Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1883915 original size:87 final size:87
Alignment explanation
Indices: 1883692--1883938 Score: 365
Period size: 87 Copynumber: 2.9 Consensus size: 87
1883682 ATCTACCATT
*
1883692 TTACGAAAATAAT-ACCATTTTAAAAATAATTACAAAAATATCACCATTTTAAAAATAATTACAA
1 TTACGAAAAT-ATCACCATTTTAAAAATAATTACAAAAATATCACCATTTTAAAAATAATTACTA
* * *
1883756 AAATAGC-GCTTTTTAAAAATAA
65 AAATAACACCATTTTAAAAATAA
* * *
1883778 TTACGAAAATAACATCATTTTAAAAATAATTACAAAAATATCACCTTTTTAAAAATAATTACTAA
1 TTACGAAAATATCACCATTTTAAAAATAATTACAAAAATATCACCATTTTAAAAATAATTACTAA
1883843 AATAACACCATTTTAAAAATAA
66 AATAACACCATTTTAAAAATAA
* * *
1883865 TTACGAAAATATCA-CATTTTTAAAAGTAATTACTAAAATATGACCATTTTAAAAATAATTACTA
1 TTACGAAAATATCACCA-TTTTAAAAATAATTACAAAAATATCACCATTTTAAAAATAATTACTA
1883929 AAATAACACC
65 AAATAACACC
1883939 CAGTCAACGG
Statistics
Matches: 146, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
85 1 0.01
86 66 0.45
87 79 0.54
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (87 bp):
TTACGAAAATATCACCATTTTAAAAATAATTACAAAAATATCACCATTTTAAAAATAATTACTAA
AATAACACCATTTTAAAAATAA
Found at i:1883968 original size:22 final size:22
Alignment explanation
Indices: 1883940--1883984 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1883930 AATAACACCC
*
1883940 AGTCAACGGTTGGGTCGGGTCG
1 AGTCAACGGTCGGGTCGGGTCG
1883962 AGTCAACGGTCGGGTCGGGTCG
1 AGTCAACGGTCGGGTCGGGTCG
1883984 A
1 A
1883985 ACCGGTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.44, T:0.20
Consensus pattern (22 bp):
AGTCAACGGTCGGGTCGGGTCG
Found at i:1884036 original size:51 final size:51
Alignment explanation
Indices: 1883980--1884086 Score: 187
Period size: 51 Copynumber: 2.1 Consensus size: 51
1883970 GTCGGGTCGG
1883980 GTCGAACCGGTCAACCCGGTTCAGACCGGTCAAACCGGTTTTCAAGCAGTA
1 GTCGAACCGGTCAACCCGGTTCAGACCGGTCAAACCGGTTTTCAAGCAGTA
* * *
1884031 GTCGAATCGGTCAACCCTGTTCAGACCGGTCAAACCGGTTTTCAAGTAGTA
1 GTCGAACCGGTCAACCCGGTTCAGACCGGTCAAACCGGTTTTCAAGCAGTA
1884082 GTCGA
1 GTCGA
1884087 TTTCAACAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (51 bp):
GTCGAACCGGTCAACCCGGTTCAGACCGGTCAAACCGGTTTTCAAGCAGTA
Found at i:1884766 original size:20 final size:21
Alignment explanation
Indices: 1884731--1884772 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1884721 ACATAATATA
1884731 ACTGAATGAGCAAAATAATCG
1 ACTGAATGAGCAAAATAATCG
* *
1884752 ACTGAAT-ATCAAAATGATCG
1 ACTGAATGAGCAAAATAATCG
1884772 A
1 A
1884773 AGTACCCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (21 bp):
ACTGAATGAGCAAAATAATCG
Found at i:1890883 original size:30 final size:31
Alignment explanation
Indices: 1890849--1890915 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
1890839 AAAATTTTAG
1890849 GTTTTAAATGAGATGAAATA-AAAAAAATAA
1 GTTTTAAATGAGATGAAATATAAAAAAATAA
*
1890879 GTTTTAAATGAGATGAAATATAAAAAATTAA
1 GTTTTAAATGAGATGAAATATAAAAAAATAA
*
1890910 ATTTTA
1 GTTTTA
1890916 TAGTAAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (31 bp):
GTTTTAAATGAGATGAAATATAAAAAAATAA
Found at i:1895832 original size:14 final size:13
Alignment explanation
Indices: 1895790--1895832 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1895780 AGACAACGGA
*
1895790 CAACAGTCAAAGT
1 CAACGGTCAAAGT
* *
1895803 CAACGGTCATATT
1 CAACGGTCAAAGT
1895816 CAACTGGTCAAAGT
1 CAAC-GGTCAAAGT
1895830 CAA
1 CAA
1895833 TAGGTTGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (13 bp):
CAACGGTCAAAGT
Found at i:1895855 original size:15 final size:15
Alignment explanation
Indices: 1895835--1895872 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1895825 AAAGTCAATA
*
1895835 GGTTGACTCAGTCTG
1 GGTTGACTCAGTCCG
1895850 GGTTGACTCAGTCCG
1 GGTTGACTCAGTCCG
1895865 GGTTGACT
1 GGTTGACT
1895873 TGGTCGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.21, G:0.34, T:0.32
Consensus pattern (15 bp):
GGTTGACTCAGTCCG
Found at i:1901153 original size:31 final size:31
Alignment explanation
Indices: 1901095--1901154 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1901085 CGAGGCCCCA
* *
1901095 AGATCTTTCTTGGGTAGGCCCTGTGGCCTTG
1 AGATCCTTCTTGGGTAGGCCCTATGGCCTTG
1901126 AGATCCTTCTTGGGTAGG-CCTCATGGCCT
1 AGATCCTTCTTGGGTAGGCCCT-ATGGCCT
1901155 CGAGTAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.12, C:0.25, G:0.30, T:0.33
Consensus pattern (31 bp):
AGATCCTTCTTGGGTAGGCCCTATGGCCTTG
Found at i:1905052 original size:32 final size:32
Alignment explanation
Indices: 1904991--1905068 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
1904981 TTAGGCGTAG
* *
1904991 GAGCCAACCTAAAGGAGTATCTTGGGGCC-TAA
1 GAGCCTACC-AAAGGAGTACCTTGGGGCCTTAA
*
1905023 GAGCCTACCAAAGGTAGTACCTTGTGGCCTTAA
1 GAGCCTACCAAAGG-AGTACCTTGGGGCCTTAA
1905056 -AGCCTACCCAAAG
1 GAGCCTA-CCAAAG
1905069 AAATGGCTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 5 0.12
32 26 0.65
33 9 0.22
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (32 bp):
GAGCCTACCAAAGGAGTACCTTGGGGCCTTAA
Found at i:1915043 original size:96 final size:96
Alignment explanation
Indices: 1914879--1915069 Score: 355
Period size: 96 Copynumber: 2.0 Consensus size: 96
1914869 ATTTGGCTTT
* *
1914879 GAACCACCAGACAAGACGCATTTTCACTATAAACAACAGCTGTAATTTGTCAATCGTACTTCCTT
1 GAACCACCAAACAAGACGCATTTTCACTATAAACAACAGCTGTAATTTGTCAACCGTACTTCCTT
1914944 TGAATATGACATTATTCCACATAAGCCAAAA
66 TGAATATGACATTATTCCACATAAGCCAAAA
*
1914975 GAACCACCAAACAAGACGCATTTTCACTATAAACGACAGCTGTAATTTGTCAACCGTACTTCCTT
1 GAACCACCAAACAAGACGCATTTTCACTATAAACAACAGCTGTAATTTGTCAACCGTACTTCCTT
1915040 TGAATATGACATTATTCCACATAAGCCAAA
66 TGAATATGACATTATTCCACATAAGCCAAA
1915070 TGGAACATAG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.27
Consensus pattern (96 bp):
GAACCACCAAACAAGACGCATTTTCACTATAAACAACAGCTGTAATTTGTCAACCGTACTTCCTT
TGAATATGACATTATTCCACATAAGCCAAAA
Found at i:1916212 original size:21 final size:21
Alignment explanation
Indices: 1916186--1916384 Score: 185
