAAAAGGAAAAGTCAT
* * *
237133 TTATTATTTGAGTAAAAAGTCACTGATTGCGGGATCTGGTACCTCCAATTCATAGCCATGTTGTG
130 TTACTATTTGAGTAAAAAGTCACTGATTGCGAGATCTGGTACCCCCAATTCATAGCCATGTTGTG
** *
237198 CTTTGGTATAGGATACCAAGAGGCTAAATTAGTATATGTCTACCATACCACTTGGATGATATCCA
195 CTTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGTATACCATACCACTTGGATGATATCCA
237263 -AACTCGATCCTTTGAA
260 GAA-TCGATCCTTTGAA
237279 ATTTCTGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACC-ATTAATCCTCTACCTG
1 ATTTCTGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGA-TAAT-CTCTACCTG
* *
237343 ACGGTCTTTGATAATTCAATGG-ATGTGTTGGGACAACAAGATGAATCTGGAAAAAAGGAAAGGA
64 ACGGTCTTTGA-AATTCAATGGAATGTGCTGGGACAACAAGATGAATCT-GAAAAAAGGAAAAG-
* * * *
237407 TCATTTACTA-TTGAGTAAAAATTTCACTGATTGCGAGATC-GGTACCCCCCAAATTTATAATCT
126 TCATTTACTATTTGAGTAAAAA-GTCACTGATTGCGAGATCTGGTA-CCCCC-AATTCAT-AGCC
* * * * *
237470 ATGTTTTGCTTTGGTATGGGATACCAAGGGGCTCAAGAAGTATATGTATACCATACCACTTGGCT
187 ATGTTGTGCTTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGTATACCATACCACTTGGAT
237535 GATATCCAGAATCGATCC
252 GATATCCAGAATCGATCC
237553 CCTTAAGTTC
Statistics
Matches: 239, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
275 1 0.00
276 72 0.30
277 46 0.19
278 38 0.16
279 6 0.03
280 74 0.31
281 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (275 bp):
ATTTCTGTCTAACGCTTTGATCATAGTGGCACCGATCCCTGATAGACCGATAATCTCTACCTGAC
GGTCTTTGAAATTCAATGGAATGTGCTGGGACAACAAGATGAATCTGAAAAAAGGAAAAGTCATT
TACTATTTGAGTAAAAAGTCACTGATTGCGAGATCTGGTACCCCCAATTCATAGCCATGTTGTGC
TTTGGTATAGGATACCAAGAGGCTAAAGAAGTATATGTATACCATACCACTTGGATGATATCCAG
AATCGATCCTTTGAA
Found at i:240094 original size:20 final size:20
Alignment explanation
Indices: 240066--240104 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
240056 TATTCAACCC
* *
240066 GAATCGAGTTAACTCGACCT
1 GAATCGAGTCAACCCGACCT
*
240086 GAATTGAGTCAACCCGACC
1 GAATCGAGTCAACCCGACC
240105 CGACCCGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (20 bp):
GAATCGAGTCAACCCGACCT
Found at i:240159 original size:22 final size:24
Alignment explanation
Indices: 240109--240171 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 24
240099 CCGACCCGAC
240109 CCGTTGACTTTGATCTGAGTCGTTAA
1 CCGTTGACTTTGA-CTGAGTC-TTAA
*
240135 CCGTTGACTTTGACT-AGT-TTGA
1 CCGTTGACTTTGACTGAGTCTTAA
240157 CCGTTGACTTTGACT
1 CCGTTGACTTTGACT
240172 TTGACAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 18 0.50
24 3 0.08
25 2 0.06
26 13 0.36
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (24 bp):
CCGTTGACTTTGACTGAGTCTTAA
Found at i:241911 original size:36 final size:35
Alignment explanation
Indices: 241820--241919 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 35
241810 TCTCTGCAGG
* * * *
241820 TTCAGCTTGATTAAACTGGTAATTCTTTATATAGG
1 TTCAGCTCGATTAAACTGGTAATTCCTTACATAGC
* ** *
241855 TTCAGATCGATCGAATTGGTAATTCCTTACAGTAGC
1 TTCAGCTCGATTAAACTGGTAATTCCTTACA-TAGC
*
241891 TTCAGCTCGGTTAAACTGGTAATTCCTTA
1 TTCAGCTCGATTAAACTGGTAATTCCTTA
241920 TAGAGGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 24 0.47
36 27 0.53
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (35 bp):
TTCAGCTCGATTAAACTGGTAATTCCTTACATAGC
