Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:3376045 original size:69 final size:69
Alignment explanation
Indices: 3375967--3376109 Score: 250
Period size: 69 Copynumber: 2.1 Consensus size: 69
3375957 TGTTGTATTT
* *
3375967 TGTATTTGGTTGGTTTAGTAGGAATGTAAGATTATCGTATTTGATTAAAGGAATAAAAGATTATT
1 TGTATTTGGTTGGTTTAGTAGGAATGTAAGATTATCGTATTTGATTAAAGAAATAAAAAATTATT
3376032 GGAA
66 GGAA
* *
3376036 TGTATTTGGTTGGTTTAGTAGGAATGTAAGATTATCGTGTTTGGTTAAAGAAATAAAAAATTATT
1 TGTATTTGGTTGGTTTAGTAGGAATGTAAGATTATCGTATTTGATTAAAGAAATAAAAAATTATT
3376101 GGAA
66 GGAA
3376105 TGTAT
1 TGTAT
3376110 ATTTTACCAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.40
Consensus pattern (69 bp):
TGTATTTGGTTGGTTTAGTAGGAATGTAAGATTATCGTATTTGATTAAAGAAATAAAAAATTATT
GGAA
Found at i:3376754 original size:42 final size:43
Alignment explanation
Indices: 3376707--3376822 Score: 155
Period size: 42 Copynumber: 2.7 Consensus size: 43
3376697 CCCGAATTCT
*
3376707 CGTGTTTGTTTCACGTAATTCGTTTTTC-GGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTTCTGAAAAATGTTTTCC
* * *
3376749 CGTGTTTGTTTCCCGTAATTC-ATTTTCTGAAAAATGTTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTTCTGAAAAATGTTTTCC
* * *
3376791 AGTGTTTGTTTCACGTAATTTGTTTTCCTGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTTCTGAA
3376823 CGTAATTCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 5 0.08
42 50 0.79
43 8 0.13
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.49
Consensus pattern (43 bp):
CGTGTTTGTTTCACGTAATTCGTTTTTCTGAAAAATGTTTTCC
Found at i:3377040 original size:31 final size:31
Alignment explanation
Indices: 3377005--3377123 Score: 87
Period size: 31 Copynumber: 4.1 Consensus size: 31
3376995 AAATATTATT
3377005 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
3377036 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
3377068 -ATTATA-TTATAATA--ATATAAGA-A-GA
1 TATTATATTTTTAATATTATATAAAATATAA
* *
3377093 TATTATATTTTT-ATTTTA-ATAATATATAA
1 TATTATATTTTTAATATTATATAAAATATAA
3377122 TA
1 TA
3377124 AAATTTTTTA
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
25 1 0.01
26 9 0.13
27 8 0.11
28 9 0.13
29 3 0.04
30 7 0.10
31 22 0.31
32 12 0.17
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:3377043 original size:22 final size:23
Alignment explanation
Indices: 3377013--3377056 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3377003 TTTATTAATT
3377013 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
3377036 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
3377057 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:3377143 original size:28 final size:28
Alignment explanation
Indices: 3377112--3377175 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
3377102 TTTATTTTAA
*
3377112 TAATATAT-AATAAAATTTTTTATATATT
1 TAATA-ATGAATAAAATTATTTATATATT
*
3377140 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAATTATTTATATATT
3377168 TAAATAAT
1 T-AATAAT
3377176 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TAATAATGAATAAAATTATTTATATATT
Found at i:3377155 original size:19 final size:19
Alignment explanation
Indices: 3377133--3377185 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
3377123 AAAATTTTTT
*
3377133 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
3377152 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
3377174 ATAT-TTTAATAA
1 ATATATTTAATAA
3377186 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:3377206 original size:23 final size:23
Alignment explanation
Indices: 3377180--3377224 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3377170 AATAATATTT
3377180 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3377203 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3377225 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3377323 original size:21 final size:21
Alignment explanation
Indices: 3377299--3377359 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3377289 AAAAATACTA
3377299 TTTAATAATAAATAAATTATT
1 TTTAATAATAAATAAATTATT
*
3377320 TTTAATAATAAA-AAA--AGT
1 TTTAATAATAAATAAATTATT
*
3377338 TTT-ATGATAAATAATATTATT
1 TTTAATAATAAATAA-ATTATT
3377359 T
1 T
3377360 ATTGTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 1 0.03
20 3 0.09
21 15 0.45
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTAATAATAAATAAATTATT
Found at i:3377519 original size:14 final size:14
Alignment explanation
Indices: 3377485--3377525 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3377475 AAATGTAATT
*
3377485 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
3377499 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
3377513 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
3377526 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:3377573 original size:20 final size:20
Alignment explanation
Indices: 3377515--3377564 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3377505 CCGGAAAACG
3377515 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3377535 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3377555 TTTTCCAGAA
1 TTTTCCAGAA
3377565 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3377589 original size:29 final size:30
Alignment explanation
Indices: 3377547--3377617 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
3377537 TTCCAGAAAT
3377547 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
3377576 GTAATTCATTTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
3377606 GTAATTCATTTT
1 GTAATTCATTTT
3377618 TCGAAAAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:3377619 original size:15 final size:15
Alignment explanation
Indices: 3377547--3377617 Score: 92
Period size: 15 Copynumber: 4.8 Consensus size: 15
3377537 TTCCAGAAAT
3377547 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
3377562 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
3377576 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
*
3377591 GTAATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
3377606 GTAATTCATTTT
1 GTAATTCATTTT
3377618 TCGAAAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
14 16 0.33
15 28 0.58
16 4 0.08
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:3378873 original size:44 final size:44
Alignment explanation
Indices: 3378801--3378915 Score: 117
Period size: 43 Copynumber: 2.6 Consensus size: 44
3378791 TAAAACATAT
* * * * * *
3378801 TTACCCTTGGATACATCAAATGAACCTGGGGGAAACTAT-AAGGC
1 TTACCCTTGCACACAACAAAGGAGCCT-GGGGAAACTATAAAGAC
*
3378845 TTACCCTTGCACACAACAAAGGAGCCT-GGGAAACTGTAAAGAC
1 TTACCCTTGCACACAACAAAGGAGCCTGGGGAAACTATAAAGAC
* * *
3378888 TTACCCTTGCACATAGCAGAGGAGCCTG
1 TTACCCTTGCACACAACAAAGGAGCCTG
3378916 ATGAAAACAG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 9 0.15
43 28 0.47
44 22 0.37
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (44 bp):
TTACCCTTGCACACAACAAAGGAGCCTGGGGAAACTATAAAGAC
Found at i:3378897 original size:43 final size:42
Alignment explanation
Indices: 3378830--3378915 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
3378820 ATGAACCTGG
*
3378830 GGGAAACTATAAGGCTTACCCTTGCACACAACAAAGGAGCCT
1 GGGAAACTATAAGACTTACCCTTGCACACAACAAAGGAGCCT
* * * *
3378872 GGGAAACTGTAAAGACTTACCCTTGCACATAGCAGAGGAGCCT
1 GGGAAACTAT-AAGACTTACCCTTGCACACAACAAAGGAGCCT
3378915 G
1 G
3378916 ATGAAAACAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 9 0.24
43 29 0.76
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (42 bp):
GGGAAACTATAAGACTTACCCTTGCACACAACAAAGGAGCCT
Found at i:3383400 original size:43 final size:43
Alignment explanation
Indices: 3383287--3383660 Score: 365
Period size: 44 Copynumber: 8.6 Consensus size: 43
3383277 TGCAAAAATA
* * * * * *
3383287 GTAAGGTCTTACCCTTGCACATAGCAAAAGAGCCTGGGGAACCG
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * ** *
3383331 GTAAGGTTTTACCCTTGCACATAGTAAAGGAACCT-GAGAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * ** **
3383374 ATAAGGTCTTACCCTTACACACAGTAAATAAACCTGGGGAAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGG-AAACT
** * * *
3383419 GTAAGGCTTACTTTTGCATACAACAAAGGAACTTGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
3383462 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG-GAAACT
* *
3383506 GTAAAGCTTACCCTTGTACACAACAAAGGAACCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGGGAAACT
* * * * *
3383550 GTAAGGCTTACCCTTACACATAGCAAATGAACATGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
* * * *
3383593 ATAAGGCTTACCCTTACACACAACAAAGGAGCCT-GGGAAACA
1 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
*
3383635 GTAAGGACTTACCCTTGCACATAACA
1 GTAAGG-CTTACCCTTGCACACAACA
3383661 GATAAGCCTG
Statistics
Matches: 276, Mismatches: 49, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
42 12 0.04
43 125 0.45
44 126 0.46
45 13 0.05
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (43 bp):
GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACT
Found at i:3383410 original size:87 final size:86
Alignment explanation
Indices: 3383288--3383655 Score: 366
Period size: 87 Copynumber: 4.2 Consensus size: 86
3383278 GCAAAAATAG
* * * * *
3383288 TAAGGTCTTACCCTTGCACATAGCAAA-AGAGCCTGGGGAACCGGTAAGGTTTTACCCTTGCACA