Period size: 21 Copynumber: 9.6 Consensus size: 21
1916176 ATTTTCAGAT
* *
1916186 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
1916207 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1916228 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1916249 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
1916270 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
1916290 TCGCAATGTGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
1916310 TCGCAATGCGATA-GTCGCCTA
1 TCGCAATGCGA-ACTTGGACTA
* * * *
1916331 TCGTAATGCGATA-GTCGCCTA
1 TCGCAATGCGA-ACTTGGACTA
1916352 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
1916373 TCGCAATACGAA
1 TCGCAATGCGAA
1916385 TATGTAAATC
Statistics
Matches: 157, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
20 33 0.21
21 124 0.79
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1916316 original size:103 final size:103
Alignment explanation
Indices: 1916206--1916561 Score: 298
Period size: 103 Copynumber: 3.5 Consensus size: 103
1916196 AACTTCGACT
* * * *
1916206 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACT
*
1916269 ATCGCAATGCGAATATGTAAATCGCAATGTGAATATGTAA
64 ATCGCAATACGAATATGTAAATCGCAATGTGAATATGTAA
* * *
1916309 ATCGCAATGCGATAGTCGCCTATCGTAATGCGATAGTCGCCTATCGCAATGCGAACTTGGACTAT
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTAT
*
1916374 CGCAATACGAATATGTAAATCGCAATGCG-ATA-GTCGAA
66 CGCAATACGAATATGTAAATCGCAATGTGAATATGT--AA
* * *
1916412 GTTCGCATTGCGATAGTC--C-A--GCAATGCGAATA-T-GTA-AATCG---TGCGAACTTGGAC
1 -ATCGCAATGCGATAGTCGACTATCGCAATGCG-ATAGTCG-ACTATCGCAATGCGAACTTGGAC
* * *
1916466 TATCGCAATGCAAATATGTAAATCGCAATGCG-ATA-GTCGAA
63 TATCGCAATACGAATATGTAAATCGCAATGTGAATATGT--AA
* * * * * *
1916507 GTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCGACTATCGCATTGCGA
1 -ATCGCAATGCGATAGT-CGACTATCGCAATGCGATAGTCGACTATCGCAATGCGA
1916562 TTTACATATT
Statistics
Matches: 215, Mismatches: 19, Indels: 37
0.79 0.07 0.14
Matches are distributed among these distances:
95 69 0.32
96 1 0.00
98 5 0.02
99 11 0.05
100 12 0.06
101 8 0.04
102 4 0.02
103 83 0.39
104 22 0.10
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (103 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTAT
CGCAATACGAATATGTAAATCGCAATGTGAATATGTAA
Found at i:1916424 original size:83 final size:82
Alignment explanation
Indices: 1916227--1916452 Score: 218
Period size: 83 Copynumber: 2.8 Consensus size: 82
1916217 AACTTGGACT
* * * * * *
1916227 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGATA-GTCGCCTATCGCAATGCGAATATGGAAA
**
1916290 TCGCAATGTGAATATGTAA
64 TCGCAATACGAATATGTAA
* * *
1916309 ATCGCAATGCGATAGTCGCCTATCGTAATGCGATAGTCGCCTATCGCAATGCGAACT-TGGACTA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGATAGTCGCCTATCGCAATGCGAA-TATGGA-AA
1916373 TCGCAATACGAATATGTAA
64 TCGCAATACGAATATGTAA
* * *
1916392 ATCGCAATGCGATAGTCGAAGT-TCGCATTGCGATAGT--CC-A--GCAATGCGAATATGTAAAT
1 ATCGCAATGCGATAGTCG-ACTATCGCAATGCGATAGTCGCCTATCGCAATGCGAATATGGAAAT
1916451 CG
65 CG
1916453 TGCGAACTTG
Statistics
Matches: 121, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
77 5 0.04
78 13 0.11
80 1 0.01
81 2 0.02
82 47 0.39
83 52 0.43
84 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (82 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGATAGTCGCCTATCGCAATGCGAATATGGAAATC
GCAATACGAATATGTAA
Found at i:1916518 original size:21 final size:21
Alignment explanation
Indices: 1916488--1916593 Score: 121
Period size: 21 Copynumber: 5.1 Consensus size: 21
1916478 AATATGTAAA
*
1916488 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
1916509 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
1916530 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
1916550 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
1916571 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
1916592 TC
1 TC
1916594 ATGTTGCGAT
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
20 17 0.24
21 54 0.75
22 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:1916606 original size:41 final size:41
Alignment explanation
Indices: 1916488--1916593 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
1916478 AATATGTAAA
* * *
1916488 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGAT-TTACAAGT
*
1916530 TCGCATTGCGATAGTCG-ACTATCGCATTGCGATTTACATA-T
1 TCGCATTGCGATAGTCGAAGT-TCGCATTGCGATTTACA-AGT
1916571 TCGCATTGCGATAGTCGAAGTTC
1 TCGCATTGCGATAGTCGAAGTTC
1916594 ATGTTGCGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
41 25 0.45
42 31 0.55
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (41 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATTTACAAGT
Found at i:1916632 original size:19 final size:20
Alignment explanation
Indices: 1916576--1916632 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
1916566 CATATTCGCA
* *
1916576 TTGCGATAGTCGAAGTTCATG
1 TTGCGATAGTCCAAATTCA-G
*
1916597 TTGCGATTTATTCCAAATTC-G
1 TTGCGA--TAGTCCAAATTCAG
1916618 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
1916633 ATCGCAACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAATTCAG
Found at i:1916747 original size:5 final size:5
Alignment explanation
Indices: 1916725--1916762 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
1916715 CGTATTACCA
1916725 CGACC ACGACC ACGACC CGACC CGACC CGACC CGACC C
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC C
1916763 AAGACGAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 21 0.66
6 11 0.34
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:1917258 original size:6 final size:6
Alignment explanation
Indices: 1917242--1917278 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1917232 TCTCGTCTCG
1917242 GGTCG- GGTCGT GGTCGT GGTCG- GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1917279 AATACATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1917264 original size:17 final size:17