Found at i:241946 original size:71 final size:71
Alignment explanation
Indices: 241820--241955 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 71
241810 TCTCTGCAGG
* * * * * *
241820 TTCAGCTTGATTAAACTGGTAATTCTTTATATAGGTTCAGATCGATCGAATTGGTAATTCCTTAC
1 TTCAGCTCGATTAAACTGGTAATTCCTTATAGAGGTTCAGACCGACCGAACTGGTAATTCCTTAC
241885 AGTAGC
66 AGTAGC
* * *
241891 TTCAGCTCGGTTAAACTGGTAATTCCTTATAGAGGTTTAGACCGACCGAGCTGGTAATTCCTTAC
1 TTCAGCTCGATTAAACTGGTAATTCCTTATAGAGGTTCAGACCGACCGAACTGGTAATTCCTTAC
241956 GGATCTAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (71 bp):
TTCAGCTCGATTAAACTGGTAATTCCTTATAGAGGTTCAGACCGACCGAACTGGTAATTCCTTAC
AGTAGC
Found at i:246024 original size:36 final size:35
Alignment explanation
Indices: 245981--246087 Score: 101
Period size: 35 Copynumber: 3.0 Consensus size: 35
245971 TTCCTTATAT
*
245981 AGGTTCAGACCGATCGAATTAGTAATTCCTTACGG
1 AGGTTCAGACCGATCGAACTAGTAATTCCTTACGG
* * * **
246016 CAGGTTCAG-CTCGGTCAAACTGGTAATTCCTTATAG
1 -AGGTTCAGAC-CGATCGAACTAGTAATTCCTTACGG
* *
246052 AGGTTCAGATCGATCGAGC-AGGTAATTCCTTACGG
1 AGGTTCAGACCGATCGAACTA-GTAATTCCTTACGG
246087 A
1 A
246088 TCGAATGTGA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
35 28 0.51
36 27 0.49
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (35 bp):
AGGTTCAGACCGATCGAACTAGTAATTCCTTACGG
Found at i:246077 original size:71 final size:70
Alignment explanation
Indices: 245946--246086 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 70
245936 GAAGTCTCTA
* * * **
245946 CAGGTTTAGCTCTATCAAACTGGTATTCCTTATATAGGTTCAGACCGATCGAATTAGTAATTCCT
1 CAGGTTCAGCTCGATCAAACTGGTATTCCTTATAGAGGTTCAGACCGATCGAAGCAGTAATTCCT
246011 TACGG
66 TACGG
* *
246016 CAGGTTCAGCTCGGTCAAACTGGTAATTCCTTATAGAGGTTCAGATCGATCG-AGCAGGTAATTC
1 CAGGTTCAGCTCGATCAAACTGGT-ATTCCTTATAGAGGTTCAGACCGATCGAAGCA-GTAATTC
246080 CTTACGG
64 CTTACGG
246087 ATCGAATGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 23 0.37
71 39 0.63
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (70 bp):
CAGGTTCAGCTCGATCAAACTGGTATTCCTTATAGAGGTTCAGACCGATCGAAGCAGTAATTCCT
TACGG
Found at i:247190 original size:13 final size:13
Alignment explanation
Indices: 247172--247197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247162 TAAATATAAG
247172 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
247185 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
247198 GAAAATTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:247191 original size:11 final size:11
Alignment explanation
Indices: 247169--247202 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
247159 CAATAAATAT
247169 AAGAAGAAAAA
1 AAGAAGAAAAA
247180 AAGAAAAGAAAAA
1 AAG--AAGAAAAA
247193 AAGAAGAAAA
1 AAGAAGAAAA
247203 TTAAGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:247194 original size:16 final size:16
Alignment explanation
Indices: 247169--247202 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
247159 CAATAAATAT
*
247169 AAGAAGAAAAAAAGAA
1 AAGAAAAAAAAAAGAA
*
247185 AAGAAAAAAAGAAGAA
1 AAGAAAAAAAAAAGAA
247201 AA
1 AA
247203 TTAAGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:248379 original size:76 final size:80