1 TAAGG-CTTACCCTTGCACACAGCAAATA-AACCTGGGGAAACTGTAAGG-CTTACCCTTGCACA
* **
3383352 TAGTAAAGGAACCT-GAGAAACTA
63 CAACAAAGGAACCTGGAGAAACTA
* * ** *
3383375 TAAGGTCTTACCCTTACACACAGTAAATAAACCTGGGGAAAACTGTAAGGCTTACTTTTGCATAC
1 TAAGG-CTTACCCTTGCACACAGCAAATAAACCTGGGG-AAACTGTAAGGCTTACCCTTGCACAC
* *
3383440 AACAAAGGAACTTGGAGAAACTG
64 AACAAAGGAACCTGGAGAAACTA
* ** * *
3383463 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAGAAACTGTAAAGCTTACCCTTGTACACA
1 TAAGGCTTACCCTTGCACACAGCAAATAAACCTGGG-GAAACTGTAAGGCTTACCCTTGCACACA
* *
3383528 ACAAAGGAACCTGGGGGAAACTG
65 ACAAAGGAACCT-GGAGAAACTA
* * * * * *
3383551 TAAGGCTTACCCTTACACATAGCAAATGAACATGGGGAAACTATAAGGCTTACCCTTACACACAA
1 TAAGGCTTACCCTTGCACACAGCAAATAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAA
*
3383616 CAAAGGAGCCTGG-GAAAC-A
66 CAAAGGAACCTGGAGAAACTA
3383635 GTAAGGACTTACCCTTGCACA
1 -TAAGG-CTTACCCTTGCACA
3383656 TAACAGATAA
Statistics
Matches: 235, Mismatches: 39, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
85 10 0.04
86 15 0.06
87 146 0.62
88 64 0.27
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (86 bp):
TAAGGCTTACCCTTGCACACAGCAAATAAACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAA
CAAAGGAACCTGGAGAAACTA
Found at i:3383670 original size:43 final size:42
Alignment explanation
Indices: 3383287--3383660 Score: 320
Period size: 43 Copynumber: 8.6 Consensus size: 42
3383277 TGCAAAAATA
* * * * *
3383287 GTAAGGTCTTACCCTTGCACATAGCAAAAGAGCCTGGGGAACCG
1 GTAAGG-CTTACCCTTGCACACAAC-AAAGAACCTGGGGAAACT
* * ** *
3383331 GTAAGGTTTTACCCTTGCACATAGTAAAGGAACCT-GAGAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAA-GAACCTGGGGAAACT
* * ** *
3383374 ATAAGGTCTTACCCTTACACACAGTAAATAAACCTGGGGAAAACT
1 GTAAGG-CTTACCCTTGCACACAACAAA-GAACCTGGGG-AAACT
** * * *
3383419 GTAAGGCTTACTTTTGCATACAACAAAGGAACTTGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAA-GAACCTGGGGAAACT
3383462 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAA-GAACCTGGG-GAAACT
* *
3383506 GTAAAGCTTACCCTTGTACACAACAAAGGAACCTGGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAA-GAACCT-GGGGAAACT
* * * *
3383550 GTAAGGCTTACCCTTACACATAGCAAATGAACATGGGGAAACT
1 GTAAGGCTTACCCTTGCACACAACAAA-GAACCTGGGGAAACT
* * * *
3383593 ATAAGGCTTACCCTTACACACAACAAAGGAGCCT-GGGAAACA
1 GTAAGGCTTACCCTTGCACACAACAAA-GAACCTGGGGAAACT
*
3383635 GTAAGGACTTACCCTTGCACATAACA
1 GTAAGG-CTTACCCTTGCACACAACA
3383661 GATAAGCCTG
Statistics
Matches: 276, Mismatches: 48, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
42 12 0.04
43 128 0.46
44 123 0.45
45 13 0.05
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACACAACAAAGAACCTGGGGAAACT
Found at i:3393629 original size:98 final size:98
Alignment explanation
Indices: 3393460--3393650 Score: 319
Period size: 98 Copynumber: 1.9 Consensus size: 98
3393450 ACTGGCTTTT
*
3393460 GGACAAATGGTTGTTGGCTTAAAGTTGTATCATTTTCTTTGAACTGTACTAAGACAAAGAATGAT
1 GGACAAATGGTTGTTGGCTTAAAGTTGTATAATTTTCTTTGAACTGTACTAAGACAAAGAATGAT
* *
3393525 CATTTATGAGTATAAGAGTTCCCTCAACAAGTA
66 AATTTATGAGCATAAGAGTTCCCTCAACAAGTA
* * * *
3393558 GGACAATTGGTTGTTGGCTTAAAGTTGTATAATTTTCTTTGAACTGTGCTAAGAGAAAGACTGAT
1 GGACAAATGGTTGTTGGCTTAAAGTTGTATAATTTTCTTTGAACTGTACTAAGACAAAGAATGAT
3393623 AATTTATGAGCATAAGAGTTCCCTCAAC
66 AATTTATGAGCATAAGAGTTCCCTCAAC
3393651 GGATCAGCTG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 86 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34
Consensus pattern (98 bp):
GGACAAATGGTTGTTGGCTTAAAGTTGTATAATTTTCTTTGAACTGTACTAAGACAAAGAATGAT
AATTTATGAGCATAAGAGTTCCCTCAACAAGTA
Found at i:3397189 original size:124 final size:124
Alignment explanation
Indices: 3397050--3397306 Score: 487
Period size: 124 Copynumber: 2.1 Consensus size: 124
3397040 GTTTATGTTC
*
3397050 GTTTGTTTATTTTTTAAGGTGTTTATGTTTGGTTTTTGTTCATTTAAATTTTTAGTATCGTATTT
1 GTTTGTTTATTTTTTAAGGTGTTTATGTTTGATTTTTGTTCATTTAAATTTTTAGTATCGTATTT
*
3397115 CTGTTCATTTATTTATTTTTGAAGTTGTCCGTGTTCGTTTATTTATTATTCCCGAACAT
66 CTGTTCATTTATTTATTTTTGAAGCTGTCCGTGTTCGTTTATTTATTATTCCCGAACAT
*
3397174 GTTTGTTTATTTTTTAAGGTGTTTATTTTTGATTTTTGTTCATTTAAATTTTTAGTATCGTATTT
1 GTTTGTTTATTTTTTAAGGTGTTTATGTTTGATTTTTGTTCATTTAAATTTTTAGTATCGTATTT
3397239 CTGTTCATTTATTTATTTTTGAAGCTGTCCGTGTTCGTTTATTTATTATTCCCGAACAT
66 CTGTTCATTTATTTATTTTTGAAGCTGTCCGTGTTCGTTTATTTATTATTCCCGAACAT
3397298 GTTTGTTTA
1 GTTTGTTTA
3397307 ATGTTCGAGA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 130 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (124 bp):
GTTTGTTTATTTTTTAAGGTGTTTATGTTTGATTTTTGTTCATTTAAATTTTTAGTATCGTATTT
CTGTTCATTTATTTATTTTTGAAGCTGTCCGTGTTCGTTTATTTATTATTCCCGAACAT
Found at i:3397985 original size:38 final size:38
Alignment explanation
Indices: 3397943--3398021 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3397933 GCCACTCGCT
3397943 GCAAGGAATTTGTTCGTCCGATTTTCTTTTCCGGTACG
1 GCAAGGAATTTGTTCGTCCGATTTTCTTTTCCGGTACG
3397981 GCAAGGAATTTGTTCGTCCGATTTTCTTTTCCGGTACG
1 GCAAGGAATTTGTTCGTCCGATTTTCTTTTCCGGTACG
3398019 GCA
1 GCA
3398022 GATCCTCCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (38 bp):
GCAAGGAATTTGTTCGTCCGATTTTCTTTTCCGGTACG
Found at i:3399836 original size:31 final size:31
Alignment explanation
Indices: 3399798--3399859 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
3399788 TCCGAATTTT
3399798 CTCCTAATAGTTATCTATGTTTCTAATTGTG
1 CTCCTAATAGTTATCTATGTTTCTAATTGTG
* * *
3399829 CTCCTAATAGTTATTTATTTTTCTGATTGTG
1 CTCCTAATAGTTATCTATGTTTCTAATTGTG
3399860 TCAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.52
Consensus pattern (31 bp):
CTCCTAATAGTTATCTATGTTTCTAATTGTG
Found at i:3406278 original size:25 final size:25
Alignment explanation
Indices: 3406227--3406280 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
3406217 TCTAAAAGTC
* **
3406227 TAATAAAAAAATAAACATTTATTTT
1 TAATAAAAAAATAAACATATAAATT
* *
3406252 TAATAAAAAAATTAATATATAAATT
1 TAATAAAAAAATAAACATATAAATT
3406277 TAAT
1 TAAT
3406281 TTAAAATATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TAATAAAAAAATAAACATATAAATT
Found at i:3406289 original size:18 final size:17
Alignment explanation
Indices: 3406263--3406296 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3406253 AATAAAAAAA
*
3406263 TTAATATATAAATTTAAT
1 TTAAAATAT-AATTTAAT
3406281 TTAAAATATAATTTAA
1 TTAAAATATAATTTAA
3406297 ATATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAATATAATTTAAT
Found at i:3409008 original size:15 final size:15
Alignment explanation
Indices: 3408964--3409012 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 15
3408954 ATCCTTCAAA
3408964 GAGTATCGATACCTAAG
1 GAGTATCGATACC--AG
3408981 GAGTAGCATCGATACCAG
1 GAGT---ATCGATACCAG
3408999 GAGTATCGATACCA
1 GAGTATCGATACCA
3409013 ATGTACAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 10 0.34
17 4 0.14
18 6 0.21
20 9 0.31
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (15 bp):
GAGTATCGATACCAG
Found at i:3414327 original size:13 final size:13
Alignment explanation
Indices: 3414309--3414333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3414299 TCCAGAGTTC
3414309 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
3414322 TCTTCTTCTTCT
1 TCTTCTTCTTCT
3414334 CCACGTGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:3415030 original size:24 final size:24
Alignment explanation
Indices: 3415003--3415080 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
3414993 GCATGGGTAG
*
3415003 TGCATCGATGCTCATGTTAAGGTA
1 TGCATCGATGCTCATGTTAAGGGA
*
3415027 TGCATCGATGCTCATATTAAGGGA
1 TGCATCGATGCTCATGTTAAGGGA
3415051 TGCATCGATGCTCATGTTAAGGGA
1 TGCATCGATGCTCATGTTAAGGGA
3415075 TGCATC
1 TGCATC
3415081 AATACACTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (24 bp):
TGCATCGATGCTCATGTTAAGGGA
Found at i:3416013 original size:14 final size:14
Alignment explanation
Indices: 3415994--3416021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3415984 CCATGTGTCT
3415994 ATGTGTATATGTGA
1 ATGTGTATATGTGA
3416008 ATGTGTATATGTGA
1 ATGTGTATATGTGA
3416022 TACAAGTTAT
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:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
ATGTGTATATGTGA
Found at i:3416205 original size:32 final size:32
Alignment explanation
Indices: 3416164--3416255 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 32
3416154 AGTCGAGGAT
*
3416164 TTACCTATGTTCTATGGAACATATGGACAAAA
1 TTACCTATGTTCTATAGAACATATGGACAAAA
* * * *
3416196 TTACCTATG-TCTTTTGAGACATAT-GA-ATAG
1 TTACCTATGTTCTATAGA-ACATATGGACAAAA
3416226 TATACCTATGTTCTA-AGAAGCATATGGACA
1 T-TACCTATGTTCTATAGAA-CATATGGACA
3416256 GTTTACCTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
30 4 0.08
31 23 0.48
32 20 0.42
33 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTATAGAACATATGGACAAAA
Found at i:3417267 original size:45 final size:46
Alignment explanation
Indices: 3417178--3417272 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 46
3417168 TGACCATACT
* *
3417178 CTATGTGTTATGTGATCTATGTGATTATATGAGAATATGATATAAG
1 CTATGTGTTATGTGACCTAAGTGATTATATGAGAATATGATATAAG
* *
3417224 CTATGTGTTAT-TGACCTAAGTGATTATATGA-ACATGTGGTATAAG
1 CTATGTGTTATGTGACCTAAGTGATTATATGAGA-ATATGATATAAG
