Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1764259 original size:35 final size:35
Alignment explanation
Indices: 1764212--1764279 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
1764202 TTATTTTACA
*
1764212 GACCAGCTACTATACACACATGAACAAGACCACAG
1 GACCAGCAACTATACACACATGAACAAGACCACAG
* *
1764247 GACCAGCAACTATAGACACATGAACAGGACCAC
1 GACCAGCAACTATACACACATGAACAAGACCAC
1764280 GGGAACAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.31, G:0.16, T:0.10
Consensus pattern (35 bp):
GACCAGCAACTATACACACATGAACAAGACCACAG
Found at i:1766114 original size:34 final size:34
Alignment explanation
Indices: 1766040--1766137 Score: 87
Period size: 34 Copynumber: 2.9 Consensus size: 34
1766030 AATTAAAATA
* * * *
1766040 ATAT-TTATTTAAGTTTAAATAGTAAAAGGTGTCT
1 ATATCTTA-TTAAATTTCAATATTAAAAGATGTCT
1766074 ATATCTT-TTGAACATTTCAA-ATTAAAAGATGT-T
1 ATATCTTATT-AA-ATTTCAATATTAAAAGATGTCT
*
1766107 ATCATCTTATTAAATTTGAATATTAAAAGAT
1 AT-ATCTTATTAAATTTCAATATTAAAAGAT
1766138 ATCTGATTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 11 0.21
34 33 0.62
35 9 0.17
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (34 bp):
ATATCTTATTAAATTTCAATATTAAAAGATGTCT
Found at i:1769279 original size:2 final size:2
Alignment explanation
Indices: 1769272--1769301 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1769262 AGATCATTTA
1769272 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
1769302 TAATTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1773962 original size:20 final size:19
Alignment explanation
Indices: 1773884--1773963 Score: 52
Period size: 20 Copynumber: 4.1 Consensus size: 19
1773874 TGGATTGAGA
*
1773884 GTTTCAATTTGGGAATTACG
1 GTTTTAATTTGGGAATTA-G
* * ***
1773904 GTTATAATATATAAATTAG
1 GTTTTAATTTGGGAATTAG
* * *
1773923 GGTTTAATTTTGAGAGTTAG
1 GTTTTAA-TTTGGGAATTAG
1773943 AGTTTTAATTTGGGAATTAG
1 -GTTTTAATTTGGGAATTAG
1773963 G
1 G
1773964 GTACTCAACT
Statistics
Matches: 42, Mismatches: 16, Indels: 5
0.67 0.25 0.08
Matches are distributed among these distances:
19 7 0.17
20 29 0.69
21 6 0.14
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (19 bp):
GTTTTAATTTGGGAATTAG
Found at i:1774574 original size:51 final size:51
Alignment explanation
Indices: 1774493--1774596 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
1774483 TCGATGTGAC
*
1774493 AAACTCATCCCTTTAAAAATATAAAAAATAATGTAAATAACTTTATTTTTA
1 AAACCCATCCCTTTAAAAATATAAAAAATAATGTAAATAACTTTATTTTTA
1774544 AAACCCATCCCTTTAAAAATATAAAAAATAATGTAAATAACTTTATTTTTA
1 AAACCCATCCCTTTAAAAATATAAAAAATAATGTAAATAACTTTATTTTTA
1774595 AA
1 AA
1774597 CAAGTTTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (51 bp):
AAACCCATCCCTTTAAAAATATAAAAAATAATGTAAATAACTTTATTTTTA
Found at i:1778973 original size:2 final size:2
Alignment explanation
Indices: 1778966--1778993 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1778956 CCTTAAAATG
1778966 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
1778994 GTTTAACTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1783284 original size:3 final size:3
Alignment explanation
Indices: 1783276--1783306 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1783266 TTGGCATTAG
1783276 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1783307 CCACATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1797670 original size:19 final size:19
Alignment explanation
Indices: 1797646--1797687 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1797636 TTCAACCACT
1797646 GAAAGAAACACAAACAATA
1 GAAAGAAACACAAACAATA
1797665 GAAAGAAACACAAACAATA
1 GAAAGAAACACAAACAATA
1797684 GAAA
1 GAAA
1797688 CCCAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.14, G:0.12, T:0.05
Consensus pattern (19 bp):
GAAAGAAACACAAACAATA
Found at i:1801976 original size:18 final size:18
Alignment explanation
Indices: 1801953--1801987 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1801943 ACTGAATATT
1801953 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1801971 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1801988 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1804397 original size:12 final size:12
Alignment explanation
Indices: 1804382--1804431 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1804372 CTTGAAAAAG
1804382 ACAAGGAAAATA
1 ACAAGGAAAATA
*
1804394 ACAAGTAAAACTA
1 ACAAGGAAAA-TA
1804407 TACAA--AAAATAA
1 -ACAAGGAAAAT-A
1804419 ACAAGGAAAATA
1 ACAAGGAAAATA
1804431 A
1 A
1804432 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.12
Consensus pattern (12 bp):
ACAAGGAAAATA
Found at i:1806166 original size:20 final size:20
Alignment explanation
Indices: 1806137--1806178 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1806127 ATTCCACCAC
1806137 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
1806157 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
1806177 AT
1 AT
1806179 AAGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:1810889 original size:27 final size:27
Alignment explanation
Indices: 1810840--1810891 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1810830 ATCAAGAATG
* *
1810840 AATCAGTGACCTAAACACGAAATACTA
1 AATCAATGACCTAAACACAAAATACTA
* *
1810867 AATCAATGACCTAAATATAAAATAC
1 AATCAATGACCTAAACACAAAATAC
1810892 ACATAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (27 bp):
AATCAATGACCTAAACACAAAATACTA
Found at i:1812403 original size:51 final size:51
Alignment explanation
Indices: 1812286--1812599 Score: 403
Period size: 51 Copynumber: 6.0 Consensus size: 51
1812276 TCAAATGGCA
* * * * *
1812286 TGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
* * ** *
1812341 AGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTTTATCTTCAATAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
* *
1812392 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
* * *
1812447 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATTTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
* *
1812498 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1812549 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1812600 AGTTTGCTTC
Statistics
Matches: 238, Mismatches: 17, Indels: 12
0.89 0.06 0.04
Matches are distributed among these distances:
51 161 0.68
55 77 0.32
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
Found at i:1812457 original size:106 final size:105
Alignment explanation
Indices: 1812286--1812599 Score: 454
Period size: 106 Copynumber: 3.0 Consensus size: 105
1812276 TCAAATGGCA
* * * * ** **
1812286 TGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGAGTCCGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-AACAATCTTCAACGAACTTGTCCGCTCC
* ** *
1812351 CTATTCCTTCAGAGAGTATAAGACTTTATCTTCAATAAACG
65 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1812392 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACGAACTTGTCCGCTCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-AACAATCTTCAACGAACTTGTCCGCTCC
* * *
1812457 CTATTCCTTCAGAGAGTATAGGACTCAATTTTCAACGAACT
65 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1812498 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCAACGAACTTGTCCGCTCCC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAACAATCTTCAACGAACTTGTCCGCTCCC
1812560 TATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
66 TATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
1812600 AGTTTGCTTC
Statistics
Matches: 189, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
102 64 0.34
106 125 0.66
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (105 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAACAATCTTCAACGAACTTGTCCGCTCCC
TATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACG
Found at i:1813959 original size:9 final size:9
Alignment explanation
Indices: 1813922--1814087 Score: 56
Period size: 9 Copynumber: 18.7 Consensus size: 9
1813912 TTTCTCTTTT
1813922 TTTTTTTCA
1 TTTTTTTCA
*
1813931 TTTTTCTCA
1 TTTTTTTCA
1813940 --TTTTTCA
1 TTTTTTTCA
1813947 --TTTTTCA
1 TTTTTTTCA
1813954 -TTTTTTC-
1 TTTTTTTCA
1813961 TTCTATTTTCCA
1 TT-T-TTTT-CA
1813973 TTTTTTTC-
1 TTTTTTTCA
*
1813981 TTCTCTTTT-T
1 TT-T-TTTTCA
1813991 TTTCTTTTCA
1 TTT-TTTTCA
*
1814001 TTTTTTCCA