Alignment explanation
Indices: 248219--248405 Score: 229
Period size: 76 Copynumber: 2.4 Consensus size: 80
248209 TTAAGGGGAC
* * * * *
248219 AAGTTCATAATGAGAATAACTTGTTCAACCTTTGCTCAATTCCATCACATAAAGAGTTGGATCAT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTCTGCTCAATTCCATCACAGAAAGAGGTGGATCAA
* * *
248284 CATTTCTAGGAGAAG
66 CATTTCCAAGAGAAA
* * * *
248299 AAGTTCATAATAAAAAGAACTTGTTCAACC-CT-CTC-A-TCCATCACAGAATGAGGTGGGTCAA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCTCTGCTCAATTCCATCACAGAAAGAGGTGGATCAA
248360 CATTTCCAAGAGAAA
66 CATTTCCAAGAGAAA
*
248375 AAGTTCATGATGAGAAGAACTTGTTCAACCT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCT
248406 TGACTTATCC
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
76 59 0.65
77 1 0.01
78 3 0.03
79 1 0.01
80 27 0.30
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (80 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCTCTGCTCAATTCCATCACAGAAAGAGGTGGATCAA
CATTTCCAAGAGAAA
Found at i:248747 original size:78 final size:78
Alignment explanation
Indices: 248610--248756 Score: 249
Period size: 78 Copynumber: 1.9 Consensus size: 78
248600 TAGCTCAAGG
* * *
248610 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATTAGAAGAACTTGTTCAACCTTGACTCAT
1 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
248675 CCATCACAGAAGA
66 CCATCACAGAAGA
* *
248688 AGGTGGATCAACATTTCCAAGAGAATAATTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
1 AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
248753 CCAT
66 CCAT
248757 AAAAAAAGAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (78 bp):
AGGTGGATCAACATTTCCAAGAGAAGAAGTTCATAATAAGAAGAACTTGATCAAACTTGACTCAT
CCATCACAGAAGA
Found at i:251251 original size:14 final size:14
Alignment explanation
Indices: 251234--251261 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
251224 TAAAATGATT
251234 TTTTAAAATTAAAA
1 TTTTAAAATTAAAA
251248 TTTTAAAATTAAAA
1 TTTTAAAATTAAAA
251262 GACGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTAAAATTAAAA
Found at i:260129 original size:18 final size:17
Alignment explanation
Indices: 260097--260134 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
260087 TAATCATAGA
260097 TAGAATTTTAACTTAGC
1 TAGAATTTTAACTTAGC
*
260114 TAGAACTTTTACCTTAGC
1 TAGAA-TTTTAACTTAGC
260132 TAG
1 TAG
260135 GACTCTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (17 bp):
TAGAATTTTAACTTAGC
Found at i:263327 original size:23 final size:23
Alignment explanation
Indices: 263290--263399 Score: 105
Period size: 23 Copynumber: 4.8 Consensus size: 23
263280 CAGCTCGTAT
*
263290 AAATGCACCGAAGTGCCACATAG
1 AAATGCACTGAAGTGCCACATAG
* * * *
263313 AATTGCACTGTAGTGCCGCGTAG
1 AAATGCACTGAAGTGCCACATAG
263336 AAATGCA-TCGAAGTGCCACATAG
1 AAATGCACT-GAAGTGCCACATAG
* * * * *
263359 AATTGCATTGTAGTGCCGCGTAG
1 AAATGCACTGAAGTGCCACATAG
*
263382 AAATGCACCGAAGTGCCA
1 AAATGCACTGAAGTGCCA
263400 TATAAGATGT
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
22 1 0.01
23 65 0.97
24 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACTGAAGTGCCACATAG
Found at i:263357 original size:46 final size:46
Alignment explanation
Indices: 263285--263399 Score: 203
