Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_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: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:1075807 original size:10 final size:10
Alignment explanation
Indices: 1075775--1075806 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1075765 TTCAACTTTC
1075775 TTTCTTTCTT
1 TTTCTTTCTT
1075785 TTTCTTTCTT
1 TTTCTTTCTT
1075795 TTTC-TTCTT
1 TTTCTTTCTT
1075804 TTT
1 TTT
1075807 TAGTGCTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:1082953 original size:28 final size:28
Alignment explanation
Indices: 1082918--1082986 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
1082908 AAGTAGGCTG
**
1082918 CCATGTGCATCATTCAAGCATGTGTACT
1 CCATGTGCATCATTCAAGCATGTAAACT
1082946 CCATGTGCATCATTCAAGCATGTAAACT
1 CCATGTGCATCATTCAAGCATGTAAACT
1082974 CCATGTGACATCA
1 CCATGTG-CATCA
1082987 AATAGGCACC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (28 bp):
CCATGTGCATCATTCAAGCATGTAAACT
Found at i:1085084 original size:19 final size:20
Alignment explanation
Indices: 1085044--1085096 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1085034 GAAACCCCTT
1085044 TGAAAATACATGATTTTTTTAA
1 TGAAAATACATGA--TTTTTAA
1085066 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
* *
1085085 TGCATATACATG
1 TGAAAATACATG
1085097 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1085814 original size:33 final size:33
Alignment explanation
Indices: 1085772--1085840 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1085762 GTTGATGAAT
*
1085772 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1085805 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1085838 GAA
1 GAA
1085841 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1091489 original size:33 final size:33
Alignment explanation
Indices: 1091447--1091515 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1091437 GTTGATGAAT
*
1091447 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1091480 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1091513 GAA
1 GAA
1091516 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1093339 original size:30 final size:31
Alignment explanation
Indices: 1093298--1093357 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1093288 ACATGCTGCC
**
1093298 ATGATATCTAAATGATATACAAACATAATAA
1 ATGATATCTAAAACATATACAAACATAATAA
**
1093329 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATACAAACATAATA
1093358 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATACAAACATAATAA
Found at i:1100721 original size:20 final size:21
Alignment explanation
Indices: 1100696--1100745 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1100686 TGATTTAAGT
1100696 AAATGGATAATT-AAGAAAGG
1 AAATGGATAATTAAAGAAAGG
*
1100716 AAATGGA-AATTGAAAGAAATG
1 AAATGGATAATT-AAAGAAAGG
1100737 AAATGGATA
1 AAATGGATA
1100746 GAAATGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 14 0.54
22 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (21 bp):
AAATGGATAATTAAAGAAAGG
Found at i:1102034 original size:8 final size:8
Alignment explanation
Indices: 1102013--1102045 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1102003 TATTATAAGC
1102013 TAAATA-A
1 TAAATATA
1102020 TATAATATA
1 TA-AATATA
1102029 TAAATATA
1 TAAATATA
1102037 TAAATATA
1 TAAATATA
1102045 T
1 T
1102046 GGTTCATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 2 0.08
8 19 0.79
9 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAAATATA
Found at i:1102045 original size:16 final size:16
Alignment explanation
Indices: 1102013--1102044 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1102003 TATTATAAGC
1102013 TAAATAATATAATATA
1 TAAATAATATAATATA
1102029 TAAAT-ATATAA-ATA
1 TAAATAATATAATATA
1102043 TA
1 TA
1102045 TGGTTCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATAATATAATATA
Found at i:1106304 original size:159 final size:159
Alignment explanation
Indices: 1106013--1106344 Score: 538
Period size: 159 Copynumber: 2.1 Consensus size: 159
1106003 AATGAGAGGG
* * * *
1106013 CTTGGCCGAATGGTTACATGATGTTTCGGCTAGAGACATGTCACTAGGATGATATATAATGCTTC
1 CTTGGCCGAATGGTAACATGATGTTTCAGCTAGAGACATGTCACTAGGAAGATACATAATGCTTC
* * * *
1106078 AAAATAAAAGAACATGTCTATAGGCTTGGTGTTGGTTAGGCTAACCCTTCATAAAGGGACTTGAT
66 AAAATAAAAGAACATGTCTACAGGCTTGGTATTGGTTAGGCTAACCCTTAATAAAGGGACTTAAT
* *
1106143 GATTCGGCTAAGGATGGGAAGGCATCTCC
131 GATTCGACTAAGGATGGGAAAGCATCTCC
* *
1106172 CTTGGCCGAATGGTAACATGATGTTTCAGCTAGATACATGTCTCTAGGAAGATACATAATGCTTC
1 CTTGGCCGAATGGTAACATGATGTTTCAGCTAGAGACATGTCACTAGGAAGATACATAATGCTTC
* *
1106237 AAAATAAAAGAACATGTCTACAGGCTTGGTATTGGTTCGGCTAACCCTTAATAAATGGACTTAAT
66 AAAATAAAAGAACATGTCTACAGGCTTGGTATTGGTTAGGCTAACCCTTAATAAAGGGACTTAAT
1106302 GATTCGACTAAGGATGGGAAAGCATCTCC
131 GATTCGACTAAGGATGGGAAAGCATCTCC
1106331 CTTGGCCGAATGGT
1 CTTGGCCGAATGGT
1106345 GATGCTTGTT
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (159 bp):
CTTGGCCGAATGGTAACATGATGTTTCAGCTAGAGACATGTCACTAGGAAGATACATAATGCTTC
AAAATAAAAGAACATGTCTACAGGCTTGGTATTGGTTAGGCTAACCCTTAATAAAGGGACTTAAT