3417269 CTAT
1 CTAT
3417273 ATGATAAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 1 0.02
45 32 0.73
46 11 0.25
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (46 bp):
CTATGTGTTATGTGACCTAAGTGATTATATGAGAATATGATATAAG
Found at i:3417337 original size:8 final size:8
Alignment explanation
Indices: 3417324--3417355 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3417314 ACTACGTTAT
3417324 TATATGAA
1 TATATGAA
3417332 TATATGAA
1 TATATGAA
3417340 TATATGAA
1 TATATGAA
*
3417348 TATGTGAA
1 TATATGAA
3417356 ATGTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (8 bp):
TATATGAA
Found at i:3417727 original size:6 final size:6
Alignment explanation
Indices: 3417716--3417805 Score: 72
Period size: 6 Copynumber: 14.8 Consensus size: 6
3417706 GAACAATGAG
* * * * *
3417716 TGATAA TGATAA TGATAA TGATAA TGGTGA TGATGA TGATGA TGAGAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
** * ** *
3417764 TAGATGT TGACAA TGATAA TGATGT TGATAA TGATGA TGATA
1 T-GATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATA
3417806 TGTATATATA
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
6 62 0.95
7 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.33
Consensus pattern (6 bp):
TGATAA
Found at i:3417737 original size:18 final size:18
Alignment explanation
Indices: 3417711--3417804 Score: 89
Period size: 18 Copynumber: 5.1 Consensus size: 18
3417701 TAAATGAACA
3417711 ATGAGTGATAATGATAATG
1 ATGA-TGATAATGATAATG
* * *
3417730 ATAATGATAATGGTGATG
1 ATGATGATAATGATAATG
* *
3417748 ATGATGATGATGAGAATAG
1 ATGATGATAATGATAAT-G
* *
3417767 ATGTTGACAATGATAATG
1 ATGATGATAATGATAATG
* *
3417785 ATGTTGATAATGATGATG
1 ATGATGATAATGATAATG
3417803 AT
1 AT
3417805 ATGTATATAT
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
18 43 0.72
19 17 0.28
ACGTcount: A:0.39, C:0.01, G:0.27, T:0.33
Consensus pattern (18 bp):
ATGATGATAATGATAATG
Found at i:3419097 original size:2 final size:2
Alignment explanation
Indices: 3419090--3419123 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3419080 AATTCAAGAA
3419090 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
3419124 TATCCTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3421711 original size:16 final size:16
Alignment explanation
Indices: 3421670--3421711 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3421660 CCTACATTTT
* *
3421670 AATACCAAATATTTCG
1 AATACCCAATATTTCA
3421686 AATACCCAATATTTCA
1 AATACCCAATATTTCA
*
3421702 AATATCCAAT
1 AATACCCAAT
3421712 TATAGACACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (16 bp):
AATACCCAATATTTCA
Found at i:3434247 original size:21 final size:21
Alignment explanation
Indices: 3434223--3434262 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3434213 AAAATAATTA
* *
3434223 AATTTATTTATTTTGAAATCT
1 AATTTAATTATTCTGAAATCT
3434244 AATTTAATTATTCTGAAAT
1 AATTTAATTATTCTGAAAT
3434263 TTACATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTAATTATTCTGAAATCT
Found at i:3434827 original size:57 final size:57
Alignment explanation
Indices: 3434727--3434862 Score: 177
Period size: 57 Copynumber: 2.4 Consensus size: 57
3434717 CCACAATTCG
*
3434727 TGCGTATGTGTTTGTTCTTGTTTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTAAT
1 TGCGTATGTGTCTGTTCTTG--TTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGT--T
** * *
3434788 TTTGTATGTGTCTGTTCTTG-TTTTT-TTTTCTTTTTTAAGTATGCAGTTATTCGTT
1 TGCGTATGTGTCTGTTCTTGTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTT
3434843 TGCGTATGTGTCTGTTCTTG
1 TGCGTATGTGTCTGTTCTTG
3434863 ATAATCACAG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
55 19 0.28
57 27 0.40
58 5 0.07
61 17 0.25
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (57 bp):
TGCGTATGTGTCTGTTCTTGTTTTTTCTTTTCTTTTCTAAGTATACAGTTATTCGTT
Found at i:3437460 original size:9 final size:9
Alignment explanation
Indices: 3437446--3437470 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3437436 ACACCTTGTA
3437446 GATGAAGAT
1 GATGAAGAT
3437455 GATGAAGAT
1 GATGAAGAT
3437464 GATGAAG
1 GATGAAG
3437471 TTGTTATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (9 bp):
GATGAAGAT
Found at i:3442993 original size:33 final size:33
Alignment explanation
Indices: 3442950--3443015 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
3442940 AGAAGGGGCG
3442950 GGGGGGGGGGGTCTTCATGAAAGACACAGATGGC
1 GGGGGGGGGGG-CTTCATGAAAGACACAGATGGC
3442984 GGGGGGGGGGGCTTCATGAAAGACACAGATGG
1 GGGGGGGGGGGCTTCATGAAAGACACAGATGG
3443016 TTCCATTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 21 0.66
34 11 0.34
ACGTcount: A:0.24, C:0.14, G:0.48, T:0.14
Consensus pattern (33 bp):
GGGGGGGGGGGCTTCATGAAAGACACAGATGGC
Found at i:3447823 original size:2 final size:2
Alignment explanation
Indices: 3447816--3447854 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3447806 ATTTAAAGAT
3447816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3447855 TCAACACAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3456431 original size:16 final size:17
Alignment explanation
Indices: 3456399--3456435 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3456389 TTCTTAGAAT
3456399 AAATTCTATCAAAAAAA
1 AAATTCTATCAAAAAAA
*
3456416 AAATTCTACCAAAAAAA
1 AAATTCTATCAAAAAAA
3456433 AAA
1 AAA
3456436 GTAGGTCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATTCTATCAAAAAAA
Found at i:3461153 original size:6 final size:7
Alignment explanation
Indices: 3461136--3461161 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3461126 AAATAGTAGA
3461136 AAAAAAC
1 AAAAAAC
3461143 AAAAAAC
1 AAAAAAC
3461150 AAAAAAC
1 AAAAAAC
3461157 AAAAA
1 AAAAA
3461162 GTAACAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:3461167 original size:17 final size:17
Alignment explanation
Indices: 3461121--3461168 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
3461111 ATAGATCAAC
*
3461121 AAAACAAATAGTAGA-AA
1 AAAACAAAAAGTA-ACAA
3461138 AAAAC-AAAA--AACAA
1 AAAACAAAAAGTAACAA
3461152 AAAACAAAAAGTAACAA
1 AAAACAAAAAGTAACAA
3461169 GAACCTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.04
14 8 0.31
15 4 0.15
16 3 0.12
17 10 0.38
ACGTcount: A:0.77, C:0.10, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAACAAAAAGTAACAA
Found at i:3462325 original size:87 final size:87
Alignment explanation
Indices: 3462179--3462341 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
3462169 TATGTTATAT
*
3462179 TATTTAACCAGAAATATTATCAAGTATAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
3462244 AGCGCTTATATAATAAAATAAG
66 AGCGCTTATATAATAAAATAAG
* *
3462266 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
3462331 AGCGCTTATAT
66 AGCGCTTATAT
3462342 TGACCTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAAG
Found at i:3462875 original size:182 final size:182
Alignment explanation
Indices: 3462477--3463318 Score: 1431
Period size: 182 Copynumber: 4.6 Consensus size: 182
3462467 TGCGTTCACC
** * * *
3462477 TTTTGTCATTTATAGACCGCTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
3462542 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCC-AAAAGTGTCG
*
3462607 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * * *
3462660 TTTGGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATTGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3462725 TTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
3462790 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
3462842 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3462907 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
3462969 ATACTTATAATAAATTATCGACACTTTCAACATAACTGGTAGCGCTTTACATG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
3463022 TTTTGTCATTTCGAGACCGGTATATGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
1 TTTTGTCATTTCGAGACCGGT-TTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* *
3463087 TTTTATAATGTATCGACACTTTATTGGCGCTATAAC-ACTTCTCTTTTAAATTCCAAAAGTGTCG
65 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
*
3463151 ATACCTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
3463204 TTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
3463269 TTTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
3463319 AAAGGTAAAA
Statistics
Matches: 621, Mismatches: 32, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
179 2 0.00
180 94 0.15
181 150 0.24
182 263 0.42
183 112 0.18
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:3463162 original size:362 final size:363
Alignment explanation
Indices: 3462477--3463317 Score: 1427
Period size: 362 Copynumber: 2.3 Consensus size: 363
3462467 TGCGTTCACC
** * * *
3462477 TTTTGTCATTTATAGACCGCTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
3462542 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTT-AATTCCAAAAAG-GTCG
* * *
3462607 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTGGTCATTTT
129 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTGGTCATTTC
* * *
3462672 GAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAATAT
194 GAGACCGGTTATGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAATAT
* *
3462737 CGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAA
259 CGACACTTTATTGGCGCTATAACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACCTATAATAA
3462802 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
324 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
3462842 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
3462907 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTCC-AAAA-GTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAATTCCAAAAAGGTCGA
* *
3462970 TACTTATAATAAATTATCGACACTTTCAACATAACTGGTAGCGCTTTACATGTTTTGTCATTTCG
130 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTGGTCATTTCG
**
3463035 AGACCGGTATATGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAATGTAT
195 AGACCGGT-TATGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAATAT
3463100 CGACACTTTATTGGCGCTATAAC-ACTTCTCTTTTAAATTCCAAAAGTGTCGATACCTATAATAA
259 CGACACTTTATTGGCGCTATAACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACCTATAATAA
3463164 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
324 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
3463204 TTTTGTCATTTCGAGACCAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
3463269 TTTATAAAGTATCGACACTTTATTGACGATATAACTTCTTCTCTTTTAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAA
3463318 AAAAGGTAAA
Statistics
Matches: 451, Mismatches: 23, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
361 4 0.01
362 257 0.57
363 74 0.16
364 4 0.01
365 110 0.24
366 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (363 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAATTCCAAAAAGGTCGAT
ACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACATGTTTGGTCATTTCGA
GACCGGTTATGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAATATCG
ACACTTTATTGGCGCTATAACTACTTCTCTTTTAAATTCCAAAAGTGTCGATACCTATAATAAAT
TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:3466288 original size:184 final size:184
Alignment explanation
Indices: 3465979--3466315 Score: 584
Period size: 184 Copynumber: 1.8 Consensus size: 184
3465969 TAAACGTATG
*
3465979 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTA
1 GACACAATATTAAAAAATGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTA
* * *
3466044 TATCGATTATATTAAAAAATTACCTATTACATTATAATTGTGGGTTTCGATGTTTTTTCAATCAA
66 TACCGATTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAATCAA
3466109 CACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACATAAAATTGC
131 CACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACATAAAATTGC
* *
3466163 GACACAATATTAAAAAATGTCGATATAGGTTTTATACCTATTCTCTCATAAAACCGGTATATTTA
1 GACACAATATTAAAAAATGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTA
* * **
3466228 TACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAATCGG
66 TACCGATTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAATCAA
3466293 CACTTTTTGAAAAGGTATCGACA
131 CACTTTTTGAAAAGGTATCGACA
3466316 CTTTATGTTG
Statistics
Matches: 143, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 143 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (184 bp):
GACACAATATTAAAAAATGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATATTTA
TACCGATTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTTTCAATCAA
CACTTTTTGAAAAGGTATCGACATTTTTTTCATCCATTCTGGACATAAAATTGC
Found at i:3467634 original size:12 final size:12
Alignment explanation
Indices: 3467604--3467673 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
3467594 ATTGTTTGGA
* *
3467604 TCATCATCATCA
1 TCATCGTCATCT
*
3467616 TCGTCGTCATCT
1 TCATCGTCATCT
3467628 TCATCGTCATCT
1 TCATCGTCATCT
*
3467640 TCATCGTCAGCT
1 TCATCGTCATCT
* *
3467652 TCATTGTCAGCT
1 TCATCGTCATCT
*
3467664 TCATCTTCAT
1 TCATCGTCAT
3467674 TGACAGCTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 49 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:3467673 original size:6 final size:6
Alignment explanation
Indices: 3467622--3467673 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
3467612 ATCATCGTCG
* * * *
3467622 TCATCT TCATCG TCATCT TCATCG TCAGCT TCAT-T GTCAGCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT -TCATCT TCATCT
3467670 TCAT
1 TCAT
3467674 TGACAGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
5 1 0.03
6 34 0.94
7 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.10, T:0.42
Consensus pattern (6 bp):
TCATCT
Found at i:3471721 original size:21 final size:21
Alignment explanation
Indices: 3471697--3471737 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3471687 CTTATGCCTC
3471697 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
3471718 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
3471738 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:3471840 original size:15 final size:15
Alignment explanation
Indices: 3471820--3471852 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3471810 ACTCTGTTTT
*
3471820 CCCTCACCGTCGTCC
1 CCCTCACCGTCATCC
3471835 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
3471850 CCC
1 CCC
3471853 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.64, G:0.09, T:0.18
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:3474356 original size:182 final size:181
Alignment explanation
Indices: 3473996--3474413 Score: 615
Period size: 182 Copynumber: 2.3 Consensus size: 181
3473986 GGTATCATTT
* *
3473996 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATC
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTG-TTGATCGATACAATTTTTGAAAGTATC
*
3474061 GACACTTTATAGGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAG
65 GACACTTTATAGGCACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAG
* * * * * **
3474126 TTTCGACACTTTCAATATATCCGGTAGCATTTTATCGGTTTCATCATTTTGA
130 TCTCGACACTTTAAATATATCCGGTACCAATTTACCGGTTTCATCATTTCAA
* *
3474178 TACCAGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATATAATTTTTGAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACAATTTTTGAAAGTATCG
* *
3474243 ACACTTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATACTAAAG
66 ACACTTTATAGGCACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-TAAAG
* *
3474308 TACT-GACACTTTAAATATATTCGGTACCAATTTACCGGTTTTATCATTTCAA
130 T-CTCGACACTTTAAATATATCCGGTACCAATTTACCGGTTTCATCATTTCAA
* * * *
3474360 TACTGGTTTTGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATAC-ATTTTT
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACAATTTTT
3474414 AATTTGGATC
Statistics
Matches: 212, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
181 87 0.41
182 124 0.58
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTTGATCGATACAATTTTTGAAAGTATCG
ACACTTTATAGGCACTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGT
CTCGACACTTTAAATATATCCGGTACCAATTTACCGGTTTCATCATTTCAA
Found at i:3478631 original size:14 final size:14
Alignment explanation
Indices: 3478608--3478637 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3478598 TACCATTGTT
3478608 CTCATATAGATCTC
1 CTCATATAGATCTC
*
3478622 CTCATCTAGATCTC
1 CTCATATAGATCTC
3478636 CT
1 CT
3478638 TTCAAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (14 bp):
CTCATATAGATCTC
Found at i:3480472 original size:22 final size:22
Alignment explanation
Indices: 3480441--3480483 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3480431 GTTTAAAAAT
3480441 ACTAACATTTATATAGCTATTA
1 ACTAACATTTATATAGCTATTA
*
3480463 ACTAATATTTATATAGCTATT
1 ACTAACATTTATATAGCTATT
3480484 TAATAAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.44
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATTA
Found at i:3487414 original size:29 final size:29
Alignment explanation
Indices: 3487367--3487435 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
3487357 AAGCTTCTAG
* * *
3487367 GTAATCTTACATTCACTCAATCAAACACT
1 GTAATCTTACACTCACTCAACCAAACACC
* * *
3487396 GTGATCTTACACTCCCTCAACCAAGCACC
1 GTAATCTTACACTCACTCAACCAAACACC
3487425 GTAATCTTACA
1 GTAATCTTACA
3487436 TTCCAACTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.33, C:0.32, G:0.07, T:0.28
Consensus pattern (29 bp):
GTAATCTTACACTCACTCAACCAAACACC
Found at i:3492532 original size:60 final size:61
Alignment explanation
Indices: 3492419--3492532 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
3492409 AATATGGTGG
* * * * *
3492419 ACTTTAGATACTTAGTTTGACAAAAAAAACTACTTTAAGTTCTTGGATGAAAAAAGTGAAT
1 ACTTTAGATACCTACTTTGACAAAAAAAACTACTTTAAGTACTTAGATAAAAAAAGTGAAT
* *
3492480 ACTTTAGGTACCTACTTTGATAAAAAAAA-TACTTTAAGTACTTAGATAAAAAA
1 ACTTTAGATACCTACTTTGACAAAAAAAACTACTTTAAGTACTTAGATAAAAAA
3492533 TATGACATGC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 21 0.46
61 25 0.54
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (61 bp):
ACTTTAGATACCTACTTTGACAAAAAAAACTACTTTAAGTACTTAGATAAAAAAAGTGAAT
Found at i:3493383 original size:20 final size:20
Alignment explanation
Indices: 3493309--3493677 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
3493299 GATTTTCCAT
* ** *
3493309 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3493329 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3493349 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493369 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