Alignment explanation
Indices: 1917242--1917278 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1917232 TCTCGTCTCG
1917242 GGTCGGGTCGTGGTCGT
1 GGTCGGGTCGTGGTCGT
1917259 GGTCGGGTCGTGGTCGT
1 GGTCGGGTCGTGGTCGT
1917276 GGT
1 GGT
1917279 AATACATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (17 bp):
GGTCGGGTCGTGGTCGT
Found at i:1917267 original size:11 final size:11
Alignment explanation
Indices: 1917239--1917274 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1917229 CCATCTCGTC
1917239 TCGGGTCG-GG
1 TCGGGTCGTGG
1917249 TCGTGGTCGTGG
1 TCG-GGTCGTGG
1917261 TCGGGTCGTGG
1 TCGGGTCGTGG
1917272 TCG
1 TCG
1917275 TGGTAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 3 0.12
11 16 0.67
12 5 0.21
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:1917417 original size:27 final size:27
Alignment explanation
Indices: 1917387--1917440 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1917377 ACGAATTTGG
*
1917387 AATAAATCGCAACGCGCACTTCGACTA
1 AATAAATCGCAACGCGAACTTCGACTA
1917414 AATAAATCGCAACGCGAACTTCGACTA
1 AATAAATCGCAACGCGAACTTCGACTA
1917441 TCGCAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.19
Consensus pattern (27 bp):
AATAAATCGCAACGCGAACTTCGACTA
Found at i:1917443 original size:21 final size:21
Alignment explanation
Indices: 1917419--1917494 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
1917409 GACTAAATAA
*
1917419 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
1917440 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
1917459 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
1917482 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1917495 TATGTAAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 10 0.21
21 26 0.55
23 11 0.23
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1917574 original size:20 final size:21
Alignment explanation
Indices: 1917529--1917575 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1917519 GAAGTTCGCG
1917529 TTGCGAATCTGAAAACTGATT
1 TTGCGAATCTGAAAACTGATT
1917550 TTGCGAATCT-AGAAACTGA-T
1 TTGCGAATCTGA-AAACTGATT
1917570 TTGCGA
1 TTGCGA
1917576 TACCGGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (21 bp):
TTGCGAATCTGAAAACTGATT
Found at i:1917904 original size:20 final size:20
Alignment explanation
Indices: 1917868--1917905 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1917858 AATCCTATTC
**
1917868 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1917888 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1917906 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1930709 original size:21 final size:21
Alignment explanation
Indices: 1930660--1930714 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1930650 GATGGTCACT
* * *
1930660 TAGCTAGCATAGTTAGTTTAGG
1 TAGCTAGC-TAGGTAGTGTAAG
*
1930682 TAACTAGCTAGGTAGTGTAAG
1 TAGCTAGCTAGGTAGTGTAAG
1930703 TAGCTAGCTAGG
1 TAGCTAGCTAGG
1930715 CACCTAATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (21 bp):
TAGCTAGCTAGGTAGTGTAAG
Found at i:1937390 original size:20 final size:20
Alignment explanation
Indices: 1937326--1937395 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1937316 CAATCTTTCG
* * *
1937326 GTATGGATACCAACCATCTT
1 GTATCGATACCAAGCATCTA
* *
1937346 GTATCGATGCCAAGCATC-C
1 GTATCGATACCAAGCATCTA
*
1937365 GATATCGATATCAAGCATCTA
1 G-TATCGATACCAAGCATCTA
*
1937386 GTATCAATAC
1 GTATCGATAC
1937396 TACAACCCTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (20 bp):
GTATCGATACCAAGCATCTA
Found at i:1938183 original size:16 final size:17
Alignment explanation
Indices: 1938162--1938199 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1938152 ATACGTAGAG
1938162 AGAAATAGAA-GAAGAA
1 AGAAATAGAAGGAAGAA
1938178 AGAAATAGAAGGAAGAA
1 AGAAATAGAAGGAAGAA
1938195 AGAAA
1 AGAAA
1938200 GAAGCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.26, T:0.05
Consensus pattern (17 bp):
AGAAATAGAAGGAAGAA
Found at i:1941631 original size:20 final size:20
Alignment explanation
Indices: 1941608--1941659 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1941598 AACGCGATCC
1941608 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1941628 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1941648 CCAAAATCGCAA
1 CCAGAATCGCAA
1941660 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1941676 original size:21 final size:20
Alignment explanation
Indices: 1941649--1941747 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1941639 AATCAGTTTC
1941649 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1941670 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1941691 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1941711 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1941732 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1941748 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1941776 original size:20 final size:20
Alignment explanation
Indices: 1941714--1941907 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1941704 CGATTTTCCA
* ** *
1941714 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1941734 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1941754 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1941774 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1941794 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1941814 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1941834 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1941854 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1941874 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1941895 AAATCGCAACGCG
1 AAATCGCAACGCG
1941908 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1941798 original size:60 final size:60
Alignment explanation
Indices: 1941714--1941907 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1941704 CGATTTTCCA
* ** * *