1 TTTTTTTCA
*
1814010 TCATTTTTC-
1 T-TTTTTTCA
1814019 TTTTTTCTCA
1 TTTTTT-TCA
1814029 --TTTTTC-
1 TTTTTTTCA
*
1814035 TTTTCTTC-
1 TTTTTTTCA
1814043 TTTTTCTTC-
1 TTTTT-TTCA
*
1814052 TTCTCATTTTTA
1 TT-T--TTTTCA
1814064 TTATTTTTCA
1 TT-TTTTTCA
1814074 -TTTTTTCA
1 TTTTTTTCA
1814082 TTTTTT
1 TTTTTT
1814088 CTCTTTTATT
Statistics
Matches: 124, Mismatches: 12, Indels: 42
0.70 0.07 0.24
Matches are distributed among these distances:
7 15 0.12
8 33 0.27
9 37 0.30
10 28 0.23
11 4 0.03
12 7 0.06
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1813976 original size:7 final size:7
Alignment explanation
Indices: 1813924--1813958 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
1813914 TCTCTTTTTT
1813924 TTTTTCA
1 TTTTTCA
1813931 TTTTTCTCA
1 -TTTT-TCA
1813940 TTTTTCA
1 TTTTTCA
1813947 TTTTTCA
1 TTTTTCA
1813954 TTTTT
1 TTTTT
1813959 TCTTCTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.58
8 8 0.31
9 3 0.12
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:1813992 original size:34 final size:35
Alignment explanation
Indices: 1813907--1814049 Score: 93
Period size: 34 Copynumber: 3.9 Consensus size: 35
1813897 TGAACCCTCC
*
1813907 TTTTA-TTTCTCTTTTTTTTTTTCATTTTTCTCAT
1 TTTTATTTTCTCTTTTTTTTCTTCATTTTTCTCAT
*
1813941 TTTTCATTTT-TC-ATTTTTTCTTC-TATTTTC-CAT
1 TTTT-ATTTTCTCTTTTTTTTCTTCAT-TTTTCTCAT
1813974 TTTT-TTCTTCTCTTTTTTTTCTTTTCATTTTTTCCATCATT
1 TTTTATT-TTCTCTTTTTTTTC--TTCA-TTTTT-C-TCA-T
*
1814015 TTTCTTTTTTCTCATTTTTCTTTTCTTC-TTTTTCT
1 TTT-TATTTTCTC--TTTT-TTTTCTTCATTTTTCT
1814050 TCTTCTCATT
Statistics
Matches: 87, Mismatches: 3, Indels: 33
0.71 0.02 0.27
Matches are distributed among these distances:
31 2 0.02
32 2 0.02
33 10 0.11
34 25 0.29
35 3 0.03
36 6 0.07
37 4 0.05
38 2 0.02
39 1 0.01
40 3 0.03
41 9 0.10
42 6 0.07
43 5 0.06
44 4 0.05
45 5 0.06
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (35 bp):
TTTTATTTTCTCTTTTTTTTCTTCATTTTTCTCAT
Found at i:1813999 original size:54 final size:54
Alignment explanation
Indices: 1813941--1814104 Score: 162
Period size: 56 Copynumber: 3.0 Consensus size: 54
1813931 TTTTTCTCAT
* *
1813941 TTTTCATTTTTCATTTTTTCTTCTATTTTCCATTTTTTTCTTC-TCTTTTTTTTC
1 TTTTCATTTTTCATTATTT-TTCTATTTTCCATTTTTTTCTTCTTCTTTTTCTTC
* *
1813995 TTTTCATTTTTTCCATCATTTTTCTTTTTTCTCATTTTTCTT-TTCTTCTTTTTCTTC
1 TTTTCA-TTTTT-CATTATTTTTCTATTTTC-CATTTTT-TTCTTCTTCTTTTTCTTC
* *
1814052 TTCTCATTTTT-ATTATTTTTC-ATTTTTTCA-TTTTTTC-TCTT-TTATTTCTTC
1 TTTTCATTTTTCATTATTTTTCTA-TTTTCCATTTTTTTCTTCTTCTT-TTTCTTC
1814103 TT
1 TT
1814105 CAAGCGAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 19
0.78 0.07 0.16
Matches are distributed among these distances:
50 2 0.02
51 15 0.16
52 4 0.04
53 2 0.02
54 19 0.20
55 14 0.15
56 21 0.22
57 17 0.18
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (54 bp):
TTTTCATTTTTCATTATTTTTCTATTTTCCATTTTTTTCTTCTTCTTTTTCTTC
Found at i:1814015 original size:40 final size:41
Alignment explanation
Indices: 1813971--1814048 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1813961 TTCTATTTTC
**
1813971 CATTTTT-TTCTTCTCTTTTTTTTCTTTTCAT-TTTTTCCAT
1 CATTTTTCTT-TTCTCTCATTTTTCTTTTCATCTTTTTCCAT
* *
1814011 CATTTTTCTTTTTTCTCATTTTTCTTTTCTTCTTTTTC
1 CATTTTTCTTTTCTCTCATTTTTCTTTTCATCTTTTTC
1814049 TTCTTCTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (41 bp):
CATTTTTCTTTTCTCTCATTTTTCTTTTCATCTTTTTCCAT
Found at i:1814078 original size:55 final size:54
Alignment explanation
Indices: 1813912--1814104 Score: 179
Period size: 55 Copynumber: 3.6 Consensus size: 54
1813902 CCTCCTTTTA
* *
1813912 TTTCTC-TTTTTTTTT-TTCATTTTTC-TCATTTTTCATTTTTCATTTTTTCTTCTAT
1 TTTCTCATTTTTTTTTCTTC-TTTTTCTTC--TTTTCATTTTTCATTATTT-TTCTTT
* *
1813967 TTTC-CATTTTTTTCTTC-TCTTTTTTTTCTTTTCATTTTTTCCATCATTTTTCTTT
1 TTTCTCATTTTTTT-TTCTTCTTTTTCTTCTTTTCA-TTTTT-CATTATTTTTCTTT
* *
1814022 TTTCTCATTTTTCTTTTCTTCTTTTTCTTCTTCTCATTTTT-ATTATTTTTCATT
1 TTTCTCATTTTT-TTTTCTTCTTTTTCTTCTTTTCATTTTTCATTATTTTTCTTT
*
1814076 TTT-TCA-TTTTTTCTCTT-TTATTTCTTCTT
1 TTTCTCATTTTTTTTTCTTCTT-TTTCTTCTT
1814105 CAAGCGAAAT
Statistics
Matches: 119, Mismatches: 9, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
50 2 0.02
51 15 0.13
52 4 0.03
53 3 0.03
54 21 0.18
55 30 0.25
56 27 0.23
57 17 0.14
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (54 bp):
TTTCTCATTTTTTTTTCTTCTTTTTCTTCTTTTCATTTTTCATTATTTTTCTTT
Found at i:1814087 original size:16 final size:16
Alignment explanation
Indices: 1813923--1814088 Score: 79
Period size: 16 Copynumber: 10.4 Consensus size: 16
1813913 TTCTCTTTTT
1813923 TTTTTTCATTTTTCTCA
1 TTTTTTCATTTTT-TCA
1813940 -TTTTTCA-TTTTTCA
1 TTTTTTCATTTTTTCA
*
1813954 TTTTTTCTTCTATTTTCCA
1 TTTTTTCAT-T-TTTT-CA
* *
1813973 TTTTTT--TCTTCTC-
1 TTTTTTCATTTTTTCA
1813986 TTTTTT--TTCTTTTCA
1 TTTTTTCATT-TTTTCA
*
1814001 TTTTTTCCATCATTTTTCT
1 TTTTTT-CAT--TTTTTCA
1814020 TTTTTCTCA-TTTTTC-
1 TTTTT-TCATTTTTTCA
1814035 TTTTCTTC--TTTTTC-
1 TTTT-TTCATTTTTTCA
* *
1814049 TTCTTCTCATTTTTATTA
1 TT-TTTTCATTTTT-TCA
1814067 -TTTTTCATTTTTTCA
1 TTTTTTCATTTTTTCA
1814082 TTTTTTC
1 TTTTTTC
1814089 TCTTTTATTT
Statistics
Matches: 119, Mismatches: 10, Indels: 41
0.70 0.06 0.24
Matches are distributed among these distances:
13 7 0.06
14 18 0.15
15 29 0.24
16 34 0.29
17 4 0.03
18 5 0.04
19 20 0.17
20 2 0.02
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTCATTTTTTCA
Found at i:1823708 original size:24 final size:24
Alignment explanation
Indices: 1823676--1823750 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
1823666 TGCTGACTAC
*
1823676 CCCATCATGCTTTATCAGATCCTA
1 CCCAACATGCTTTATCAGATCCTA
* *
1823700 CCCAACATG--ATATC-TA-CC--
1 CCCAACATGCTTTATCAGATCCTA
*
1823718 CCCATCATGCTTTATCAGATCCTA
1 CCCAACATGCTTTATCAGATCCTA
1823742 CCCAACATG
1 CCCAACATG
1823751 ATATCTACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 8 0.21
20 6 0.16
21 2 0.05
22 6 0.16
24 16 0.42
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (24 bp):
CCCAACATGCTTTATCAGATCCTA
Found at i:1823721 original size:42 final size:42
Alignment explanation
Indices: 1823675--1823763 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
1823665 ATGCTGACTA
1823675 CCCCATCATGCTTTATCAGATCCTACCCAACATGATATCTAC
1 CCCCATCATGCTTTATCAGATCCTACCCAACATGATATCTAC
1823717 CCCCATCATGCTTTATCAGATCCTACCCAACATGATATCTAC
1 CCCCATCATGCTTTATCAGATCCTACCCAACATGATATCTAC
1823759 CCCCA
1 CCCCA
1823764 GGTTTTGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.28, C:0.38, G:0.07, T:0.27
Consensus pattern (42 bp):
CCCCATCATGCTTTATCAGATCCTACCCAACATGATATCTAC
Found at i:1823845 original size:46 final size:47
Alignment explanation
Indices: 1823779--1823880 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 47
1823769 TGTTATCCAC
*
1823779 AAAAAGAAATCCTAATCGCATGATATCTAATTCGCATGCTTATTCAA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
* * * *
1823826 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTTCGA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
*
1823872 AAAATGAAA
1 AAAAAGAAA
1823881 ATAAATGACT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 40 0.83
47 8 0.17
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTATTCAA
Found at i:1825657 original size:27 final size:27
Alignment explanation
Indices: 1825608--1825659 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1825598 ATCAAGAATG
* *
1825608 AATCAGTGACCTAAACACGAAATACTA
1 AATCAATGACCTAAACACAAAATACTA
* *
1825635 AATCAATGACCTAAATATAAAATAC
1 AATCAATGACCTAAACACAAAATAC
1825660 ACATAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (27 bp):
AATCAATGACCTAAACACAAAATACTA
Found at i:1828968 original size:23 final size:23
Alignment explanation
Indices: 1828942--1829019 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1828932 CACCACAACT
*
1828942 CATATAATTGCACTGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
1828965 CATATAATTACACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
1828988 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
1829011 TATAATAAT
1 CAT-ATAAT
1829020 GTCCATAAGG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 38 0.90
24 4 0.10
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:1829209 original size:103 final size:103