3493389 AATCACAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3493409 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493429 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3493449 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493469 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
3493489 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493509 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3493529 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493549 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3493569 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3493589 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3493609 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3493629 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3493649 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3493669 AATCACAAC
1 AATCGCAAC
3493678 ACTTAAATTT
Statistics
Matches: 303, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 295 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3494399 original size:24 final size:24
Alignment explanation
Indices: 3494360--3494406 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3494350 AAATTTGGTC
3494360 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3494384 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3494407 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3494598 original size:12 final size:12
Alignment explanation
Indices: 3494581--3494605 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3494571 ATATAATCCT
3494581 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3494593 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3494605 G
1 G
3494606 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3496910 original size:19 final size:19
Alignment explanation
Indices: 3496888--3497180 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
3496878 CGGAAAATAC
*
3496888 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3496907 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3496921 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3496941 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3496955 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3496974 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3496993 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
3497007 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
3497026 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497045 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497064 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497083 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497102 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497121 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3497135 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3497173 AATCGCAA
1 AATCGCAA
3497181 CGAGATAATC
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 165 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3497003 original size:52 final size:55
Alignment explanation
Indices: 3496916--3497202 Score: 356
Period size: 52 Copynumber: 5.4 Consensus size: 55
3496906 AAATCCCAAC
*
3496916 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
3496969 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
*
3497021 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
3497078 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
3497133 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
3497183 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
3497203 TATAAACGCA
Statistics
Matches: 222, Mismatches: 2, Indels: 21
0.91 0.01 0.09
Matches are distributed among these distances:
50 2 0.01
52 127 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 64 0.29
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:3497099 original size:128 final size:128
Alignment explanation
Indices: 3496888--3497202 Score: 462
Period size: 128 Copynumber: 2.6 Consensus size: 128
3496878 CGGAAAATAC
* *
3496888 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
3496948 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
3497007 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
3497072 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
3497135 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
3497195 TGCGAAAT
66 TGCGAAAT
3497203 TATAAACGCA
Statistics
Matches: 179, Mismatches: 7, Indels: 16
0.89 0.03 0.08
Matches are distributed among these distances:
119 24 0.13
121 1 0.01
123 34 0.19
124 17 0.09
125 2 0.01
126 2 0.01
127 1 0.01
128 98 0.55
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:3497318 original size:19 final size:19
Alignment explanation
Indices: 3497209--3497310 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3497199 AAATTATAAA
3497209 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3497228 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3497248 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3497264 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3497281 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3497300 CGCATTGCGAT
1 CGCATTGCGAT
3497311 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3497436 original size:14 final size:14
Alignment explanation
Indices: 3497417--3497453 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3497407 CATCAATTAC
3497417 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3497431 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3497445 ACAAATCAA
1 ACAAATCAA
3497454 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3499450 original size:19 final size:19
Alignment explanation
Indices: 3499356--3499488 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
3499346 TAGTTTACTT
* *
3499356 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3499376 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3499395 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3499414 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3499428 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3499447 TCGCAA--CGAAA-G---A
1 TCGCAACGCGAAATGAAAA
3499460 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
3499478 TCGCAATGCGA
1 TCGCAACGCGA
3499489 TTTTTTCGCG
Statistics
Matches: 95, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.07
14 8 0.08
15 5 0.05
16 7 0.07
17 10 0.11
18 11 0.12
19 35 0.37
20 12 0.13
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3499471 original size:32 final size:33
Alignment explanation
Indices: 3499393--3499483 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3499383 GCGAAACCAA
*
3499393 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3499426 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3499459 -ATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3499484 TGCGATTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 9 0.16
32 15 0.27
33 31 0.56
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3499533 original size:33 final size:33
Alignment explanation
Indices: 3499492--3499572 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
3499482 AATGCGATTT
**
3499492 TTTCGCGTTGCGA-TCTTGTCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTC-TGTCGTTGCGATTTTCA
3499525 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
3499558 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
3499573 TTGGTTTCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.07, C:0.20, G:0.27, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
Found at i:3499535 original size:19 final size:19
Alignment explanation
Indices: 3499511--3499609 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
3499501 GCGATCTTGT
3499511 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
3499530 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
3499544 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
3499563 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
3499582 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
3499602 TGTTGCGA
1 CGTTGCGA
3499610 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.60
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:3499824 original size:92 final size:92
Alignment explanation
Indices: 3499653--3500123 Score: 897
Period size: 92 Copynumber: 5.1 Consensus size: 92
3499643 TTGAATGGAT
*
3499653 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAATGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
3499718 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
3499746 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
3499811 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
3499838 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
3499903 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
*
3499930 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATATACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
3499995 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
3500022 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
3500087 AGTTTAGCAGAATTGGCAGCAACCGAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