GATTCGACTAAGGATGGGAAAGCATCTCC
Found at i:1108274 original size:34 final size:34
Alignment explanation
Indices: 1108229--1108405 Score: 158
Period size: 34 Copynumber: 4.9 Consensus size: 34
1108219 CCATAGCTGA
*
1108229 AATGCACATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
1108263 AATGCATATGGGTGCATTATCAGCTTAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
1108297 AATACATATGGGTGCATTAT-TGCATGAAAGGGTGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA---AG--A-A--T
1108339 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
** * *
1108375 AATATATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
1108406 GATGCCATAT
Statistics
Matches: 117, Mismatches: 14, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
33 3 0.03
34 80 0.68
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.02
40 1 0.01
41 1 0.01
42 1 0.01
44 22 0.19
45 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:1108439 original size:79 final size:79
Alignment explanation
Indices: 1108263--1108765 Score: 359
Period size: 79 Copynumber: 6.4 Consensus size: 79
1108253 ATAAAAGAAT
* *
1108263 AATGCATATGGGTGCATTATCAGCTTAAAAGAATAATACATATGGGTGCATTATT-GCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAG
* *
1108327 GGTGCCATAGCTGA
66 GATGCCATAGATGA
*
1108341 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATATATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAG
*
1108406 GATGCCATATATGA
66 GATGCCATAGATGA
* * ** * * ** *
1108420 AATGCATATGGGTGCATTAT--TCTTTTATGTCGATAATGCACCCATATGCATTTCAGTTA-TGG
1 AATGCATATGGGTGCATTATCGGCATAAAAG--AATAAT--A--CATATG-GGTGCA-TTATTGG
******
1108482 CATCCTTTCATGCCAATA-ATG-
58 CATGAAAGGATGCC-ATAGATGA
* ** * * ** * * **
1108503 CACCCAT-T---TGCATTAT--TCTTTTATGTCGATAATGTATATGGGTGCATTATTGGCATGAA
1 AATGCATATGGGTGCATTATCGGCATAAAAG--AATAATACATATGGGTGCATTATTGGCATGAA
* *
1108562 AAGATGCCATAGCTGA
64 AGGATGCCATAGATGA
* * * * * * *
1108578 AATGCATATGGATGCATTATTGACAAAAAAGAATAATGCATATGGGTGCATTACTAGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAG
1108643 GATGCCATAGATGA
66 GATGCCATAGATGA
* ** *
1108657 AATGCATATGGGTGCATTGTCGGCATAAAAGAATAATGTATAAT--GTGCATTATTCGCATGAAA
1 AATGCATATGGGTGCATTATCGGCATAAAAGAATAATACAT-ATGGGTGCATTATTGGCATGAAA
* *
1108720 GGATGCCATGGCTGA
65 GGATGCCATAGATGA
* *
1108735 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
1108766 GATACCATAA
Statistics
Matches: 340, Mismatches: 65, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
73 6 0.02
74 16 0.05
75 9 0.03
76 1 0.00
77 4 0.01
78 110 0.32
79 155 0.46
80 2 0.01
81 4 0.01
82 1 0.00
83 9 0.03
84 17 0.05
85 6 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAG
GATGCCATAGATGA
Found at i:1108470 original size:34 final size:34
Alignment explanation
Indices: 1108432--1108536 Score: 84
Period size: 45 Copynumber: 2.8 Consensus size: 34
1108422 TGCATATGGG
1108432 TGCATTATTCTTTTATGTCGATAATGCACCCATA
1 TGCATTATTCTTTTATGTCGATAATGCACCCATA
* * *
1108466 TGCATTTCAGTTATGGCATCCTTTCATGCCAATAATGCACCCATT
1 TGCA-TT-A--T-T--C-T--TTT-ATGTCGATAATGCACCCATA
1108511 TGCATTATTCTTTTATGTCGATAATG
1 TGCATTATTCTTTTATGTCGATAATG
1108537 TATATGGGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
34 14 0.25
35 5 0.09
36 1 0.02
37 1 0.02
38 2 0.04
39 1 0.02
40 1 0.02
41 2 0.04
42 1 0.02
43 1 0.02
44 5 0.09
45 21 0.38
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (34 bp):
TGCATTATTCTTTTATGTCGATAATGCACCCATA
Found at i:1108663 original size:45 final size:45
Alignment explanation
Indices: 1108612--1108786 Score: 158
Period size: 45 Copynumber: 4.2 Consensus size: 45
1108602 AAAAAAGAAT
* *
1108612 AATGCATATGGGTGCATTACTAGCATGAAAGGATGCCATAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
* * *
1108657 AATGCATATGGGTGCATTGTCGGCAT-AAA--A-G-AATA-ATG-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
* * * *
1108695 TAT--A-AT--GTGCATTATTCGCATGAAAGGATGCCATGGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
* * *
1108735 AATGCATATGGGTGCATTATTGGCATGAAAGGATACCATAAATAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
1108780 AATGCAT
1 AATGCAT
1108787 GAAAGGATGG
Statistics
Matches: 99, Mismatches: 19, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
33 12 0.12
34 3 0.03
35 2 0.02
36 2 0.02
37 1 0.01
38 4 0.04
39 5 0.05
40 5 0.05
41 1 0.01
42 2 0.02
43 2 0.02
44 3 0.03
45 57 0.58
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGATGA
Found at i:1108808 original size:20 final size:20
Alignment explanation
Indices: 1108783--1108993 Score: 145
Period size: 20 Copynumber: 9.7 Consensus size: 20
1108773 TAAATAAAAT
* *
1108783 GCATGAAAGGATGGATTCAG
1 GCATGAAAGGATGCATTAAG
1108803 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1108823 GCATGAAAGCATGACATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
1108849 GCATGAAATGATGCATTCAG
1 GCATGAAAGGATGCATTAAG
*
1108869 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