Alignment explanation
Indices: 1829026--1829243 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
1829016 TAATGTCCAT
* *
1829026 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1829091 TACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
* * *
1829129 AAGGATCATATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
1829194 GACTTCACACTTGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
1829232 AAGGACCACATA
1 AAGGACCACATA
1829244 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:1832826 original size:18 final size:18
Alignment explanation
Indices: 1832803--1832855 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1832793 ACTGAATATT
*
1832803 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1832821 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1832839 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1832856 GATAATCCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1833214 original size:55 final size:55
Alignment explanation
Indices: 1833149--1833266 Score: 218
Period size: 55 Copynumber: 2.1 Consensus size: 55
1833139 GAATGCGAAA
*
1833149 TCATAAGTTTAACTATAAGAGATAGACTCATCGCAAGTCTTATCTCAATACAATT
1 TCATAAGTTTAACTAGAAGAGATAGACTCATCGCAAGTCTTATCTCAATACAATT
*
1833204 TCATAAGTTTAACTAGAAGAGATAGATTCATCGCAAGTCTTATCTCAATACAATT
1 TCATAAGTTTAACTAGAAGAGATAGACTCATCGCAAGTCTTATCTCAATACAATT
1833259 TCATAAGT
1 TCATAAGT
1833267 AATACATTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (55 bp):
TCATAAGTTTAACTAGAAGAGATAGACTCATCGCAAGTCTTATCTCAATACAATT
Found at i:1833562 original size:21 final size:21
Alignment explanation
Indices: 1833538--1833588 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1833528 GAGAATGCAT
*
1833538 CGATACACATTGAATGTGTAC
1 CGATGCACATTGAATGTGTAC
1833559 CGATGCACATTGAATGTGTAC
1 CGATGCACATTGAATGTGTAC
1833580 CGATGCACA
1 CGATGCACA
1833589 CAGCCCAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
CGATGCACATTGAATGTGTAC
Found at i:1837800 original size:2 final size:2
Alignment explanation
Indices: 1837793--1837830 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1837783 GTATACACTT
*
1837793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1837831 AATAAATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1838318 original size:22 final size:22
Alignment explanation
Indices: 1838292--1838336 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1838282 TTTATTAAAT
*
1838292 TTTTTAATAAATATAATAGTATA
1 TTTTTAAT-AATATAATAATATA
*
1838315 TTTTTAATATTATAATAATATA
1 TTTTTAATAATATAATAATATA
1838337 CTCAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTAATAATATAATAATATA
Found at i:1838367 original size:23 final size:23
Alignment explanation
Indices: 1838321--1838371 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1838311 TATATTTTTA
**
1838321 ATATTATAATAATATACTCAATT
1 ATATTATAATAATATACAAAATT
1838344 ATATTATAATAATATA-AAATATT
1 ATATTATAATAATATACAAA-ATT
1838367 ATATT
1 ATATT
1838372 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTATAATAATATACAAAATT
Found at i:1838492 original size:20 final size:18
Alignment explanation
Indices: 1838450--1838498 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1838440 TCATAAAATA
1838450 TTTAAAAA-AT-ATTTTT
1 TTTAAAAATATAATTTTT
1838466 TTTAAAAATATAATTTATT
1 TTTAAAAATATAATTT-TT
1838485 TTTAAAAAATATAA
1 TTT-AAAAATATAA
1838499 AATATTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.28
17 2 0.07
18 4 0.14
19 5 0.17
20 10 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAATATAATTTTT
Found at i:1838504 original size:20 final size:20
Alignment explanation
Indices: 1838463--1838506 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1838453 AAAAAATATT
* **
1838463 TTTTTTAAAAATATAATTTA
1 TTTTTAAAAAATATAAAATA
1838483 TTTTTAAAAAATATAAAATA
1 TTTTTAAAAAATATAAAATA
1838503 TTTT
1 TTTT
1838507 CCATAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTAAAAAATATAAAATA
Found at i:1855743 original size:12 final size:11
Alignment explanation
Indices: 1855716--1855748 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1855706 ACCTGAATGC
1855716 ATTGACAAAAA
1 ATTGACAAAAA
1855727 ATTGACAAAAA
1 ATTGACAAAAA
1855738 AGTTGA-AAAAA
1 A-TTGACAAAAA
1855749 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (11 bp):
ATTGACAAAAA
Found at i:1859043 original size:2 final size:2
Alignment explanation
Indices: 1859036--1859063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1859026 TGCACCTTTC
1859036 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
1859064 CCATGCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1862198 original size:31 final size:31
Alignment explanation
Indices: 1862160--1862250 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 31
1862150 GGGTCGAGGG
*
1862160 TTACCTATATTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1862191 TTACCTATGTTCTTC-GGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1862221 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1862251 GTCCTTCGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
30 28 0.53
31 24 0.45
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1864639 original size:16 final size:16
Alignment explanation
Indices: 1864618--1864651 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1864608 TTAACATCTG
1864618 ATTTTA-TACATGTTTT
1 ATTTTATTA-ATGTTTT
1864634 ATTTTATTAATGTTTT
1 ATTTTATTAATGTTTT
1864650 AT
1 AT
1864652 ACGATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (16 bp):
ATTTTATTAATGTTTT
Found at i:1867128 original size:46 final size:46
Alignment explanation
Indices: 1867052--1867150 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
1867042 GGATTACCGA
* *
1867052 AAGCA-GACTGAGATGTTTATCCTGATATTCAAACATTGCTAATTG
1 AAGCAGGACTGAAATGTTTATCCTGACATTCAAACATTGCTAATTG
1867097 AAGCAGGACTGAAATGTTTATACC-GACATTCAAACATTGCTAATTG
1 AAGCAGGACTGAAATGTTTAT-CCTGACATTCAAACATTGCTAATTG
1867143 AAGCAGGA
1 AAGCAGGA
1867151 ACTGTAATTC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
45 5 0.10
46 43 0.86
47 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (46 bp):
AAGCAGGACTGAAATGTTTATCCTGACATTCAAACATTGCTAATTG
Found at i:1870693 original size:18 final size:18
Alignment explanation
Indices: 1870668--1870705 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1870658 ATTTTTATTG
1870668 AAATTTTAATTAATT-TA
1 AAATTTTAATTAATTATA
*
1870685 AAATCTTTATTTAATTATA
1 AAAT-TTTAATTAATTATA
1870704 AA
1 AA
1870706 TTAAAGCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTTAATTAATTATA
Found at i:1870971 original size:16 final size:17
Alignment explanation
Indices: 1870941--1870972 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1870931 TCTTAAAAAT
1870941 TTTAAATTATTATTTAG
1 TTTAAATTATTATTTAG
1870958 TTTAAATT-TTATTTA
1 TTTAAATTATTATTTA
1870973 TATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAAATTATTATTTAG
Found at i:1872368 original size:24 final size:24
Alignment explanation
Indices: 1872341--1872396 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1872331 AAACGGAGAT
* *
1872341 ATCAGAAAACAAAACATAATTCAG
1 ATCAGAAAACAAAACAGAATCCAG
* *
1872365 ATCAGATATCAAAACAGAATCCAG
1 ATCAGAAAACAAAACAGAATCCAG
*
1872389 GTCAGAAA
1 ATCAGAAA
1872397 TTAGAACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (24 bp):
ATCAGAAAACAAAACAGAATCCAG
Found at i:1879786 original size:17 final size:17
Alignment explanation
Indices: 1879766--1879799 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1879756 TCAGATTTGT
1879766 TAAATATAAAAATTAGG
1 TAAATATAAAAATTAGG
*
1879783 TAAATATAGAAATTAGG
1 TAAATATAAAAATTAGG
1879800 CCCCTAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (17 bp):
TAAATATAAAAATTAGG
Found at i:1882648 original size:22 final size:22
Alignment explanation
Indices: 1882607--1882648 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1882597 TCTATTATAA
* * *
1882607 TTATATTTTTGTTTTTATTTTT
1 TTATATTTTTATTATAATTTTT
1882629 TTATATTTTTATTATAATTT
1 TTATATTTTTATTATAATTT
1882649 AAATTGATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TTATATTTTTATTATAATTTTT
Found at i:1882670 original size:26 final size:26
Alignment explanation