3500115 AAATTTACT
1 AAATTTACT
3500124 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 274 0.73
93 99 0.27
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (92 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3501848 original size:14 final size:14
Alignment explanation
Indices: 3501829--3501918 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3501819 TTGAAATGAA
3501829 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3501843 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3501860 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3501876 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3501895 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3501909 AATCGCAACG
1 AATCGCAACG
3501919 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3501866 original size:33 final size:33
Alignment explanation
Indices: 3501821--3501935 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3501811 TCTTTTGGTT
3501821 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3501854 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3501887 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3501920 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3501936 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3501867 original size:19 final size:18
Alignment explanation
Indices: 3501828--3501940 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
3501818 GTTGAAATGA
3501828 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3501843 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3501860 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3501876 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3501893 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
3501909 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
3501926 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3501941 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3501971 original size:14 final size:14
Alignment explanation
Indices: 3501952--3502006 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3501942 TTTGGTTTCG
3501952 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3501966 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3501985 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3501999 CGTTGCGA
1 CGTTGCGA
3502007 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3501984 original size:33 final size:33
Alignment explanation
Indices: 3501936--3502006 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3501926 AAAATCGCAA
**
3501936 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3501969 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3502002 TGCGA
1 TGCGA
3502007 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3502014 original size:33 final size:33
Alignment explanation
Indices: 3501947--3502028 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
3501937 GCGATTTTGG
***
3501947 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
3501980 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
3502013 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
3502029 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:3502033 original size:20 final size:20
Alignment explanation
Indices: 3501959--3502047 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3501949 TCGCGTTGCG
3501959 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3501979 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
3501992 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3502012 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3502032 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3502048 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3502169 original size:33 final size:33
Alignment explanation
Indices: 3502127--3502197 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3502117 AATACTAACT
*
3502127 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3502160 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3502193 TGAAA
1 TGAAA
3502198 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3502430 original size:22 final size:22
Alignment explanation
Indices: 3502378--3502432 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3502368 TGGTTGTGAG
**
3502378 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3502400 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3502422 GGATTTCTTCG
1 GGATTTCTTCG
3502433 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3502603 original size:20 final size:20
Alignment explanation
Indices: 3502578--3502770 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
3502568 CTTTAAATAT
3502578 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
3502598 CGCGTTGCAATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3502620 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3502639 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3502659 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3502679 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3502699 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3502719 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3502739 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3502759 CGCGTTGCGATT
1 CGCGTTGCGATT
3502771 ATGGAAAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3502765 original size:60 final size:60
Alignment explanation
Indices: 3502578--3502770 Score: 242
Period size: 60 Copynumber: 3.2 Consensus size: 60
3502568 CTTTAAATAT
* **
3502578 CGCGTTGCGATTTACGGATACGCGTTGCAATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3502639 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3502699 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3502759 CGCGTTGCGATT
1 CGCGTTGCGATT
3502771 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 22, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3502876 original size:20 final size:20
Alignment explanation
Indices: 3502826--3502877 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3502816 AAGAATCGCG
* *
3502826 TTGCGATTTTAGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3502846 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3502866 TTGCGATTCTGG
1 TTGCGATTCTGG
3502878 GGATCGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3506504 original size:17 final size:17
Alignment explanation
Indices: 3506480--3506521 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3506470 ATATTGATTA
3506480 TGCCATAAGGAAAAATG
1 TGCCATAAGGAAAAATG
*
3506497 TTCCATAAGGAAAAATG
1 TGCCATAAGGAAAAATG
3506514 TGCCATAA
1 TGCCATAA
3506522 ATTCAATTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (17 bp):
TGCCATAAGGAAAAATG
Found at i:3510186 original size:23 final size:23
Alignment explanation
Indices: 3510160--3510204 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3510150 TGGATACAGA
3510160 AGGAAAATGATAATTGATATGGT
1 AGGAAAATGATAATTGATATGGT
3510183 AGGAAAATGATAATTGATATGG
1 AGGAAAATGATAATTGATATGG
3510205 ATTAAAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (23 bp):
AGGAAAATGATAATTGATATGGT
Found at i:3511572 original size:20 final size:20
Alignment explanation
Indices: 3511547--3511586 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3511537 TGAATAGTAC
*
3511547 AATATTAAATTATGTTTTTA
1 AATATTAAATTATGATTTTA
**
3511567 AATATTTCATTATGATTTTA
1 AATATTAAATTATGATTTTA
3511587 TGTGATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
AATATTAAATTATGATTTTA
Found at i:3514108 original size:22 final size:20
Alignment explanation
Indices: 3514082--3514127 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
3514072 AAGAAATCAC
* *
3514082 TTTTAATGTTTTTTATAATGTT
1 TTTTAATGCTTGTTAT-AT-TT
3514104 TTTTAATGCTTGTTATATTT
1 TTTTAATGCTTGTTATATTT
3514124 TTTT
1 TTTT
3514128 GATATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 2 0.09
22 14 0.64
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.70
Consensus pattern (20 bp):
TTTTAATGCTTGTTATATTT
Found at i:3514932 original size:2 final size:2
Alignment explanation
Indices: 3514925--3514965 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3514915 GAGAACATGC
3514925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3514966 ATTTAATCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3518156 original size:15 final size:15
Alignment explanation
Indices: 3518136--3518165 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3518126 ATATATTATG
3518136 TTGCTTTGTTAAGTC
1 TTGCTTTGTTAAGTC
3518151 TTGCTTTGTTAAGTC
1 TTGCTTTGTTAAGTC
3518166 ACTCTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.20, T:0.53
Consensus pattern (15 bp):
TTGCTTTGTTAAGTC
Found at i:3529095 original size:9 final size:9
Alignment explanation
Indices: 3529083--3529134 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
3529073 TAATATTTTG
3529083 TATTTAATT
1 TATTTAATT
*
3529092 TATTTAA-G
1 TATTTAATT
3529100 TATTTAATT
1 TATTTAATT
3529109 TATTTAA--
1 TATTTAATT
* *
3529116 TATTTTACT
1 TATTTAATT
3529125 TATTTAATT
1 TATTTAATT
3529134 T
1 T
3529135 TTTTGAAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:3529104 original size:17 final size:17