1108895 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1108915 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1108935 GCATG-AACGATGCCATAAATAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1108960 GCATGAAAGGATGCAATAAG
1 GCATGAAAGGATGCATTAAG
*
1108980 GAATGAAAGGATGC
1 GCATGAAAGGATGC
1108994 CATAAACAAA
Statistics
Matches: 153, Mismatches: 19, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
19 6 0.04
20 87 0.57
21 6 0.04
22 3 0.02
23 1 0.01
24 2 0.01
25 15 0.10
26 33 0.22
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1108841 original size:66 final size:67
Alignment explanation
Indices: 1108747--1108882 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 67
1108737 TGCATATGGG
* * *
1108747 TGCATTATTGGCATGAAAGGATACCATAAATAAAATGCATGAAAGGATGGATTCAGGCATGAAAG
1 TGCATTATAGGCATGAAAGCATACCATAAATAAAATGCATGAAAGGATGCATTCAGGCATGAAAG
1108812 GA
66 GA
*
1108814 TGCATTA-AGGCATGAAAGCATGA-CATAAATAAAATGCATGAAATGATGCATTCAGGCATGAAA
1 TGCATTATAGGCATGAAAGCAT-ACCATAAATAAAATGCATGAAAGGATGCATTCAGGCATGAAA
1108877 GGA
65 GGA
1108880 TGC
1 TGC
1108883 CATAAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
66 56 0.88
67 8 0.12
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (67 bp):
TGCATTATAGGCATGAAAGCATACCATAAATAAAATGCATGAAAGGATGCATTCAGGCATGAAAG
GA
Found at i:1108853 original size:46 final size:46
Alignment explanation
Indices: 1108803--1108922 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
1108793 ATGGATTCAG
1108803 GCATGAAAGGATGCATTAAGGCATGAAAGCATGACATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGCATGACATAAATAAAAT
* * * *
1108849 GCATGAAATGATGCATTCAGGCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGCATGACATAAATAAAAT
1108895 GCATGAAAGGATGCATTAAGGCATGAAA
1 GCATGAAAGGATGCATTAAGGCATGAAA
1108923 TGATGCATTA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 68 1.00
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGCATGACATAAATAAAAT
Found at i:1108854 original size:26 final size:24
Alignment explanation
Indices: 1108823--1108910 Score: 69
Period size: 26 Copynumber: 3.6 Consensus size: 24
1108813 ATGCATTAAG
1108823 GCATGAAAGCATGACATAAATAAAAT
1 GCATGAAAG-ATG-CATAAATAAAAT
* *
1108849 GCATGAAATGATGCAT---T--CAG
1 GCATGAAA-GATGCATAAATAAAAT
1108869 GCATGAAAGGATGCCATAAATAAAAT
1 GCATGAAA-GATG-CATAAATAAAAT
1108895 GCATGAAAGGATGCAT
1 GCATGAAA-GATGCAT
1108911 TAAGGCATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
20 13 0.26
21 3 0.06
22 1 0.02
24 1 0.02
25 6 0.12
26 25 0.50
27 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (24 bp):
GCATGAAAGATGCATAAATAAAAT
Found at i:1108877 original size:112 final size:111
Alignment explanation
Indices: 1108756--1109006 Score: 394
Period size: 112 Copynumber: 2.3 Consensus size: 111
1108746 GTGCATTATT
* * *
1108756 GGCATGAAAGGATACCATAAATAAAATGCATGAAAGGATGGATTCAGGCATGAAAGGATGCATTA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTA
* * *
1108821 AGGCATGAAAGCATGACATAAATAAAATGCATGAAATGATGCATTCA
66 AGGCATGAAAG-ATGACATAAATAAAATGCATGAAAGGATGCAATAA
*
1108868 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCATTA
1 GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTA
* *
1108933 AGGCATGAACGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
66 AGGCATGAAAGATGACATAAATAAAATGCATGAAAGGATGCAATAA
* *
1108979 GGAATGAAAGGATGCCATAAACAAAATG
1 GGCATGAAAGGATGCCATAAATAAAATG
1109007 AAATTTAACG
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 57 0.45
112 71 0.55
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (111 bp):
GGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCATTA
AGGCATGAAAGATGACATAAATAAAATGCATGAAAGGATGCAATAA
Found at i:1108968 original size:65 final size:66
Alignment explanation
Indices: 1108849--1108993 Score: 238
Period size: 65 Copynumber: 2.2 Consensus size: 66
1108839 TAAATAAAAT
* * *
1108849 GCATGAAATGATGCATTCAGGCATGAAAGGATGCCATAAATAAAATGCATGAAAGGATGCATTAA
1 GCATGAAATGATGCATTAAGGCATGAAACGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
1108914 G
66 G
1108915 GCATGAAATGATGCATTAAGGCATG-AACGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
1 GCATGAAATGATGCATTAAGGCATGAAACGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
1108979 G
66 G
* *
1108980 GAATGAAAGGATGC
1 GCATGAAATGATGC
1108994 CATAAACAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 50 0.68
66 24 0.32
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (66 bp):
GCATGAAATGATGCATTAAGGCATGAAACGATGCCATAAATAAAATGCATGAAAGGATGCAATAA
G
Found at i:1108973 original size:45 final size:46
Alignment explanation
Indices: 1108915--1109006 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 46
1108905 ATGCATTAAG
* * * *
1108915 GCATGAAATGATGCATTAAGGCATG-AACGATGCCATAAATAAAAT
1 GCATGAAAGGATGCAATAAGGAATGAAACGATGCCATAAACAAAAT
*
1108960 GCATGAAAGGATGCAATAAGGAATGAAAGGATGCCATAAACAAAAT
1 GCATGAAAGGATGCAATAAGGAATGAAACGATGCCATAAACAAAAT
1109006 G
1 G
1109007 AAATTTAACG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.18
Consensus pattern (46 bp):
GCATGAAAGGATGCAATAAGGAATGAAACGATGCCATAAACAAAAT
Found at i:1109514 original size:29 final size:29