Indices: 1882641--1882722 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
1882631 ATATTTTTAT
1882641 TATAATTTAAATTGATATAATTCATA
1 TATAATTTAAATTGATATAATTCATA
* ** * *
1882667 TATAA--CAATATTTTTTTGAATTTAT-
1 TATAATTTAA-ATTGATAT-AATTCATA
* *
1882692 TATAGTTTAAATTGATATGATTCATA
1 TATAATTTAAATTGATATAATTCATA
1882718 TATAA
1 TATAA
1882723 GGGTGTGTTT
Statistics
Matches: 38, Mismatches: 13, Indels: 10
0.62 0.21 0.16
Matches are distributed among these distances:
24 2 0.05
25 14 0.37
26 20 0.53
27 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (26 bp):
TATAATTTAAATTGATATAATTCATA
Found at i:1891233 original size:2 final size:2
Alignment explanation
Indices: 1891226--1891259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1891216 ATTACATTGA
1891226 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
1891260 TATCTTCATA
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:1897871 original size:23 final size:23
Alignment explanation
Indices: 1897827--1897871 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1897817 ATTATTATAT
*
1897827 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1897850 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1897872 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1899049 original size:24 final size:25
Alignment explanation
Indices: 1899021--1899067 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1899011 GTAAATGAAG
1899021 TTTTAAATG-TTTATTATTAAATCA
1 TTTTAAATGTTTTATTATTAAATCA
1899045 TTTTAAATGTTTTATTATTAAAT
1 TTTTAAATGTTTTATTATTAAAT
1899068 TGTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTAAATGTTTTATTATTAAATCA
Found at i:1899067 original size:15 final size:16
Alignment explanation
Indices: 1899047--1899076 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1899037 TTAAATCATT
1899047 TTAAA-TGTTTTATTA
1 TTAAATTGTTTTATTA
1899062 TTAAATTGTTTTATT
1 TTAAATTGTTTTATT
1899077 TAAAGAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
TTAAATTGTTTTATTA
Found at i:1899073 original size:25 final size:24
Alignment explanation
Indices: 1899020--1899074 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
1899010 AGTAAATGAA
1899020 GTTTTAAATGTTTATTATTAAATC
1 GTTTTAAATGTTTATTATTAAATC
* *
1899044 ATTTTAAATGTTTTATTATTAAATT
1 GTTTTAAATG-TTTATTATTAAATC
1899069 GTTTTA
1 GTTTTA
1899075 TTTAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (24 bp):
GTTTTAAATGTTTATTATTAAATC
Found at i:1900998 original size:20 final size:20
Alignment explanation
Indices: 1900975--1901026 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1900965 AACGCGATCC
1900975 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1900995 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1901015 CCAAAATCGCAA
1 CCAGAATCGCAA
1901027 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:1901043 original size:21 final size:20
Alignment explanation
Indices: 1901016--1901114 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1901006 AATCAGTTTC
1901016 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1901037 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1901058 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1901078 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1901099 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1901115 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:1901143 original size:20 final size:20
Alignment explanation
Indices: 1901081--1901274 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1901071 CGATTTTCCA
* ** *
1901081 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1901101 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1901121 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1901141 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1901161 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1901181 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1901201 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1901221 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1901241 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1901262 AAATCGCAACGCG
1 AAATCGCAACGCG
1901275 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:1901165 original size:60 final size:60
Alignment explanation
Indices: 1901081--1901274 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1901071 CGATTTTCCA
* ** * *
1901081 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1901141 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1901201 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1901262 AAATCGCAACGCG
1 AAATCGCAACGCG
1901275 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:1901695 original size:33 final size:33
Alignment explanation
Indices: 1901656--1901726 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1901646 TTCACTTAGA
*
1901656 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1901689 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1901722 TTTCA
1 TTTCA
1901727 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:1901866 original size:14 final size:14
Alignment explanation
Indices: 1901847--1901901 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1901837 AGAATGACTG
1901847 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1901861 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1901880 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1901894 TCGCAACG
1 TCGCAACG
1901902 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1901884 original size:33 final size:33
Alignment explanation
Indices: 1901847--1901917 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1901837 AGAATGACTG
**
1901847 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1901880 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1901913 TCGCA
1 TCGCA
1901918 TTGCGATTTT
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:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1901935 original size:19 final size:19
Alignment explanation
Indices: 1901913--1902010 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1901903 GAAACCAAAA
*
1901913 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1901932 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1901946 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1901965 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1901979 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1901998 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1902011 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:1901954 original size:14 final size:14
Alignment explanation
Indices: 1901935--1902024 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1901925 TTTCATTTCG
1901935 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1901949 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1901968 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1901982 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1901999 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1902015 CGTTGCGATT
1 CGTTGCGATT
1902025 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:1901960 original size:33 final size:33
Alignment explanation
Indices: 1901918--1902032 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1901908 CAAAATCGCA
1901918 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1901951 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1901984 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1902017 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1902033 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:1903960 original size:185 final size:186
Alignment explanation
Indices: 1903731--1904110 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
1903721 TAGATTGCTT
1903731 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1903796 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1903861 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1903916 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1903981 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1904046 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1904102 AGTAAATTT
1 AGTAAATTT