1941714 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1941774 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1941834 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1941895 AAATCGCAACGCG
1 AAATCGCAACGCG
1941908 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1942328 original size:33 final size:33
Alignment explanation
Indices: 1942289--1942359 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1942279 TTCACTTAGA
*
1942289 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1942322 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1942355 TTTCA
1 TTTCA
1942360 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1942499 original size:14 final size:14
Alignment explanation
Indices: 1942480--1942534 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1942470 AGAATGACTG
1942480 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1942494 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1942513 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1942527 TCGCAACG
1 TCGCAACG
1942535 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1942547 original size:33 final size:33
Alignment explanation
Indices: 1942480--1942550 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1942470 AGAATGACTG
***
1942480 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1942513 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1942546 TCGCA
1 TCGCA
1942551 TTGCGATTTT
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:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1942568 original size:19 final size:19
Alignment explanation
Indices: 1942546--1942643 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1942536 GAAACCAAAA
*
1942546 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1942565 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1942579 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1942598 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1942612 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1942631 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1942644 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1942587 original size:14 final size:14
Alignment explanation
Indices: 1942568--1942657 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1942558 TTTCATTTCG
1942568 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1942582 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1942601 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1942615 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1942632 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1942648 CGTTGCGATT
1 CGTTGCGATT
1942658 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1942593 original size:33 final size:33
Alignment explanation
Indices: 1942551--1942665 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1942541 CAAAATCGCA
1942551 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1942584 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1942617 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1942650 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1942666 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1944594 original size:185 final size:186
Alignment explanation
Indices: 1944364--1944745 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
1944354 TAGATTGCTT
1944364 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944429 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1944494 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1944549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944614 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1944679 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1944735 AGTAAATTTAT
1 AGTAAATTTAT
1944746 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1944678 original size:93 final size:93
Alignment explanation
Indices: 1944364--1944743 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
1944354 TAGATTGCTT
*
1944364 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944429 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1944457 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944521 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1944549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944614 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1944642 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1944707 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1944735 AGTAAATTT
1 AGTAAATTT
1944744 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1944907 original size:19 final size:19
Alignment explanation
Indices: 1944787--1944901 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
1944777 TAGTTTACTT
* *
1944787 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1944807 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1944826 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
1944845 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1944864 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1944878 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1944897 TCGCA
1 TCGCA
1944902 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 53 0.65
20 13 0.16
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1944919 original size:19 final size:19
Alignment explanation
Indices: 1944897--1945031 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1944887 GAAACCAAAA
*
1944897 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1944916 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1944932 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1944949 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1944965 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1944982 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1945001 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1945021 TCGTGTTGCGA