Alignment explanation
Indices: 3529082--3529131 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
3529072 TTAATATTTT
3529082 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
3529099 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
3529116 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
3529132 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:3529127 original size:16 final size:16
Alignment explanation
Indices: 3529091--3529136 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3529081 TGTATTTAAT
* *
3529091 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
3529108 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
3529124 TTATTTAAT-TTTT
1 TTATTTAATATTTT
3529137 TTGAAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:3530852 original size:27 final size:27
Alignment explanation
Indices: 3530822--3530880 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
3530812 GATGCCACCA
* * *
3530822 CGCCTTTCCATTACCAGATGTCGCCGT
1 CGCCATTCCATTACCAGATGTCACCGC
* *
3530849 CGCCATTCCCTTACCCGATGTCACCGC
1 CGCCATTCCATTACCAGATGTCACCGC
3530876 CGCCA
1 CGCCA
3530881 CCATCACCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (27 bp):
CGCCATTCCATTACCAGATGTCACCGC
Found at i:3533911 original size:26 final size:24
Alignment explanation
Indices: 3533875--3533924 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
3533865 CAGGCTCACG
*
3533875 AAGCGGTTCTTCTACATATTAAGGTC
1 AAGCGGTTCTTCCACAT-TT-AGGTC
3533901 AAGCGGTTCTTCCACATTTAGGTC
1 AAGCGGTTCTTCCACATTTAGGTC
3533925 GAAGAACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 2 0.09
26 16 0.70
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (24 bp):
AAGCGGTTCTTCCACATTTAGGTC
Found at i:3543499 original size:22 final size:23
Alignment explanation
Indices: 3543456--3543499 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3543446 CCTTAGGGGA
* *
3543456 TTATTTTTAACATTATACCTTTT
1 TTATTTATAACATTAGACCTTTT
*
3543479 TTATTTATAA-ATTAGAGCTTT
1 TTATTTATAACATTAGACCTTT
3543500 AAATATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (23 bp):
TTATTTATAACATTAGACCTTTT
Found at i:3543951 original size:15 final size:15
Alignment explanation
Indices: 3543931--3543960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3543921 ATATGAAATG
3543931 AATTTAAAATTTTAT
1 AATTTAAAATTTTAT
*
3543946 AATTTAATATTTTAT
1 AATTTAAAATTTTAT
3543961 TAATACATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTAAAATTTTAT
Found at i:3546248 original size:23 final size:20
Alignment explanation
Indices: 3546222--3546281 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
3546212 ACTAAATTAC
3546222 TAAAAAATTAAATATATATATGT
1 TAAAAAATTAAA-ATAT-TAT-T
* *
3546245 TAAAATACTAAAATATTATT
1 TAAAAAATTAAAATATTATT
*
3546265 AAAAAAATTAAAA-ATTA
1 TAAAAAATTAAAATATTA
3546282 AATATATATC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
21 3 0.09
22 4 0.12
23 10 0.31
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAAAATTAAAATATTATT
Found at i:3546471 original size:25 final size:25
Alignment explanation
Indices: 3546431--3546481 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3546421 GGGTTAATCG
3546431 AGACTTACAAAATTTGAATTAGTCA
1 AGACTTACAAAATTTGAATTAGTCA
* * *
3546456 AGACTTATAAATTTTGGATTAGTCA
1 AGACTTACAAAATTTGAATTAGTCA
3546481 A
1 A
3546482 AATGTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (25 bp):
AGACTTACAAAATTTGAATTAGTCA
Found at i:3546543 original size:2 final size:2
Alignment explanation
Indices: 3546536--3546590 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
3546526 GTCTCGACTG
3546536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
3546577 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3546591 TATTTTGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3546657 original size:16 final size:16
Alignment explanation
Indices: 3546635--3546681 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
3546625 TAATTTTTAG
3546635 TATTTTTATATTT-AA
1 TATTTTTATATTTGAA
*
3546650 TTTCTTTTAAATATTTGAA
1 TAT-TTTT--ATATTTGAA
3546669 TATTTTTATATTT
1 TATTTTTATATTT
3546682 CAAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.08
16 10 0.38
18 10 0.38
19 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTTTTATATTTGAA
Found at i:3548715 original size:74 final size:74
Alignment explanation
Indices: 3548577--3548733 Score: 163
Period size: 74 Copynumber: 2.1 Consensus size: 74
3548567 TGTTTAAAGC
* * * *
3548577 ATCCAAAAAACTATGAAAAATTATTATACATATTCAATTATATAAATAGCGGTACATTTGCTTAT
1 ATCC-AAAAACTATGAAAAATTATTATACATATTCAATTATAGAAATAACAGTACATTTCCTTAT
*
3548642 AT-AAATTACT
65 -TCAAATAACT
* * * ** * * *
3548652 ATCCAAAAACTATGAAAAGTTATTATGCATTTTCAATTATAGGGATAATATTATATTTCCTTATT
1 ATCCAAAAACTATGAAAAATTATTATACATATTCAATTATAGAAATAACAGTACATTTCCTTATT
*
3548717 CGAATAACT
66 CAAATAACT
3548726 ATCCAAAA
1 ATCCAAAA
3548734 TAAATATTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
73 1 0.01
74 62 0.93
75 4 0.06
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (74 bp):
ATCCAAAAACTATGAAAAATTATTATACATATTCAATTATAGAAATAACAGTACATTTCCTTATT
CAAATAACT
Found at i:3556573 original size:17 final size:17
Alignment explanation
Indices: 3556551--3556584 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3556541 GGTCAACTAT
*
3556551 GGTCAACACCGGTCAAC
1 GGTCAACACAGGTCAAC
*
3556568 GGTCAACGCAGGTCAAC
1 GGTCAACACAGGTCAAC
3556585 AGTCGACCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.26, T:0.12
Consensus pattern (17 bp):
GGTCAACACAGGTCAAC
Found at i:3557515 original size:2 final size:2
Alignment explanation
Indices: 3557508--3557542 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3557498 CAAATTTTAT
3557508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3557543 TTACTTGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3558395 original size:16 final size:17
Alignment explanation
Indices: 3558365--3558400 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3558355 TCTTGTTTGG
3558365 ATTATATTTAAATTAAA
1 ATTATATTTAAATTAAA
*
3558382 ATTAT-TTTATATTAAA
1 ATTATATTTAAATTAAA
3558398 ATT
1 ATT
3558401 TTATCATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATTTAAATTAAA
Found at i:3559259 original size:32 final size:32
Alignment explanation
Indices: 3559220--3559285 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
3559210 AATAAACAGG
3559220 TAAATAAAAAAT-AAGAAGA-AAATACAAATAAA
1 TAAATAAAAAATAAAGAAGATAAA-A-AAATAAA
**
3559252 TAAATAAAATGTAAAGAAGATAAAAAAATAAA
1 TAAATAAAAAATAAAGAAGATAAAAAAATAAA
3559284 TA
1 TA
3559286 TAAGGAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 19 0.63
33 8 0.27
34 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (32 bp):
TAAATAAAAAATAAAGAAGATAAAAAAATAAA
Found at i:3559316 original size:25 final size:23
Alignment explanation
Indices: 3559275--3559337 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
3559265 AAGAAGATAA
*
3559275 AAAAATAAATATAAGGAATAAAAAT
1 AAAAATAAA-ATAAGGAA-AAAAAG
3559300 AAAAATAAAATAGAGGAAAAAAAG
1 AAAAATAAAATA-AGGAAAAAAAG
*
3559324 ATAAATAGAAATAA
1 AAAAATA-AAATAA
3559338 ATAAAATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAAATAAAATAAGGAAAAAAAG
Found at i:3559355 original size:3 final size:3
Alignment explanation
Indices: 3559347--3559378 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3559337 AATAAAATAG
*
3559347 AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3559379 AAACAATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3559386 original size:12 final size:12
Alignment explanation
Indices: 3559337--3559447 Score: 55
Period size: 12 Copynumber: 8.9 Consensus size: 12
3559327 AATAGAAATA
*
3559337 AATAAAATAGAAT
1 AATAAAA-ATAAT
*
3559350 AATAATAATAAT
1 AATAAAAATAAT
**
3559362 AATACTAATAAT
1 AATAAAAATAAT
*
3559374 AATAAAAACAAT
1 AATAAAAATAAT
*
3559386 AAGTAAAGAGTAAT
1 AA-TAAA-AATAAT
* *
3559400 AAAAGAAAATAAA
1 AATA-AAAATAAT
* *
3559413 AATAGAAAT-GT
1 AATAAAAATAAT
*
3559424 -ATAAGAATAAT
1 AATAAAAATAAT
3559435 AAATAAAATATAA
1 -AATAAAA-ATAA
3559448 GTATATATGT
Statistics
Matches: 72, Mismatches: 19, Indels: 13
0.69 0.18 0.12
Matches are distributed among these distances:
10 6 0.08
11 1 0.01
12 30 0.42
13 23 0.32
14 12 0.17
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:3559439 original size:29 final size:30
Alignment explanation
Indices: 3559406--3559468 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 30
3559396 TAATAAAAGA
*
3559406 AAATAAAAATAGAAATGTATAAG-AATAAT
1 AAATAAAAATAGAAATATATAAGTAATAAT
* * *
3559435 AAAT-AAAATATAAGTATATATGTAATAAT
1 AAATAAAAATAGAAATATATAAGTAATAAT
3559464 AAATA
1 AAATA
3559469 TAATATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATAAAAATAGAAATATATAAGTAATAAT
Found at i:3559562 original size:21 final size:20
Alignment explanation
Indices: 3559536--3559605 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 20
3559526 CATATAGATA
*
3559536 AATAATAGAGAGAAAAAATAT
1 AATAATA-AGAGAAAATATAT
*
3559557 AATAATGATAGAGAAATTATAT
1 AATAAT-A-AGAGAAAATATAT
*
3559579 AA-AATAAGATAAAATATAT
1 AATAATAAGAGAAAATATAT
3559598 AATGAATA
1 AAT-AATA