1904111 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1904045 original size:93 final size:93
Alignment explanation
Indices: 1903731--1904110 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
1903721 TAGATTGCTT
1903731 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1903796 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1903824 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1903888 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1903916 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1903981 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1904009 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1904074 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1904102 AGTAAATTT
1 AGTAAATTT
1904111 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1904194 original size:19 final size:19
Alignment explanation
Indices: 1904154--1904282 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1904144 TAGTTTACTT
* *
1904154 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1904174 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1904193 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1904212 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1904226 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1904245 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1904259 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1904278 TCGCA
1 TCGCA
1904283 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1904233 original size:33 final size:32
Alignment explanation
Indices: 1904190--1904282 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1904180 CGCGAAACCA
**
1904190 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1904222 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1904255 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1904283 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1904280 original size:52 final size:52
Alignment explanation
Indices: 1904154--1904282 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1904144 TAGTTTACTT
**
1904154 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1904206 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1904259 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1904283 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1904300 original size:19 final size:18
Alignment explanation
Indices: 1904278--1904396 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
1904268 GAAACCAAAA
*
1904278 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
1904297 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
1904313 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
1904330 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
1904346 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
1904363 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
1904382 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1904397 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:1904319 original size:14 final size:14
Alignment explanation
Indices: 1904300--1904356 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1904290 TTTCATTTCG
1904300 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
1904314 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
1904331 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
1904347 CGTTGCGATT
1 CGTTGCGATT
1904357 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1904325 original size:33 final size:33
Alignment explanation
Indices: 1904283--1904375 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1904273 CAAAATCGCA
*
1904283 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
1904316 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1904349 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1904376 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1904404 original size:20 final size:19
Alignment explanation
Indices: 1904278--1904412 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
1904268 GAAACCAAAA
*
1904278 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1904297 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
1904313 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
1904330 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
1904346 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
1904363 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
1904382 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
1904402 TCGTGTTGCGA
1 TCGCGTTGCGA
1904413 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:1906270 original size:38 final size:38
Alignment explanation
Indices: 1906227--1906299 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1906217 AATTGATTGT
*
1906227 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1906265 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1906300 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:1906286 original size:19 final size:19
Alignment explanation
Indices: 1906222--1906286 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1906212 AGTTTAATTG
*
1906222 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1906241 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1906259 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1906279 ATTGATTT
1 ATTGATTT
1906287 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:1906300 original size:14 final size:14
Alignment explanation
Indices: 1906281--1906316 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1906271 ATTGTTTAAT
1906281 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1906295 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1906309 TGATTTGT
1 TGATTTGT
1906317 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:1906439 original size:19 final size:19
Alignment explanation
Indices: 1906423--1906524 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1906413 AAAAATGACT
1906423 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1906442 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1906461 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1906475 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1906494 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1906514 ATCGCAATGCG
1 ATCGCAATGCG
1906525 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:1906577 original size:19 final size:19
Alignment explanation
Indices: 1906553--1906878 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
1906543 GATTATCTCG
1906553 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906591 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1906605 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906624 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1906643 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1906662 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906681 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1906700 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1906714 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906733 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1906752 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1906766 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1906785 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1906804 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1906818 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1906838 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1906852 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1906871 TTGCGATT
1 TTGCGATT
1906879 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:1906593 original size:52 final size:52
Alignment explanation
Indices: 1906531--1906850 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1906521 TGCGTTTATA
*
1906531 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1906583 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1906635 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1906692 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1906744 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1906796 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1906849 AT