1 TCGCGTTGCGA
1945032 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1944938 original size:14 final size:14
Alignment explanation
Indices: 1944919--1944975 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1944909 TTTCATTTCG
1944919 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1944933 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1944950 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1944966 CGTTGCGATT
1 CGTTGCGATT
1944976 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1944944 original size:33 final size:33
Alignment explanation
Indices: 1944902--1944994 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1944892 CAAAATCGCA
*
1944902 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1944935 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1944968 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1944995 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1946891 original size:38 final size:38
Alignment explanation
Indices: 1946848--1946920 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1946838 AATTGATTGT
*
1946848 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1946886 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1946921 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1946907 original size:19 final size:19
Alignment explanation
Indices: 1946843--1946907 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1946833 AGTTTAATTG
*
1946843 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1946862 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1946880 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1946900 ATTGATTT
1 ATTGATTT
1946908 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1946921 original size:14 final size:14
Alignment explanation
Indices: 1946902--1946937 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1946892 ATTGTTTAAT
1946902 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1946916 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1946930 TGATTTGT
1 TGATTTGT
1946938 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1947060 original size:19 final size:19
Alignment explanation
Indices: 1947044--1947145 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1947034 AAAAATGACT
1947044 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1947063 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1947082 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1947096 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1947115 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1947135 ATCGCAATGCG
1 ATCGCAATGCG
1947146 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1947198 original size:19 final size:19
Alignment explanation
Indices: 1947174--1947499 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
1947164 GATTATCTCG
1947174 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947193 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947212 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1947226 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947245 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1947264 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1947283 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947302 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1947321 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1947335 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947354 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1947373 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1947387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1947406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1947425 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1947439 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1947459 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1947473 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1947492 TTGCGATT
1 TTGCGATT
1947500 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1947214 original size:52 final size:52
Alignment explanation
Indices: 1947152--1947471 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1947142 TGCGTTTATA
*
1947152 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1947204 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1947256 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1947313 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1947365 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1947417 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1947470 AT
1 AT
1947472 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1947249 original size:71 final size:72
Alignment explanation
Indices: 1947174--1947499 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
1947164 GATTATCTCG
1947174 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1947238 TTTCGCA
66 TTTCGCA
* *
1947245 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
1947310 TTCATTTCGCA
62 TTCATTTCGCA
*
1947321 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
1947379 TTC-TCTCG--
62 TTCATTTCGCA
*
1947387 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1947451 TTTCCGCA
66 TTT-CGCA
* *
1947459 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1947500 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:1947417 original size:161 final size:157
Alignment explanation
Indices: 1947152--1947471 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1947142 TGCGTTTATA
1947152 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1947217 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1947282 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1947313 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1947378 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1947443 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1947470 AT