Alignment explanation
Indices: 1109389--1109507 Score: 166
Period size: 29 Copynumber: 4.1 Consensus size: 29
1109379 TATGTCAGTT
* *
1109389 AGATGAACGGTGAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
*
1109418 AGATGAAAGGCCAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
* **
1109447 AGATTAAAGGTCAAACACCATTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
* *
1109476 AGATGAATGGTTAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
1109505 AGA
1 AGA
1109508 ATAATGGACT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (29 bp):
AGATGAAAGGTCAAACACTGTTGAGTAAA
Found at i:1110959 original size:10 final size:10
Alignment explanation
Indices: 1110946--1110972 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1110936 AAACAAAACA
1110946 AAAAAAAGGC
1 AAAAAAAGGC
1110956 AAAAAAAGGC
1 AAAAAAAGGC
1110966 AAAAAAA
1 AAAAAAA
1110973 AAACAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:1110979 original size:11 final size:11
Alignment explanation
Indices: 1110932--1110982 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1110922 TAATTTTTTT
1110932 CAAAAAACAAAA
1 CAAAAAA-AAAA
**
1110944 CAAAAAAAAGG
1 CAAAAAAAAAA
**
1110955 C-AAAAAAAGG
1 CAAAAAAAAAA
1110965 CAAAAAAAAAA
1 CAAAAAAAAAA
1110976 CAAAAAA
1 CAAAAAA
1110983 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 10 0.29
11 17 0.50
12 7 0.21
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:1131339 original size:23 final size:23
Alignment explanation
Indices: 1131313--1131366 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
1131303 AAAAATCATA
*
1131313 AAAGAAAGTCAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
1131336 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
1131360 -AAGAAAA
1 AAAGAAAA
1131367 AACAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 7 0.25
24 17 0.61
ACGTcount: A:0.61, C:0.17, G:0.15, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:1139111 original size:24 final size:25
Alignment explanation
Indices: 1139065--1139119 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1139055 ACAGTTATGC
*
1139065 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1139089 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1139114 CA-TTGA
1 CACTTGA
1139120 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:1144773 original size:23 final size:23
Alignment explanation
Indices: 1144745--1144798 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1144735 AAAAATCAGA
* *
1144745 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
1144768 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
1144792 -AAGAAAA
1 AAAGAAAA
1144799 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:1148707 original size:10 final size:10
Alignment explanation
Indices: 1148692--1148720 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1148682 AAATTCATCC
1148692 ATTCATGCAT
1 ATTCATGCAT
1148702 ATTCATGCAT
1 ATTCATGCAT
1148712 ATTCATGCA
1 ATTCATGCA
1148721 AGAAGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (10 bp):
ATTCATGCAT
Found at i:1157978 original size:44 final size:46
Alignment explanation
Indices: 1157858--1157983 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 46
1157848 TATAAAATCT
*
1157858 CTTACCATTT-A-TCACATAAGCTCCTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTC-CATAAGCTCATAAGCTTATTTTACCAAAATA
** * * *
1157903 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
* *
1157950 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
1157984 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
44 22 0.32
45 10 0.14
46 2 0.03
47 33 0.48
48 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:1163119 original size:16 final size:16
Alignment explanation
Indices: 1163098--1163129 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1163088 AATCGTAACC
1163098 ATTGATGATATCACTT
1 ATTGATGATATCACTT
*
1163114 ATTGATGATTTCACTT
1 ATTGATGATATCACTT
1163130 TTTCATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTGATGATATCACTT
Found at i:1168431 original size:2 final size:2
Alignment explanation
Indices: 1168424--1168471 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1168414 TGGTAGCAGA
1168424 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
1168466 AT AT AT
1 AT AT AT
1168472 GTTGGTGATA
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:1168868 original size:37 final size:37
Alignment explanation
Indices: 1168827--1168898 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1168817 ACATCAAGGA
1168827 AGCATCATTATAAACCATTTCATTAGTTCATATGCGC
1 AGCATCATTATAAACCATTTCATTAGTTCATATGCGC
* *
1168864 AGCATCATTATAAACTATTTCATTAGTTTATATGC
1 AGCATCATTATAAACCATTTCATTAGTTCATATGC
1168899 ATTCATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (37 bp):
AGCATCATTATAAACCATTTCATTAGTTCATATGCGC
Found at i:1173762 original size:20 final size:20
Alignment explanation
Indices: 1173717--1173772 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
1173707 GTTGTAGGAG
1173717 TCTTTTATTTTCTCTTTTGT