1 AT
1906851 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:1906628 original size:71 final size:72
Alignment explanation
Indices: 1906553--1906878 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
1906543 GATTATCTCG
1906553 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1906617 TTTCGCA
66 TTTCGCA
* *
1906624 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
1906689 TTCATTTCGCA
62 TTCATTTCGCA
*
1906700 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
1906758 TTC-TCTCG--
62 TTCATTTCGCA
*
1906766 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1906830 TTTCCGCA
66 TTT-CGCA
* *
1906838 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1906879 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:1906796 original size:161 final size:157
Alignment explanation
Indices: 1906531--1906850 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1906521 TGCGTTTATA
1906531 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1906596 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1906661 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1906692 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1906757 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1906822 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1906849 AT
1 AT
1906851 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:1906822 original size:33 final size:33
Alignment explanation
Indices: 1906572--1906878 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
1906562 TCATTTCGCA
*
1906572 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1906605 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1906641 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1906679 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1906714 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1906750 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1906785 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1906818 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1906852 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1906879 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:1909202 original size:12 final size:12
Alignment explanation
Indices: 1909185--1909209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1909175 TCTTCGGGGA
1909185 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1909197 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1909209 C
1 C
1909210 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:1909418 original size:24 final size:24
Alignment explanation
Indices: 1909384--1909430 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1909374 CTGAAACATC
1909384 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1909408 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1909431 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1910132 original size:20 final size:20
Alignment explanation
Indices: 1910104--1910472 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1910094 AAATTTCAGT
* * * *
1910104 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1910124 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1910144 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1910164 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1910184 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1910204 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1910224 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1910244 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1910264 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1910284 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1910304 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1910324 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1910344 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1910364 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1910384 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1910404 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1910424 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1910444 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1910464 GTTGCGATT
1 GTTGCGATT
1910473 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
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:1913904 original size:44 final size:44
Alignment explanation
Indices: 1913841--1913930 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1913831 TCTGCCGTTA
1913841 ACATATAAATATATATCTAAGACTACGTAGAGATTTAAAGATTT
1 ACATATAAATATATATCTAAGACTACGTAGAGATTTAAAGATTT
1913885 ACATATAAATATATATCTAAGACTACGTAGAGATTTAAAGATTT
1 ACATATAAATATATATCTAAGACTACGTAGAGATTTAAAGATTT
1913929 AC
1 AC
1913931 TTTCATTTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (44 bp):
ACATATAAATATATATCTAAGACTACGTAGAGATTTAAAGATTT
Found at i:1929154 original size:114 final size:115
Alignment explanation
Indices: 1928954--1929186 Score: 450
Period size: 114 Copynumber: 2.0 Consensus size: 115
1928944 TGAAAAAAGA
1928954 TAGTCTACTAGCCCAAACTCCATAGTTCCAGACATAAGGAAAAAGACACTAGATGCATTTGAAAT
1 TAGTCTACTAGCCCAAACTCCATAGTTCCAGACATAAGGAAAAAGACACTAGATGCATTTGAAAT
1929019 CATTTAGCAACATAAGGGCTTTATTTATCTACAAATTAAAGATCATATT-
66 CATTTAGCAACATAAGGGCTTTATTTATCTACAAATTAAAGATCATATTC
1929068 TAGTCTACTAGCCCAAACTCCATAGTTCCAGACATAAGGAAAAAGACACTAGATGCATTTGAAAT
1 TAGTCTACTAGCCCAAACTCCATAGTTCCAGACATAAGGAAAAAGACACTAGATGCATTTGAAAT
*
1929133 CATTTAGCAACATGAGGGCTTTATTTATCTACAAATTAAAGATCATATTC
66 CATTTAGCAACATAAGGGCTTTATTTATCTACAAATTAAAGATCATATTC
1929183 TAGT
1 TAGT
1929187 AAAAACAAAA
Statistics
Matches: 117, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
114 113 0.97
115 4 0.03
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (115 bp):
TAGTCTACTAGCCCAAACTCCATAGTTCCAGACATAAGGAAAAAGACACTAGATGCATTTGAAAT
CATTTAGCAACATAAGGGCTTTATTTATCTACAAATTAAAGATCATATTC
Found at i:1931838 original size:2 final size:2
Alignment explanation
Indices: 1931831--1931878 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1931821 CGTAGGATGA
1931831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1931873 AT AT AT
1 AT AT AT
1931879 CATAAATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1932119 original size:4 final size:4
Alignment explanation
Indices: 1932112--1932137 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1932102 TATATATATA
1932112 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
1932138 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1938067 original size:16 final size:18
Alignment explanation
Indices: 1938035--1938068 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1938025 TATTAATGTA
1938035 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1938053 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1938069 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1938740 original size:130 final size:130
Alignment explanation
Indices: 1938537--1938784 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
1938527 AATTTTCTTC
*
1938537 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
* * *
1938602 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTATGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
1938667 TAATTAGGTGGTGACATGTGTTACCAATGACATGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
1938732 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1938785 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1939231 original size:35 final size:35
Alignment explanation
Indices: 1939184--1939252 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
1939174 TGAATTTAAT
* *
1939184 TGAATTATTTTGGAATTTAGGGTTTAGAATGAAAA
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAA
*
1939219 TGAATTACTTTGGAAATTGGGGTTTAGAATGAAA
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAA
1939253 TTGAGGACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAA
Found at i:1939818 original size:17 final size:18
Alignment explanation
Indices: 1939777--1939818 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1939767 TTTCTATTTT
*