1 AT
1947472 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:1947443 original size:33 final size:33
Alignment explanation
Indices: 1947193--1947499 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
1947183 TCATTTCGCA
*
1947193 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1947226 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1947262 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1947300 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1947335 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1947371 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1947406 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1947439 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1947473 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1947500 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1949822 original size:12 final size:12
Alignment explanation
Indices: 1949805--1949829 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1949795 TCTTCGGGGA
1949805 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1949817 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1949829 C
1 C
1949830 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1950037 original size:23 final size:23
Alignment explanation
Indices: 1950004--1950048 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1949994 CTGAAACATC
1950004 ATCAAAATCCGTG-TATTGACCAT
1 ATCAAAATCCG-GATATTGACCAT
*
1950027 ATCAAAGTCCGGATATTGACCA
1 ATCAAAATCCGGATATTGACCA
1950049 AGACCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (23 bp):
ATCAAAATCCGGATATTGACCAT
Found at i:1950751 original size:20 final size:20
Alignment explanation
Indices: 1950723--1951090 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
1950713 AAATTTCAGT
* * * *
1950723 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1950743 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1950763 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1950783 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1950803 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1950823 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1950843 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1950863 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1950883 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1950903 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1950923 GTTGCGGTTTACGGATAC-C
1 GTTGCGATTTACGGATACGC
1950942 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1950962 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1950982 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1951002 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1951022 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1951042 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1951062 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1951082 GTTGCGATT
1 GTTGCGATT
1951091 ATGGAAAATC
Statistics
Matches: 308, Mismatches: 31, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
19 23 0.07
20 280 0.91
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1952106 original size:23 final size:22
Alignment explanation
Indices: 1952066--1952113 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1952056 TGATTTGTAA
* *
1952066 AAAAAATCAATTTGCAATACCC
1 AAAAAATCAATATCCAATACCC
*
1952088 AAAAAATCAAATATCCAATACTC
1 AAAAAATC-AATATCCAATACCC
1952111 AAA
1 AAA
1952114 CTAACAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAAATCAATATCCAATACCC
Found at i:1956451 original size:26 final size:27
Alignment explanation
Indices: 1956422--1956489 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
1956412 AATCGAAACC
1956422 TTTTGCATTTGCATTTACA-TTCACAT
1 TTTTGCATTTGCATTTACATTTCACAT
* * * **
1956448 TTTTACGTTTGTATTTACATTTTCATTT
1 TTTTGCATTTGCATTTACA-TTTCACAT
1956476 TTTTGCATTTGCAT
1 TTTTGCATTTGCAT
1956490 CTTTGCATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 16 0.50
28 16 0.50
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (27 bp):
TTTTGCATTTGCATTTACATTTCACAT
Found at i:1958920 original size:5 final size:5
Alignment explanation
Indices: 1958903--1958960 Score: 72
Period size: 5 Copynumber: 12.6 Consensus size: 5
1958893 CATCCATCAA
*
1958903 AAAAG AAAA- AAAAG AAAAG AAAAG AAAA- AAGA- AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1958949 -AAAG AAAAG AAA
1 AAAAG AAAAG AAA
1958961 TAAAATGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
4 18 0.38
5 29 0.62
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1958937 original size:26 final size:26
Alignment explanation
Indices: 1958901--1958956 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
1958891 TTCATCCATC
1958901 AAAAAAGAAAAA-AAAGAAAAGAAAAG
1 AAAAAAGAAAAAGAAAGAAAAG-AAAG
1958927 AAAAAAGAAAAAGAAAGAAAAGAAAG
1 AAAAAAGAAAAAGAAAGAAAAGAAAG
1958953 AAAA
1 AAAA
1958957 GAAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAGAAAGAAAAGAAAG
Found at i:1958957 original size:9 final size:9
Alignment explanation
Indices: 1958904--1958970 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
1958894 ATCCATCAAA
*
1958904 AAAGAAAAA
1 AAAGAAAAG
1958913 AAAGAAAAG
1 AAAGAAAAG
1958922 AAA-AGAAA-
1 AAAGA-AAAG
1958930 AAAGAAAAAG
1 AAAG-AAAAG
1958940 AAAGAAAAG
1 AAAGAAAAG
1958949 AAAGAAAAG
1 AAAGAAAAG
*
1958958 AAATAAAATG
1 AAAGAAAA-G
1958968 AAA
1 AAA
1958971 TTGAATCAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
8 4 0.08
9 38 0.75
10 9 0.18
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1960530 original size:28 final size:28
Alignment explanation
Indices: 1960490--1960547 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
1960480 GTAATCCAAG
1960490 TGGGGCATCTTGAAGGCTCACA-TCAGCA