1 TCTTTTATTTTCTCTTTTGT
*
1173737 TTTTTTATTCTT-TCTTTT-T
1 TCTTTTATT-TTCTCTTTTGT
1173756 CTCTTTT-TGTTTCTCTT
1 -TCTTTTAT-TTTCTCTT
1173773 GTTGCAGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (20 bp):
TCTTTTATTTTCTCTTTTGT
Found at i:1174935 original size:18 final size:18
Alignment explanation
Indices: 1174912--1174948 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1174902 ATCATTTGAG
1174912 CATCCTCATCCTTACAAA
1 CATCCTCATCCTTACAAA
1174930 CATCCTCATCCTTACAAA
1 CATCCTCATCCTTACAAA
1174948 C
1 C
1174949 TTCAGTGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (18 bp):
CATCCTCATCCTTACAAA
Found at i:1177063 original size:11 final size:13
Alignment explanation
Indices: 1177031--1177060 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1177021 TTGCCAAAGA
1177031 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1177044 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1177056 TGAAA
1 TGAAA
1177061 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:1178338 original size:37 final size:37
Alignment explanation
Indices: 1178288--1178361 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1178278 ATACATCAAG
1178288 GCAGCACCATTATAAACCATTTCATTAGTTCATATGC
1 GCAGCACCATTATAAACCATTTCATTAGTTCATATGC
*
1178325 GCAGCATCATTATAAACCATTTCATTAGTTCATATGC
1 GCAGCACCATTATAAACCATTTCATTAGTTCATATGC
1178362 ATTCATATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (37 bp):
GCAGCACCATTATAAACCATTTCATTAGTTCATATGC
Found at i:1193396 original size:15 final size:16
Alignment explanation
Indices: 1193368--1193397 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1193358 CGATGGGAGT
1193368 CATCCCATCACTCTAC
1 CATCCCATCACTCTAC
1193384 CATCCCA-CACTCTA
1 CATCCCATCACTCTA
1193398 GGTGAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (16 bp):
CATCCCATCACTCTAC
Found at i:1195597 original size:18 final size:18
Alignment explanation
Indices: 1195574--1195609 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1195564 TGGAAGGGAG
*
1195574 AATAAAATGATAGAAAGT
1 AATAAAAAGATAGAAAGT
1195592 AATAAAAAGATAGAAAGT
1 AATAAAAAGATAGAAAGT
1195610 GAAAGGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (18 bp):
AATAAAAAGATAGAAAGT
Found at i:1211024 original size:47 final size:45
Alignment explanation
Indices: 1210954--1211079 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1210944 TATAAAATCT
*
1210954 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1210999 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** * *
1211046 CTTGGCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1211080 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1215108 original size:19 final size:20
Alignment explanation
Indices: 1215071--1215109 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1215061 TCATTTACTT
*
1215071 GCATATTATATGATTTTCAC
1 GCATAATATATGATTTTCAC
1215091 GCATAATATATG-TTTTCAC
1 GCATAATATATGATTTTCAC
1215110 ATCTTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
GCATAATATATGATTTTCAC
Found at i:1221056 original size:19 final size:20
Alignment explanation
Indices: 1221032--1221082 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1221022 CGGCCAAGAG
* *
1221032 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
1221051 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
1221071 CATGTATTTTCA
1 CATGTATTTTCA
1221083 AAGGGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:1225555 original size:19 final size:17
Alignment explanation
Indices: 1225494--1225556 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 17
1225484 TTGGAGTGCA
* **
1225494 AAAAGAAAGAAAAAGAC
1 AAAAGAAAAAAAAATTC
1225511 AAAAGAAAAAAAAATTC
1 AAAAGAAAAAAAAATTC
*
1225528 AGAAAAGAAAAAGAAATTTC
1 --AAAAGAAAAA-AAAATTC
1225548 AAAGAGAAA
1 AAA-AGAAA
1225557 GCAAACCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 14 0.37
18 3 0.08
19 15 0.39
20 6 0.16
ACGTcount: A:0.73, C:0.05, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAAGAAAAAAAAATTC
Found at i:1232670 original size:19 final size:20
Alignment explanation
Indices: 1232608--1232679 Score: 101
Period size: 21 Copynumber: 3.6 Consensus size: 20
1232598 GAAACCCCTT
*
1232608 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
1232628 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-TTTTTAA
1232649 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1232668 TGAAGATACATG
1 TGAAAATACATG
1232680 CTCTTGGCCG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 16 0.33
20 13 0.27
21 19 0.40
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1233607 original size:30 final size:31
Alignment explanation
Indices: 1233568--1233627 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1233558 ACATGCTACC
**
1233568 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
1233599 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
1233628 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:1234688 original size:24 final size:24
Alignment explanation