Period size: 46 Copynumber: 2.5 Consensus size: 46
263275 CACCACAGCT
*
263285 CGTATAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
* *
263331 CGTAGAAATGCATCGAAGTGCCACATAGAATTGCATTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
263377 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
263400 TATAAGATGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (46 bp):
CGTAGAAATGCACCGAAGTGCCACATAGAATTGCACTGTAGTGCCG
Found at i:268696 original size:23 final size:23
Alignment explanation
Indices: 268670--268734 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
268660 CACCACAGCT
* *
268670 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGACA
* * * *
268693 CGTAGAATTGCACTGTAGT-ACG
1 CGTAGAAATGCACCGAAGTGACA
268715 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
268735 TCATATAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 17 0.53
23 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGACA
Found at i:275148 original size:34 final size:34
Alignment explanation
Indices: 275103--275171 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
275093 GTGAAACAAT
**
275103 GACAACATCCAAAAATCTGGCATCTCACGGTCAA
1 GACAACATCCAAAAATCCAGCATCTCACGGTCAA
*
275137 GACAACTTCCAAAAATCCAGCATCTCACGGTCAA
1 GACAACATCCAAAAATCCAGCATCTCACGGTCAA
275171 G
1 G
275172 TCATATCACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.17
Consensus pattern (34 bp):
GACAACATCCAAAAATCCAGCATCTCACGGTCAA
Found at i:277663 original size:26 final size:27
Alignment explanation
Indices: 277634--277686 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
277624 TAATATGGTA
277634 ATTTTGAAAAT-TTAT-TTTTTAAAAAG
1 ATTTT-AAAATATTATATTTTTAAAAAG
*
277660 ATTTTAAAATATTTTATTTTTAAAAAG
1 ATTTTAAAATATTATATTTTTAAAAAG
277687 CCCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (27 bp):
ATTTTAAAATATTATATTTTTAAAAAG
Found at i:281921 original size:6 final size:6
Alignment explanation
Indices: 281910--281944 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
281900 TGTTGATAAT
*
281910 TTCTCC TTCTCC TTCTCC TTCTCC TTCTTC TTCTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTC
281945 AACTCATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TTCTCC
Found at i:284894 original size:21 final size:20
Alignment explanation
Indices: 284870--284935 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
284860 CTGATAGATG
284870 ACCCAAAGAATTTTACAAATT
1 ACCCAAAG-ATTTTACAAATT
**
284891 ACCCAAAGGCTTTACAAATT
1 ACCCAAAGATTTTACAAATT
* *
284911 ACCCAGAGGATTTT-CAAATG
1 ACCCA-AAGATTTTACAAATT
284931 ACCCA
1 ACCCA
284936 GAGGCTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.24
Consensus pattern (20 bp):
ACCCAAAGATTTTACAAATT
Found at i:284906 original size:20 final size:20
Alignment explanation
Indices: 284881--284943 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
284871 CCCAAAGAAT
*
284881 TTTACAAATTACCCAAAGGC
1 TTTACAAATTACCCAGAGGC
*
284901 TTTACAAATTACCCAGAGGA
1 TTTACAAATTACCCAGAGGC
* *
284921 TTTTCAAATGACCCAGAGGC
1 TTTACAAATTACCCAGAGGC
284941 TTT
1 TTT
284944 TAATTTTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (20 bp):
TTTACAAATTACCCAGAGGC
Done.