1 TGGGGCATCTTGAAGGCTCACACT-AGCA
1960518 TGGGGCATCTTGAAGGCTCACACTAGCA
1 TGGGGCATCTTGAAGGCTCACACTAGCA
1960546 TG
1 TG
1960548 AAAAGGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (28 bp):
TGGGGCATCTTGAAGGCTCACACTAGCA
Found at i:1961898 original size:40 final size:40
Alignment explanation
Indices: 1961841--1962465 Score: 800
Period size: 40 Copynumber: 15.8 Consensus size: 40
1961831 ATATGGAGGA
**
1961841 TTTATCTCACTGGAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
1961881 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACATAAAAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * * *
1961921 TTTATTTCATTTAAAATTATTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * * *
1961961 TTTATTTCATTGAAGATTGTTTTTCTTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1962001 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
1962041 TTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
1962081 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
1962121 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACGGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1962161 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
1962201 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
1962241 TTTATCTCGCTCAAGATTG-TTTTCCCTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
1962280 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAATAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
** *
1962320 TTTATCTTGCTCAAGATTGTTTTTCCTTAAAACA-AAGA-
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* ** * * * * *
1962358 TTTATCTCGCTTGAGATAG-TTTCCCTCGAAATAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* ** * *
1962397 TTTATCTCGCTTTAGATAG-TTTCCCTTGAAAC--AA-AT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * *
1962433 TTTGTCTCACTTAAGATAG-TTTCCCTTGAAACA
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
1962466 AGTTTTGTCT
Statistics
Matches: 533, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
36 31 0.06
37 12 0.02
38 19 0.04
39 70 0.13
40 401 0.75
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (40 bp):
TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
Found at i:1962082 original size:20 final size:20
Alignment explanation
Indices: 1962020--1962083 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1962010 CTCAAGATTG
1962020 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
* ** **
1962040 TTTTAT-C-TCACTCAAGATTA
1 TTTT-TCCTTGAAAC-AGAAGA
1962060 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
1962080 TTTT
1 TTTT
1962084 ATCTCACTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTCCTTGAAACAGAAGA
Found at i:1962199 original size:23 final size:23
Alignment explanation
Indices: 1962173--1962241 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
1962163 TATCTCACTC
1962173 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
1962196 AAGA-T-TTTAT-CTCG---CTC
1 AAGATTGTTTTTCCTTGAAACAG
1962213 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
1962236 AAGATT
1 AAGATT
1962242 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 4 0.12
20 6 0.19
21 4 0.12
22 1 0.03
23 11 0.34
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:1962342 original size:20 final size:20
Alignment explanation
Indices: 1962279--1962342 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1962269 AAACAGAAGA
*
1962279 TTTTATCTCGCTCAAGATTG
1 TTTTATCTTGCTCAAGATTG
** * *
1962299 TTTT-TCCTTG-AAACAGAATA
1 TTTTAT-CTTGCTCA-AGATTG
1962319 TTTTATCTTGCTCAAGATTG
1 TTTTATCTTGCTCAAGATTG
1962339 TTTT
1 TTTT
1962343 TCCTTAAAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 8
0.65 0.19 0.17
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (20 bp):
TTTTATCTTGCTCAAGATTG
Found at i:1962608 original size:133 final size:132
Alignment explanation
Indices: 1962395--1962633 Score: 300
Period size: 133 Copynumber: 1.8 Consensus size: 132
1962385 GAAATAAAAG
* * *
1962395 ATTTTATCTCGCTTTAGATAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
* * * *
1962460 GAAACAAGTTTTGTCTCCCTTGAAATAGTTTCTCTTGAAAATTTTGAGAACATTTCCCTTGAAAC
66 AAAACAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAATTTTGAGAACATTTCCCTTGAAAC
1962525 GA
131 GA
* * * * * **
1962527 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAGAGTTTTGTCTCCCTTAAGATGGTTTTTCT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA-AATTTTGTCTCACTTAAGATAGTTTCCCT
* * *
1962592 TAAAACCAA-ATTTGTCTCACTTGAGATGGTTTTTCTTAAAAA
65 TAAAA-CAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAA
1962634 CCCTTGAGAC
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
132 30 0.34
133 55 0.62
134 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (132 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
AAAACAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAATTTTGAGAACATTTCCCTTGAAAC
GA
Found at i:1962649 original size:61 final size:61
Alignment explanation
Indices: 1962594--1962917 Score: 319
Period size: 61 Copynumber: 5.4 Consensus size: 61
1962584 GTTTTTCTTA
* *
1962594 AAACCAAATTTGTCTCACTTGAGATGGTTTTTCTTAAAAACCCTTGAGACAGTTTTCCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTT-AAAACCCTTGAGACAGTTTTCCTTTG
* ** * *** * *
1962656 AAAC--AA-GT-T-T---TTGAGACAGTTTCTCTTGAAACAAGTTTTTGAGACAATTTTCCTTCG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTT--AA-AA-CCCTTGAGACAGTTTTCCTTTG
* *
1962713 AAATAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTGCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
* * * *
1962774 AAACAAAATTTATCTCAATTAATATGGTTTTTCTTAAAACCCTTGAGAC-GATTTTTCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAG-TTTTCCTTTG
* * * *
1962835 AAATAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CCTTGAGACAATTTTCCTTCG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
*
1962895 AAGC-AAATTTATCTCACTTGAGA
1 AAACAAAATTTATCTCACTTGAGA
1962918 GAGCTTCTCT