Indices: 1234655--1234738 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
1234645 TGTAATGAAC
*
1234655 TTGGAGCTTCAA-TGATCATAACTT
1 TTGGAACTTCAAGTGA-CATAACTT
* *
1234679 TTGGCACTTCAAGTGACATATCTT
1 TTGGAACTTCAAGTGACATAACTT
* * *
1234703 TTTGAACTTCAAGTGCCATAACTG
1 TTGGAACTTCAAGTGACATAACTT
*
1234727 TTGGAACGTCAA
1 TTGGAACTTCAA
1234739 TGGACATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
24 46 0.94
25 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (24 bp):
TTGGAACTTCAAGTGACATAACTT
Found at i:1236020 original size:19 final size:19
Alignment explanation
Indices: 1236015--1236059 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1236005 TATTTTCTTT
1236015 TCTTCTTTTCTAATTTTTC
1 TCTTCTTTTCTAATTTTTC
* *
1236034 TCTTCTTTTGT-CTTTTTC
1 TCTTCTTTTCTAATTTTTC
1236052 T-TTCTTTT
1 TCTTCTTTT
1236060 TGCACTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 10 0.42
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (19 bp):
TCTTCTTTTCTAATTTTTC
Found at i:1236055 original size:22 final size:20
Alignment explanation
Indices: 1235998--1236056 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 20
1235988 TTTTGAACTT
1235998 TTCTTTT-TATTTTCTTT-TC
1 TTCTTTTCT-TTTTCTTTCTC
**
1236017 TTCTTTTCTAATT-TTTCTC
1 TTCTTTTCTTTTTCTTTCTC
1236036 TTCTTTTGTCTTTTTCTTTCT
1 TTC-TTT-TCTTTTTCTTTCT
1236057 TTTTGCACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.10
19 14 0.45
20 4 0.13
21 5 0.16
22 5 0.16
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.75
Consensus pattern (20 bp):
TTCTTTTCTTTTTCTTTCTC
Found at i:1236753 original size:19 final size:20
Alignment explanation
Indices: 1236706--1236756 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1236696 GAAACCCCTT
*
1236706 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1236726 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
1236745 T-AAAGATACATG
1 TGAAA-ATACATG
1236757 CTCTTGGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
20 13 0.45
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1238273 original size:24 final size:24
Alignment explanation
Indices: 1238246--1238297 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1238236 GAAAAATCAT
*
1238246 AAAAGAAAGCACTCCAAAAGAAGA
1 AAAAGAAAGCACTCAAAAAGAAGA
***
1238270 AAAATCCAGCACTCAAAAAGAAGA
1 AAAAGAAAGCACTCAAAAAGAAGA
1238294 AAAA
1 AAAA
1238298 ACAAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.63, C:0.17, G:0.13, T:0.06
Consensus pattern (24 bp):
AAAAGAAAGCACTCAAAAAGAAGA
Found at i:1239327 original size:202 final size:202
Alignment explanation
Indices: 1238981--1239386 Score: 749
Period size: 202 Copynumber: 2.0 Consensus size: 202
1238971 CAGTGGCTCA
1238981 ATGATGTGGGGGAAGCCAAGATAACCAAACAAGTTATTATTCCTTTTTCAATTGGAAGATACAAT
1 ATGATGTGGGGGAAGCCAAGATAACCAAACAAGTTATTATTCCTTTTTCAATTGGAAGATACAAT
* * *
1239046 GATGAAGTCCTTTGTGATGTGGTGCCCATGAGTGCAAGCCACATTATATTAGGACGTCCTTGGTA
66 GATGAAGTCCTTTGTGACGTGGTGCCCATGAGTGCAAGCCACATTATATTAGGACGTCATTGGCA
* *
1239111 ATTTGACAAGAAGGCTACTCACGATGGATTTTCTAATAAGTATGCATTCCAACACCATGGGAGGA
131 ATTTGACAAGAAGGCTACTCACGATGGATTTTCTAATAAGTATGCATTCCAACACAAAGGGAGGA
1239176 AAATCAT
196 AAATCAT
*
1239183 ATGATGTGGGGGAAGCCAAGATAACCAAACAAGTTATTTTTCCTTTTTCAATTGGAAGATACAAT
1 ATGATGTGGGGGAAGCCAAGATAACCAAACAAGTTATTATTCCTTTTTCAATTGGAAGATACAAT
1239248 GATGAAGTCCTTTGTGACGTGGTGCCCATGAGTGCAAGCCACATTATATTAGGACGTCATTGGCA
66 GATGAAGTCCTTTGTGACGTGGTGCCCATGAGTGCAAGCCACATTATATTAGGACGTCATTGGCA
*
1239313 ATTTGACAAGAAGGCTACTCACGATGGATTTTCTAATAAGTATTCATTCCAACACAAAGGGAGGA
131 ATTTGACAAGAAGGCTACTCACGATGGATTTTCTAATAAGTATGCATTCCAACACAAAGGGAGGA
1239378 AAATCAT
196 AAATCAT
1239385 AT
1 AT
1239387 TAGCATCGAT
Statistics
Matches: 197, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
202 197 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29
Consensus pattern (202 bp):
ATGATGTGGGGGAAGCCAAGATAACCAAACAAGTTATTATTCCTTTTTCAATTGGAAGATACAAT
GATGAAGTCCTTTGTGACGTGGTGCCCATGAGTGCAAGCCACATTATATTAGGACGTCATTGGCA
ATTTGACAAGAAGGCTACTCACGATGGATTTTCTAATAAGTATGCATTCCAACACAAAGGGAGGA
AAATCAT
Found at i:1247208 original size:14 final size:15
Alignment explanation
Indices: 1247189--1247220 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1247179 GCAAGCACAC
1247189 AAAAGAAG-AAAACA
1 AAAAGAAGAAAAACA
1247203 AAAAGAAGAAAAACA
1 AAAAGAAGAAAAACA
1247218 AAA
1 AAA
1247221 GAAAAGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAACA
Found at i:1247225 original size:20 final size:20
Alignment explanation
Indices: 1247197--1247234 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1247187 ACAAAAGAAG
1247197 AAAACAAAA-AGAAGAAAAAC
1 AAAACAAAAGA-AAGAAAAAC
*
1247217 AAAAGAAAAGAAAGAAAA
1 AAAACAAAAGAAAGAAAA
1247235 GTTGAAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAACAAAAGAAAGAAAAAC
Found at i:1247235 original size:14 final size:14
Alignment explanation
Indices: 1247187--1247223 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1247177 TTGCAAGCAC
1247187 ACAAAAGAAG-AAA
1 ACAAAAGAAGAAAA
1247200 ACAAAAAGAAGAAAA
1 AC-AAAAGAAGAAAA