1939777 TATTGAATAAAAATATTA
1 TATTTAATAAAAATATTA
*
1939795 TAATTTAATAAATATATTA
1 T-ATTTAATAAAAATATTA
1939814 T-TTTA
1 TATTTA
1939819 GGTTGGGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 1 0.05
19 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTAATAAAAATATTA
Found at i:1944912 original size:2 final size:2
Alignment explanation
Indices: 1944899--1944957 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1944889 AAAAATATGA
*
1944899 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1944941 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1944958 GTTATAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1945072 original size:25 final size:25
Alignment explanation
Indices: 1945044--1945092 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1945034 ATTCAAAAAT
*
1945044 TAAACTCAAATCGACTCGAATTTTA
1 TAAACTCAAATCAACTCGAATTTTA
* *
1945069 TAAACTCGACTCAACTCGAATTTT
1 TAAACTCAAATCAACTCGAATTTT
1945093 TTTGACTCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAACTCAAATCAACTCGAATTTTA
Found at i:1949980 original size:21 final size:21
Alignment explanation
Indices: 1949947--1949988 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1949937 AGTAATACAA
1949947 AAAAATGAGAAGTGAAGAAAGC
1 AAAAATGAGAAGTGAA-AAAGC
*
1949969 AAAAGTGA-AAGTGAAAAAGC
1 AAAAATGAGAAGTGAAAAAGC
1949989 CGTTAGGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 7 0.37
22 7 0.37
ACGTcount: A:0.60, C:0.05, G:0.26, T:0.10
Consensus pattern (21 bp):
AAAAATGAGAAGTGAAAAAGC
Found at i:1952323 original size:21 final size:21
Alignment explanation
Indices: 1952284--1952322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1952274 TACTAAGTTC
1952284 GTATATAAATAAATTTTTTGA
1 GTATATAAATAAATTTTTTGA
*
1952305 GTATAT-AATGAATTTTTT
1 GTATATAAATAAATTTTTT
1952323 TACATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (21 bp):
GTATATAAATAAATTTTTTGA
Found at i:1953094 original size:21 final size:21
Alignment explanation
Indices: 1953055--1953117 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1953045 TACATTCTAC
**
1953055 AACCATTTTAGATATCACCGT
1 AACCATTTTAGATGCCACCGT
**
1953076 AACCATTTTAGATGCCACCAC
1 AACCATTTTAGATGCCACCGT
1953097 AACCGA-TTTAGATGCCACCGT
1 AACC-ATTTTAGATGCCACCGT
1953118 CGTAGGGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 34 0.97
22 1 0.03
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
AACCATTTTAGATGCCACCGT
Found at i:1953655 original size:13 final size:13
Alignment explanation
Indices: 1953637--1953661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1953627 AATTGTATCA
1953637 TTTGTATTTAATG
1 TTTGTATTTAATG
1953650 TTTGTATTTAAT
1 TTTGTATTTAAT
1953662 TATTTTTATT
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:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (13 bp):
TTTGTATTTAATG
Found at i:1953671 original size:27 final size:27
Alignment explanation
Indices: 1953581--1953671 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
1953571 AATTATAGAC
* *
1953581 TTTTTATTT-AT-TTTGTTTGTTAATGTT
1 TTTTTATTTAATGTTTGTAT-TTAAT-TA
* *
1953608 TTTATTATTTAATTGTTTGAATTGT-ATCA
1 TTT-TTATTTAA-TGTTTGTATT-TAATTA
*
1953637 TTTGTATTTAATGTTTGTATTTAATTA
1 TTTTTATTTAATGTTTGTATTTAATTA
1953664 TTTTTATT
1 TTTTTATT
1953672 ATTTATTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
26 1 0.02
27 22 0.44
28 13 0.26
29 4 0.08
30 4 0.08
31 6 0.12
ACGTcount: A:0.22, C:0.01, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTTTATTTAATGTTTGTATTTAATTA
Found at i:1955070 original size:38 final size:38
Alignment explanation
Indices: 1955019--1955093 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
1955009 GAAATGAAAA
1955019 GAGAAAAGGTTCCAGTTTCCAGAGTTATCTTCTTCTCC
1 GAGAAAAGGTTCCAGTTTCCAGAGTTATCTTCTTCTCC
* *
1955057 GAGAAAATGTTCCAGTTTCCAGAGTTCTCTTCTTCTC
1 GAGAAAAGGTTCCAGTTTCCAGAGTTATCTTCTTCTC
1955094 ATTCCTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (38 bp):
GAGAAAAGGTTCCAGTTTCCAGAGTTATCTTCTTCTCC
Found at i:1961526 original size:16 final size:16
Alignment explanation
Indices: 1961505--1961541 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1961495 AATGATCAGC
*
1961505 TTCTCAAGAGTTATGT
1 TTCTCAAGAGTGATGT
1961521 TTCTCAAGAGTGATGT
1 TTCTCAAGAGTGATGT
1961537 TTCTC
1 TTCTC
1961542 TTGAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (16 bp):
TTCTCAAGAGTGATGT
Found at i:1977998 original size:2 final size:2
Alignment explanation
Indices: 1977991--1978032 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1977981 AAGTTATTTG
1977991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1978033 TATGATAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1978128 original size:22 final size:21
Alignment explanation
Indices: 1978082--1978128 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
1978072 ATCACAAATT
**
1978082 ATAAAACCTAAAAAAATTACC
1 ATAAAACCTAAAAAAATTAAA
1978103 ATAAAATCCTAAAATAAA-TAAA
1 ATAAAA-CCTAAAA-AAATTAAA
1978125 ATAA
1 ATAA
1978129 TCTTCATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 13 0.59
23 3 0.14
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (21 bp):
ATAAAACCTAAAAAAATTAAA
Found at i:1980389 original size:26 final size:24
Alignment explanation
Indices: 1980347--1980417 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1980337 TTTTTAACAT
* *
1980347 CATTA-TCGTTTTCATTTTATTCTA
1 CATTATTCTTTTTTATTTTATT-TA
*
1980371 CTATATATT-TTTTTTATTTTATTTT
1 C-AT-TATTCTTTTTTATTTTATTTA
1980396 CATTATTCCTTTTTTATTTTAT
1 CATTATT-CTTTTTTATTTTAT
1980418 ATGTACATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 4 0.10
24 3 0.08
25 17 0.44
26 14 0.36
27 1 0.03
ACGTcount: A:0.20, C:0.11, G:0.01, T:0.68
Consensus pattern (24 bp):
CATTATTCTTTTTTATTTTATTTA
Found at i:1980428 original size:26 final size:25
Alignment explanation
Indices: 1980355--1980417 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
1980345 ATCATTATCG
*
1980355 TTTTCATTTTATTCTACTATATATT--T
1 TTTTTATTTTATT-TAC-AT-TATTCCT
*
1980381 TTTTTATTTTATTTTCATTATTCCT
1 TTTTTATTTTATTTACATTATTCCT
1980406 TTTTTATTTTAT
1 TTTTTATTTTAT
1980418 ATGTACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 2 0.06
25 15 0.45
26 12 0.36
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTTATTTTATTTACATTATTCCT
Found at i:1980537 original size:27 final size:27
Alignment explanation
Indices: 1980466--1980546 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
1980456 TTTTAGTTTT
*
1980466 TTTATTTATTTATTACTATTATATATATC
1 TTTA-TTA-TTATTACCATTATATATATC
* * * *
1980495 TTT-TTATTTTTCCCATTGTTTATATC
1 TTTATTATTATTACCATTATATATATC
*
1980521 TTTATTATTATTACCATCATATATAT
1 TTTATTATTATTACCATTATATATAT
1980547 TATTTATTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 18 0.44
27 20 0.49
29 3 0.07
ACGTcount: A:0.27, C:0.11, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTATTATTATTACCATTATATATATC
Found at i:1985050 original size:14 final size:13
Alignment explanation
Indices: 1985031--1985085 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
1985021 ATTCAATCAG
1985031 AACAAAAAGAAAAA
1 AACAAAAA-AAAAA
*
1985045 AACAAAAAAAAGA
1 AACAAAAAAAAAA
*
1985058 AGCAAAAAAAAGAA
1 AACAAAAAAAA-AA
1985072 AACAAAAGAAAAAA
1 AACAAAA-AAAAAA
1985086 GAAAGAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 14 0.40
14 17 0.49
15 4 0.11
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (13 bp):
AACAAAAAAAAAA
Found at i:1985063 original size:13 final size:12
Alignment explanation
Indices: 1985029--1985098 Score: 65
Period size: 13 Copynumber: 5.8 Consensus size: 12
1985019 AGATTCAATC
1985029 AGAACAAAAAGAAA
1 AGAAC-AAAA-AAA
*
1985043 AAAACAAAAAAA
1 AGAACAAAAAAA
1985055 AGAAGCAAAAAAA
1 AGAA-CAAAAAAA
*
1985068 AG-A-AAACAAA
1 AGAACAAAAAAA
*
1985078 AGAA-AAAAGAA
1 AGAACAAAAAAA
1985089 AGAACAAAAA
1 AGAACAAAAA
1985099 TCGAAAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
10 8 0.17
11 10 0.21
12 11 0.23
13 14 0.30
14 4 0.09
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (12 bp):
AGAACAAAAAAA
Found at i:1985064 original size:10 final size:9
Alignment explanation
Indices: 1985029--1985085 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
1985019 AGATTCAATC
*