Statistics
Matches: 214, Mismatches: 35, Indels: 29
0.77 0.13 0.10
Matches are distributed among these distances:
54 14 0.07
55 3 0.01
56 2 0.01
57 21 0.10
58 1 0.00
59 21 0.10
60 23 0.11
61 106 0.50
62 7 0.03
63 2 0.01
65 14 0.07
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (61 bp):
AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
Found at i:1962695 original size:29 final size:29
Alignment explanation
Indices: 1962637--1962715 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
1962627 TTAAAAACCC
1962637 TTGAGACAGTTTTCCTTTGAAACAAGTTT
1 TTGAGACAGTTTTCCTTTGAAACAAGTTT
1962666 TTGAGACAG-TTT-CTCTTGAAACAAGTTT
1 TTGAGACAGTTTTCCT-TTGAAACAAGTTT
* *
1962694 TTGAGACAATTTTCCTTCGAAA
1 TTGAGACAGTTTTCCTTTGAAA
1962716 TAAAATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 2 0.04
28 24 0.53
29 17 0.38
30 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (29 bp):
TTGAGACAGTTTTCCTTTGAAACAAGTTT
Found at i:1962702 original size:13 final size:13
Alignment explanation
Indices: 1962652--1962706 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
1962642 ACAGTTTTCC
1962652 TTTGAAACAAGTT
1 TTTGAAACAAGTT
*
1962665 TTTGAGAC-AGTTT
1 TTTGAAACAAG-TT
1962678 CTCTTGAAACAAGTT
1 -T-TTGAAACAAGTT
*
1962693 TTTGAGACAA-TT
1 TTTGAAACAAGTT
1962705 TT
1 TT
1962707 CCTTCGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
12 6 0.17
13 17 0.49
14 2 0.06
15 8 0.23
16 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (13 bp):
TTTGAAACAAGTT
Found at i:1962952 original size:122 final size:121
Alignment explanation
Indices: 1962599--1962939 Score: 353
Period size: 122 Copynumber: 2.8 Consensus size: 121
1962589 TCTTAAAACC
*
1962599 AAATTTGTCTCACTTGAGATGGTTTTTCTTAAAAACCCTTGAGACAGTTTTCCTTTGAAAC-AA-
1 AAATTTATCTCACTTGAGATGGTTTTTCTT-AAAACCCTTGAGACAGTTTTCCTTTGAAACAAAT
* * *
1962662 GT-T-T--TTGAGACAGTTTCTCTTGAAACAAGTTTTTGAGACAATTTTCCTTCGAAATA
65 TTATCTCATTGAGAGAGTTTCTCTTAAAACAAGTTTTT-A-ACAATTTT-CTTCGAAATA
*
1962718 AAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTGCTTTGAAACAAAAT
1 AAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTGAAAC-AAAT
* * * ** * * *
1962783 TTATCTCAATTAATATG-GTTTTTCTTAAAAC---CCTTGAGACGATTTTTCTTTGAAATA
65 TTATCTC-ATTGAGA-GAGTTTCTCTTAAAACAAGTTTTTA-AC-AATTTTCTTCGAAATA
* * * *
1962840 AAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CCTTGAGACAATTTTCCTTCGAAGCAAATT
1 AAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTGAAACAAATT
*
1962904 TATCTCACTTGAGAGAGCTTCTCTTAAAACAAGTTT
66 TATCTCA-TTGAGAGAGTTTCTCTTAAAACAAGTTT
1962940 CTTATTAATT
Statistics
Matches: 183, Mismatches: 24, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
118 29 0.16
119 31 0.17
120 29 0.16
121 22 0.12
122 47 0.26
123 9 0.05
126 16 0.09
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (121 bp):
AAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTGAAACAAATT
TATCTCATTGAGAGAGTTTCTCTTAAAACAAGTTTTTAACAATTTTCTTCGAAATA
Found at i:1963528 original size:136 final size:136
Alignment explanation
Indices: 1963279--1963864 Score: 872
Period size: 136 Copynumber: 4.3 Consensus size: 136
1963269 TTTCCAATGG
* * *
1963279 AGAGTGGAGAAGAAATTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCATGACATTTC
1 AGAG-GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTC
*
1963344 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTTCAATTGAGAGTTCATAATGAGAAGAACTC
65 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTC
1963409 ATCCGAC
130 ATCCGAC
* * * **
1963416 AGAGGGAGAAGAAGTTCCTAATGAGAATAACTTGTTCGACATATCACTCGATTCACGGTATTTCG
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
1963481 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
66 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
1963546 TCCGAC
131 TCCGAC
* * * *
1963552 AGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCTACCTATCACTCGATTCAC-AGTATTTT
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGA-CATTTC
* * *
1963616 GAATTAGTGACGCCTCGCTTGAGGGATTAACATTTCCAA-TGAAGAGTTCATAATGAGAAGAACT
65 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTG-AGAGTTCATAATGAGAAGAACT
1963680 CATCCGAC
129 CATCCGAC
** *
1963688 AGAGGGAGAAGAAGTTCATAATGAGAAGGGCTTGTTCGACCTATCACTCGATTCACGACATTTTG
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
** * * * * *
1963753 AATCAGTGATGCCTTGCTTGAGGGATTGACATTTCTAATGGAGAGTTCATAATGAAAAGAATTCA
66 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
*
1963818 TCCAAC
131 TCCGAC
*
1963824 A-AGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCT
1963865 CAGATCAACA
Statistics
Matches: 411, Mismatches: 34, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
135 39 0.09
136 366 0.89
137 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (136 bp):
AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
TCCGAC
Found at i:1965161 original size:36 final size:35
Alignment explanation
Indices: 1965077--1965161 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 35
1965067 TTCCATCTTA
* *
1965077 ATTTTAACATTTAGTTTTGAATTTTATTTTTAGTCT
1 ATTTTAA-ATTTAGATTTGAATTTTAGTTTTAGTCT
* * *
1965113 ATTTTAATTTTAGATTTGTATGTTTAGTTTTATGTTT
1 ATTTTAAATTTAGATTTGAAT-TTTAGTTTTA-GTCT
1965150 A-TTTAAATTTAG
1 ATTTTAAATTTAG
1965162 TAATTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 11 0.27
36 26 0.63
37 4 0.10
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (35 bp):
ATTTTAAATTTAGATTTGAATTTTAGTTTTAGTCT
Found at i:1969454 original size:21 final size:23
Alignment explanation
Indices: 1969430--1969474 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1969420 TTACAATTCC
1969430 TTAATCTT-TAT-TTATCTTGTT
1 TTAATCTTATATCTTATCTTGTT
*
1969451 TTAATCTTATTTCTTATCTTGTT
1 TTAATCTTATATCTTATCTTGTT
1969474 T
1 T
1969475 CCAGCACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.18, C:0.11, G:0.04, T:0.67
Consensus pattern (23 bp):
TTAATCTTATATCTTATCTTGTT
Done.