1247215 ACAAAAGAA
1 ACAAAAGAA
1247224 AAGAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.68
15 5 0.23
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (14 bp):
ACAAAAGAAGAAAA
Found at i:1250123 original size:23 final size:23
Alignment explanation
Indices: 1250075--1250124 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1250065 CAAAGAAATC
* * *
1250075 AAAGCACTCAAAATAATAAATTA
1 AAAGCACTAAAAAAAATAAATGA
1250098 AAAGCACTAAAAAAAATGAAA-GA
1 AAAGCACTAAAAAAAAT-AAATGA
1250121 AAAG
1 AAAG
1250125 TTGAAGCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (23 bp):
AAAGCACTAAAAAAAATAAATGA
Found at i:1253885 original size:16 final size:17
Alignment explanation
Indices: 1253859--1253890 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1253849 ATTATACCTC
1253859 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
1253876 TACC-TAACCATTTCT
1 TACCATAACCATTTCT
1253891 TTTAAGACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:1254206 original size:20 final size:20
Alignment explanation
Indices: 1254181--1254218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1254171 ATGTCTTACG
1254181 TATGTTT-CATATTCATTTGT
1 TATGTTTGCATA-TCATTTGT
1254201 TATGTTTGCATATCATTT
1 TATGTTTGCATATCATTT
1254219 AAATATCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
TATGTTTGCATATCATTTGT
Found at i:1264108 original size:20 final size:20
Alignment explanation
Indices: 1264079--1264121 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1264069 ATGTAGGAGT
*
1264079 CTTTTTC-T-TTTCTTTTTG
1 CTTTTTCTTCTTTCTTGTTG
1264097 -TTTTTCTTCTTTCTTGTTG
1 CTTTTTCTTCTTTCTTGTTG
1264116 CTTTTT
1 CTTTTT
1264122 GTTGTTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 9 0.43
20 5 0.24
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTCTTCTTTCTTGTTG
Found at i:1264410 original size:16 final size:16
Alignment explanation
Indices: 1264389--1264422 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1264379 GACTTATCCG
1264389 TCAAATGTAAGAGAAT
1 TCAAATGTAAGAGAAT
1264405 TCAAATGTAAGAGAAT
1 TCAAATGTAAGAGAAT
1264421 TC
1 TC
1264423 GGCCAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (16 bp):
TCAAATGTAAGAGAAT
Found at i:1272534 original size:24 final size:24
Alignment explanation
Indices: 1272483--1272534 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1272473 GGCACATGTG
****
1272483 TGGGATGGTCACGAGGCACATGTG
1 TGGGATGGTCACGAGGCACACACA
*
1272507 TGGGCTGGTCACGAGGCACACACA
1 TGGGATGGTCACGAGGCACACACA
1272531 TGGG
1 TGGG
1272535 TGGAATAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (24 bp):
TGGGATGGTCACGAGGCACACACA
Found at i:1272537 original size:28 final size:24
Alignment explanation
Indices: 1272473--1272526 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1272463 CCATATGTAT
1272473 GGCACATGTGTGGGATGGTCACGA
1 GGCACATGTGTGGGATGGTCACGA
*
1272497 GGCACATGTGTGGGCTGGTCACGA
1 GGCACATGTGTGGGATGGTCACGA
1272521 GGCACA
1 GGCACA
1272527 CACATGGGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.41, T:0.19
Consensus pattern (24 bp):
GGCACATGTGTGGGATGGTCACGA
Found at i:1273169 original size:22 final size:22
Alignment explanation
Indices: 1273129--1273170 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1273119 AAATATATGG
*
1273129 TTCATAATAATAACTTCATACA
1 TTCATAATAATAACATCATACA
* *
1273151 TTCATAATATTATCATCATA
1 TTCATAATAATAACATCATA
1273171 GCTATAAATA
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:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATAACATCATACA
Found at i:1273935 original size:18 final size:18
Alignment explanation
Indices: 1273896--1273937 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1273886 TCTTAACACT
* *
1273896 TAAAATAAAATTTTAAAG
1 TAAAATAAAATATAAAAG
1273914 TAAAATAAAA-ATAAAAG
1 TAAAATAAAATATAAAAG
1273931 ATAAAAT
1 -TAAAAT
1273938 TCAACAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
TAAAATAAAATATAAAAG
Found at i:1275697 original size:17 final size:20
Alignment explanation
Indices: 1275662--1275700 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
1275652 TTAATTCCTA
1275662 ATAAAATAATAAATCTGATC
1 ATAAAATAATAAATCTGATC
1275682 ATAAAAT-AT-AAT-TGATC
1 ATAAAATAATAAATCTGATC
1275699 AT
1 AT
1275701 CCTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 2 0.11
20 7 0.37
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAAATAATAAATCTGATC
Found at i:1294661 original size:19 final size:20
Alignment explanation
Indices: 1294623--1294663 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1294613 GAAACCCCTT
*
1294623 TGAAAATACTTGATTTTTAA
1 TGAAAATACATGATTTTTAA
1294643 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
1294662 TG
1 TG
1294664 GAGCTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1300453 original size:16 final size:17
Alignment explanation
Indices: 1300430--1300471 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1300420 GAAAATAATA
*
1300430 AAAGATGAAAGAATAAG
1 AAAGATGAAACAATAAG
*
1300447 AAA-ATGAAACAGTAAG
1 AAAGATGAAACAATAAG
1300463 AAAGATGAA
1 AAAGATGAA