3559606 TGTATATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 13 0.32
20 1 0.02
21 13 0.32
22 14 0.34
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (20 bp):
AATAATAAGAGAAAATATAT
Found at i:3559580 original size:19 final size:20
Alignment explanation
Indices: 3559550--3559602 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
3559540 ATAGAGAGAA
3559550 AAAATATAATAATGAT-AGAG
1 AAAATAT-ATAATGATAAGAG
* * *
3559570 AAATTATATAA-AATAAGAT
1 AAAATATATAATGATAAGAG
3559589 AAAATATATAATGA
1 AAAATATATAATGA
3559603 ATATGTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 2 0.08
19 17 0.65
20 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAATATATAATGATAAGAG
Found at i:3559650 original size:21 final size:21
Alignment explanation
Indices: 3559626--3559682 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3559616 TAAAATGTTT
3559626 TAAATAATAATAATAAATAAA
1 TAAATAATAATAATAAATAAA
*
3559647 TAAAATAA-AATAAAAAATAAA
1 T-AAATAATAATAATAAATAAA
* *
3559668 TATAGAAT-ATAATAA
1 TAAATAATAATAATAA
3559683 TGATAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.33
21 14 0.47
22 6 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAATAATAATAATAAATAAA
Found at i:3559679 original size:25 final size:27
Alignment explanation
Indices: 3559627--3559689 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
3559617 AAAATGTTTT
*
3559627 AAATAATAATAATAAATAAATAAAATA
1 AAATAATAATAATAAATAAAGAAAATA
* *
3559654 AAATAA-AA-AATAAATATAGAATATA
1 AAATAATAATAATAAATAAAGAAAATA
*
3559679 ATAATGATAAT
1 A-AATAATAAT
3559690 GAAGTATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 15 0.52
26 6 0.21
27 8 0.28
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (27 bp):
AAATAATAATAATAAATAAAGAAAATA
Found at i:3560115 original size:37 final size:37
Alignment explanation
Indices: 3560065--3560174 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
3560055 ATGCTTATGG
*
3560065 ATCCTATTTTTAGGAGTTTGAATCTTAGTAAAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTTT
*
3560102 ATCCTATTTTTAGGAGCTTGAATCATAGTAAAA--TT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTTT
* *
3560137 ATCATATTTTTAGGAGTTTGAATAATAGTAAAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTTT
3560174 A
1 A
3560175 ACGTTATGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 32 0.48
37 34 0.52
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTTT
Found at i:3560146 original size:35 final size:36
Alignment explanation
Indices: 3560069--3560172 Score: 156
Period size: 35 Copynumber: 2.9 Consensus size: 36
3560059 TTATGGATCC
* *
3560069 TATTTTTAGGAGTTTGAATCTTAGTAAAACTTTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAAC-TTATCA
*
3560106 TATTTTTAGGAGCTTGAATCATAGTAAAA-TTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTTATCA
*
3560141 TATTTTTAGGAGTTTGAATAATAGTAAAACTT
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTT
3560173 TAACGTTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
35 32 0.52
36 2 0.03
37 27 0.44
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (36 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTTATCA
Found at i:3560706 original size:311 final size:312
Alignment explanation
Indices: 3560143--3560767 Score: 1135
Period size: 311 Copynumber: 2.0 Consensus size: 312
3560133 AATTATCATA
*
3560143 TTTTTAGGAGTTTGAATAATAGTAAAACTTTAACGTTATGTTTGTTTTCTGAATCCACTAAATCT
1 TTTTTAGGAGTTTGAATAATAGTAAAACTTTAACGTTATGTTTGTTTTCTGAATCCACTAAATCG
* *
3560208 GGGTTGTTGAGAGTTTTGTACTCGGACGAAAATGTGTGTTGACAATTTTACTATAGTTAATTTAT
66 GGGTTGTTGAGAGTGTTGTACTCGGACGAAAAGGTGTGTTGACAATTTTACTATAGTTAATTTAT
*
3560273 ATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATTTAATTTTTTTACAAAATTGAAAAGATA
131 ATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATTTAATTTTTTTACAAAATTAAAAAGATA
3560338 AATAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCATGAACTTCATATAAAATTCTAATTAT
196 AATAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCATGAACTTCATATAAAATTCTAATTAT
* *
3560403 GGA-TTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTGTTTTTTAAAAT
261 GAATTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTATTTTTTAAAAT
**
3560454 TTTTTAGGAGTTTGAATCCTAGTAAAACTTTAACGTTATGTTTGTTTTCTGAATCCACTAAATCG
1 TTTTTAGGAGTTTGAATAATAGTAAAACTTTAACGTTATGTTTGTTTTCTGAATCCACTAAATCG
*
3560519 GGGTTGTTGAGAGTGTTGTACTCGGATGAAAAGGTGTGTTGACAATTTTACTATAGTTAATTTAT
66 GGGTTGTTGAGAGTGTTGTACTCGGACGAAAAGGTGTGTTGACAATTTTACTATAGTTAATTTAT
*
3560584 ATATTTTCTTTAAAAAATTTAAATTCATAAAGTTTATTTAATTTTTTTACAAAATTAAAAAGATA
131 ATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATTTAATTTTTTTACAAAATTAAAAAGATA
*
3560649 AATAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCATGAACTTTATATAAAATTCTAATTAT
196 AATAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCATGAACTTCATATAAAATTCTAATTAT
3560714 GAATTTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTATTTTTTAAAAT
261 GAA-TTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTATTTTTTAAAAT
3560767 T
1 T
3560768 CGTAGAATTT
Statistics
Matches: 301, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
311 253 0.84
313 48 0.16
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (312 bp):
TTTTTAGGAGTTTGAATAATAGTAAAACTTTAACGTTATGTTTGTTTTCTGAATCCACTAAATCG
GGGTTGTTGAGAGTGTTGTACTCGGACGAAAAGGTGTGTTGACAATTTTACTATAGTTAATTTAT
ATATTTTCTTTAAAAAATTTAAATTCATAAAATTTATTTAATTTTTTTACAAAATTAAAAAGATA
AATAGGTTTAATGAAAGGGTAAAATTTTATTTTAACCCATGAACTTCATATAAAATTCTAATTAT
GAATTTTTTTGTAAATCTAAAATAGTTTAAGGATAAATTTATTTTTTAAAAT
Found at i:3562929 original size:17 final size:18
Alignment explanation
Indices: 3562898--3562944 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3562888 AATTTTTATA
*
3562898 ATTTTAAAATAAAAAAAT-
1 ATTTT-AAATTAAAAAATC
3562916 ATTTTAAATT-AAAAATC
1 ATTTTAAATTAAAAAATC
*
3562933 ACTTTAAATTAA
1 ATTTTAAATTAA
3562945 TCTTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 6 0.24
17 13 0.52
18 6 0.24
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTTAAATTAAAAAATC
Found at i:3565205 original size:25 final size:25
Alignment explanation
Indices: 3565172--3565220 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3565162 TTGGATGAAT
*
3565172 TGTTGTAATTGTTGTGATGAAATTC
1 TGTTCTAATTGTTGTGATGAAATTC
*
3565197 TGTTCTAATTGTTGTGATTAAATT
1 TGTTCTAATTGTTGTGATGAAATT
3565221 GTAGATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.04, G:0.20, T:0.51
Consensus pattern (25 bp):
TGTTCTAATTGTTGTGATGAAATTC
Found at i:3567160 original size:67 final size:68
Alignment explanation
Indices: 3567074--3567210 Score: 172
Period size: 69 Copynumber: 2.0 Consensus size: 68
3567064 GAGAATAATT
* * * *
3567074 TCCTTTTTTATCACCGAGACCATTTAAT-GAGTTC-ATTCTTGTAATA-TTTGGATTTGGATTTT
1 TCCTCTTTTATCACCGAGA-CACTTAATAGA-TTCAATTCTTGTAATATTTTGAATTTAGATTTT
3567136 TTTAA
64 TTTAA
* *
3567141 TCCTCTTTTATCACTGAGACACTTAATAGATTCAAATTTTTGTAATATTTTGAATTTAGATTTTT
1 TCCTCTTTTATCACCGAGACACTTAATAGATTC-AATTCTTGTAATATTTTGAATTTAGATTTTT
3567206 TTAA
65 TTAA
3567210 T
1 T
3567211 TATAATTTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
66 10 0.17
67 19 0.32
68 11 0.18
69 20 0.33
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (68 bp):
TCCTCTTTTATCACCGAGACACTTAATAGATTCAATTCTTGTAATATTTTGAATTTAGATTTTTT
TAA
Found at i:3570440 original size:23 final size:23
Alignment explanation
Indices: 3570407--3570489 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
3570397 CATCTTATAT
* *
3570407 GGCACTACGGTACAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
3570430 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
3570453 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
3570476 AGCACTTCGGTGCA
1 GGCACTTCGGTGCA
3570490 TTTATACAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:3577323 original size:23 final size:23
Alignment explanation
Indices: 3577209--3577315 Score: 178
Period size: 23 Copynumber: 4.7 Consensus size: 23
3577199 ACATCTTATA
* *
3577209 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3577232 GGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
3577255 TGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3577278 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
3577301 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
3577316 TTTATACGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3588250 original size:22 final size:22
Alignment explanation
Indices: 3588190--3588250 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
3588180 ATAAGGCAGA
* * *
3588190 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
*
3588212 GGGAACCTATTTCCCCTTTGAAG
1 GGGAACCGA-TTCCCCTTTGAAG
3588235 GGGAACCGATTCCCCT
1 GGGAACCGATTCCCCT
3588251 AGGGGAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:3592447 original size:15 final size:13
Alignment explanation
Indices: 3592401--3592447 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3592391 CATTACACAT
3592401 TCACATA-TTCATA
1 TCACATAGTTC-TA
*
3592414 TCACATAGTTCTT
1 TCACATAGTTCTA
3592427 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
3592442 TCACAT
1 TCACAT
3592448 TTCATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Done.