1985029 AGAACAAAA
1 AGAAAAAAA
1985038 AGAAAAAAA
1 AGAAAAAAA
*
1985047 CAAAAAAAAGA
1 -AGAAAAAA-A
1985058 AGCAAAAAAA
1 AG-AAAAAAA
1985068 AGAAAACAAA
1 AGAAAA-AAA
1985078 AGAAAAAA
1 AGAAAAAA
1985086 GAAAGAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 14 0.34
10 20 0.49
11 7 0.17
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:1985073 original size:27 final size:27
Alignment explanation
Indices: 1985029--1985083 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1985019 AGATTCAATC
1985029 AGAACAAAAAGAAAAAAACAAAA-AAA
1 AGAACAAAAAGAAAAAAACAAAAGAAA
1985055 AGAAGCAAAAA-AAAGAAAACAAAAGAAA
1 AGAA-CAAAAAGAAA-AAAACAAAAGAAA
1985083 A
1 A
1985084 AAGAAAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
27 15 0.58
28 4 0.15
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (27 bp):
AGAACAAAAAGAAAAAAACAAAAGAAA
Found at i:1985085 original size:21 final size:21
Alignment explanation
Indices: 1985040--1985098 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1985030 GAACAAAAAG
*
1985040 AAAAAAACAAAAAAAAGAAGCA
1 AAAAAAAGAAAAAAAAGAA-CA
1985062 AAAAAAAGAAAACAAAAGAA-A
1 AAAAAAAGAAAA-AAAAGAACA
* *
1985083 AAAGAAAGAACAAAAA
1 AAAAAAAGAAAAAAAA
1985099 TCGAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 11 0.33
22 11 0.33
23 7 0.21
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAGAACA
Found at i:1985098 original size:30 final size:29
Alignment explanation
Indices: 1985029--1985098 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
1985019 AGATTCAATC
1985029 AGAACAAAAAGAAAAAAACAAAAAAAAGA
1 AGAACAAAAAGAAAAAAACAAAAAAAAGA
* *
1985058 AGCAAAAAAAAGAAAACAAA-AGAAAAAAGAA
1 AG-AACAAAAAGAAAA-AAACAAAAAAAAG-A
1985089 AGAACAAAAA
1 AGAACAAAAA
1985099 TCGAAAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 27 0.77
31 6 0.17
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (29 bp):
AGAACAAAAAGAAAAAAACAAAAAAAAGA
Found at i:1985768 original size:22 final size:22
Alignment explanation
Indices: 1985740--1985795 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1985730 AGCTACCCCA
1985740 TCAAACCTTTGAACATCAAATG
1 TCAAACCTTTGAACATCAAATG
1985762 TCAAACCTTTGAACATCAAATG
1 TCAAACCTTTGAACATCAAATG
*
1985784 CCAAACCTTTGA
1 TCAAACCTTTGA
1985796 CCAAACACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (22 bp):
TCAAACCTTTGAACATCAAATG
Found at i:1987234 original size:65 final size:65
Alignment explanation
Indices: 1987013--1987430 Score: 648
Period size: 65 Copynumber: 6.5 Consensus size: 65
1987003 GTGCCACTCA
1987013 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
*
1987077 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCTCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
*
1987141 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTGTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * *
1987206 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCGACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
1987271 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCACTGGTTGTCAACAAAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* * * * *
1987336 AGACATCACAAGTTCAACTTCACAACGAATGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAAA-TTTCCCAGTT
1987401 TC
64 TC
* * *
1987403 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAACACAAGTTCAACTTCACAACGAAGG
1987431 ATATTGGACT
Statistics
Matches: 329, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
64 131 0.40
65 182 0.55
66 5 0.02
67 11 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
Found at i:1987554 original size:105 final size:107
Alignment explanation
Indices: 1987344--1987558 Score: 308
Period size: 105 Copynumber: 2.0 Consensus size: 107
1987334 TAAGACATCA
*
1987344 CAAGTTCAACTTCACAACGAATGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATTTCAGAGCC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATTTCAGAGCC
*
1987409 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
* * ** * * * *
1987451 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAA-TAAACGCTT-TCCAGTTTGAGAGTC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATTTCAGAGCC
* *
1987514 AGTTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACG
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
1987556 CAA
1 CAA
1987559 CTTGCATTGG
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 53 0.55
106 6 0.06
107 37 0.39
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (107 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAAAACTTCCCCAATTTCAGAGCC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACG
Found at i:1989331 original size:27 final size:27
Alignment explanation
Indices: 1989260--1989340 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
1989250 TTTTTAGTTT
*
1989260 TTTATTTATTTATTACTATTATATATATC
1 TTTA-TTA-TTATTACCATTATATATATC
* * * *
1989289 TTT-TTATTTTTCCCATTGTTTATATC
1 TTTATTATTATTACCATTATATATATC
*
1989315 TTTATTATTATTACCATCATATATAT
1 TTTATTATTATTACCATTATATATAT
1989341 TATATTTTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 18 0.44
27 20 0.49
29 3 0.07
ACGTcount: A:0.27, C:0.11, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTATTATTATTACCATTATATATATC
Found at i:1992090 original size:13 final size:13
Alignment explanation
Indices: 1992072--1992096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1992062 ACTTGACCAG
1992072 TAAACAATTTTTA
1 TAAACAATTTTTA
1992085 TAAACAATTTTT
1 TAAACAATTTTT
1992097 TTTGAGCAAG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAACAATTTTTA
Found at i:2011106 original size:49 final size:49
Alignment explanation
Indices: 2011014--2011112 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
2011004 TATCAAAAAC
* * * *
2011014 ATCAAATATCTTCAACTCTTTAGAGGAATCCTTAGACAGCAAATTTCTG
1 ATCAAATATCTCCAACTATTTAGAGGAATCCTCAGACAACAAATTTCTG
**
2011063 ATCAAATATCTCCAACTATTTAGAGGAAT-CTCCAGGTAACAAATTTCTG
1 ATCAAATATCTCCAACTATTTAGAGGAATCCT-CAGACAACAAATTTCTG
2011112 A
1 A
2011113 AATTCCGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 2 0.05
49 41 0.95
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (49 bp):
ATCAAATATCTCCAACTATTTAGAGGAATCCTCAGACAACAAATTTCTG
Found at i:2015960 original size:80 final size:80
Alignment explanation
Indices: 2015841--2015999 Score: 257
Period size: 80 Copynumber: 2.0 Consensus size: 80
2015831 TGGGCCCAAA
2015841 ACCAAGAGGATTTAAACGGAGAAAAAAAAAGCCATTCTAAATGT-TATAGGACAATGCTTATAAG
1 ACCAAGAGGATTTAAACGGAGAAAAAAAAAGCCATTCTAAATGTGT-TAGGACAATGCTTATAAG
2015905 GCAACAATGCCACAAT
65 GCAACAATGCCACAAT
* * **
2015921 ACCAAGAGGATTTAAATGGAGAAAAAAGAAGCCATTCTAAATGTGTTAGGACAATGCTTATGGGG
1 ACCAAGAGGATTTAAACGGAGAAAAAAAAAGCCATTCTAAATGTGTTAGGACAATGCTTATAAGG
*
2015986 GAACAATGCCACAA
66 CAACAATGCCACAA
2016000 CAGAACTGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
80 72 0.99
81 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (80 bp):
ACCAAGAGGATTTAAACGGAGAAAAAAAAAGCCATTCTAAATGTGTTAGGACAATGCTTATAAGG
CAACAATGCCACAAT
Found at i:2016437 original size:6 final size:6
Alignment explanation
Indices: 2016426--2016457 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
2016416 CCCAGTCAGA
2016426 GCCTTT GCCTTT GCCTTT GCCTTT GCCCTTT G
1 GCCTTT GCCTTT GCCTTT GCCTTT G-CCTTT G
2016458 ATGAGGAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.00, C:0.34, G:0.19, T:0.47
Consensus pattern (6 bp):
GCCTTT
Found at i:2040949 original size:22 final size:22
Alignment explanation
Indices: 2040919--2040960 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2040909 AAGAACTATC
2040919 ATCTTTCATG-AATAACAAGAT
1 ATCTTTCATGTAATAACAAGAT
*
2040940 ATCTCTTCATGTCATAACAAG
1 ATCT-TTCATGTAATAACAAG
2040961 TTCACCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 6 0.33
23 8 0.44
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCTTTCATGTAATAACAAGAT
Found at i:2060508 original size:2 final size:2
Alignment explanation
Indices: 2060501--2060554 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2060491 CACGAGACCA
*
2060501 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2060543 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2060555 CATCACTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.