1300472 GTTAACTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.12
Consensus pattern (17 bp):
AAAGATGAAACAATAAG
Found at i:1300703 original size:20 final size:20
Alignment explanation
Indices: 1300674--1300716 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1300664 ATGTATGAGT
*
1300674 CTTTTTC-T-TTTCTTTTTG
1 CTTTTTCTTCTTTCTTGTTG
1300692 -TTTTTCTTCTTTCTTGTTG
1 CTTTTTCTTCTTTCTTGTTG
1300711 CTTTTT
1 CTTTTT
1300717 TTGTTATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 9 0.43
20 5 0.24
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTCTTCTTTCTTGTTG
Found at i:1324581 original size:6 final size:6
Alignment explanation
Indices: 1324553--1324610 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
1324543 GTGTTTTAAC
* * * *
1324553 AAAAGC AAAA-A AAAA-A AAGAGA AAAAGA AAGTAGA AAAACA AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA
1324599 AAAAGA AAAAGA
1 AAAAGA AAAAGA
1324611 CTCCTACATC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
5 13 0.31
6 24 0.57
7 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:1324832 original size:16 final size:15
Alignment explanation
Indices: 1324800--1324860 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
1324790 TGAGTTATAA
*
1324800 CTTATCTTCATTTTT
1 CTTATTTTCATTTTT
1324815 CTTACTATTTCA-TTTT
1 CTTA-T-TTTCATTTTT
1324831 CTTATTCTTTCATCTTTT
1 CTTA-T-TTTCAT-TTTT
1324849 CTTATTTTCATT
1 CTTATTTTCATT
1324861 ACTTTATCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.13
16 21 0.54
17 5 0.13
18 8 0.21
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTATTTTCATTTTT
Found at i:1324850 original size:18 final size:17
Alignment explanation
Indices: 1324801--1324854 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
1324791 GAGTTATAAC
1324801 TTATCTTCATTTTTCTTA
1 TTAT-TTCATTTTTCTTA
*
1324819 CTATTTCA-TTTTCTTA
1 TTATTTCATTTTTCTTA
*
1324835 TTCTTTCATCTTTTCTTA
1 TTATTTCAT-TTTTCTTA
1324853 TT
1 TT
1324855 TTCATTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 14 0.45
17 4 0.13
18 13 0.42
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTTTTCTTA
Found at i:1329830 original size:13 final size:13
Alignment explanation
Indices: 1329812--1329841 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1329802 ATACTATCCA
1329812 TTCATCACCATCT
1 TTCATCACCATCT
*
1329825 TTCATCACCATTT
1 TTCATCACCATCT
1329838 TTCA
1 TTCA
1329842 CGCCTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (13 bp):
TTCATCACCATCT
Found at i:1331535 original size:324 final size:324
Alignment explanation
Indices: 1330942--1331591 Score: 941
Period size: 324 Copynumber: 2.0 Consensus size: 324
1330932 TTTGGTTCCT
* * *
1330942 AGTTTTTATAACTTGTGGGTCAAAGTACTTAATACCACCCCTTAAAGAAGCAATATAAAGTCTGG
1 AGTTCTTATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTAAAGAAGCAATATAAAGTATGG
*
1331007 GTCTTTGCTCTCTATAGCATTGGTTATTCTTTGAGTCTTCTTTAAGATACTATCTTCACAACAAT
66 GTCTTTGCTCTCTATAGCATTGGTTATTCTTTGAGTCTTCTTTAAGATACTATCCTCACAACAAT
* * * ** * *
1331072 TCCTTTGTTTCATCAGCCATAACCCATTGCCATATCAATCATCCTCCACTTCCGTCTCTCATTTA
131 CCCTTTGTTTCATCAACCATAAACCACAGCCATATCAATCATCCTCCACTTCCATCACTCATTTA
* * *
1331137 AACAACCTACCTATTGACCCTTACGTTTACCACCCTTAACCATCTCTTTTTGAGCCATTCACTTG
196 AACAACCTACCTATTCACCCATACGTTTACCACCCTTAACCATCTCTTCTTGAGCCATTCACTTG
* *
1331202 TGCAGGTTGTTTTGCTTCCTTCCTAGATCCATAATCAATT-ATAAGGTACAAGTTCCTTACATC
261 TGCAGGTTGTTTTACTTCCTTCATAGATCCATAATCAATTGATAAGGTACAAGTTCCTTACATC
**
1331265 AGTTCTTATAACTAGTGGGTCAAAGT-CATTGTTTACCACCCCTTAAAGAAGCAATATAAAGTAT
1 AGTTCTTATAACTAGTGGGTCAAAGTAC-TT-AATACCACCCCTTAAAGAAGCAATATAAAGTAT
* * *
1331329 GGGTCTTTGCTCTTTATAGCATTGGTTCTTCTTTGAGTCTTCTTTAAGATACTA-CCTCACAACT
64 GGGTCTTTGCTCTCTATAGCATTGGTTATTCTTTGAGTCTTCTTTAAGATACTATCCTCACAACA
* * *
1331393 ATCCCTTTGTTTCATCAACCATAAACCACAGCCATATC-ATCCATCTTTCGCTTCCATCACTCAT
129 ATCCCTTTGTTTCATCAACCATAAACCACAGCCATATCAAT-CATCCTCCACTTCCATCACTC--
* * * *
1331457 ATTTAAATAGCCTACCTATTCACCCATACTTTTACCAGCCTTAACCATCTC-TCTTGAGCCATTC
191 ATTTAAACAACCTACCTATTCACCCATACGTTTACCACCCTTAACCATCTCTTCTTGAGCCATTC
* * *
1331521 ACTTGTGTAGGTTGTTTTATTTCCTTCATAGATCCATAATCAATTGATATGGTACAAGTTCCTTA
256 ACTTGTGCAGGTTGTTTTACTTCCTTCATAGATCCATAATCAATTGATAAGGTACAAGTTCCTTA
1331586 CATC
321 CATC
1331590 AG
1 AG
1331592 CATCACTTCC
Statistics
Matches: 290, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
322 3 0.01
323 83 0.29
324 135 0.47
325 69 0.24
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (324 bp):
AGTTCTTATAACTAGTGGGTCAAAGTACTTAATACCACCCCTTAAAGAAGCAATATAAAGTATGG
GTCTTTGCTCTCTATAGCATTGGTTATTCTTTGAGTCTTCTTTAAGATACTATCCTCACAACAAT
CCCTTTGTTTCATCAACCATAAACCACAGCCATATCAATCATCCTCCACTTCCATCACTCATTTA
AACAACCTACCTATTCACCCATACGTTTACCACCCTTAACCATCTCTTCTTGAGCCATTCACTTG
TGCAGGTTGTTTTACTTCCTTCATAGATCCATAATCAATTGATAAGGTACAAGTTCCTTACATC
Found at i:1333389 original size:21 final size:21
Alignment explanation
Indices: 1333330--1333401 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1333320 TCAAGTAAAG
* *
1333330 AAATAAAAAATCAACAAAGAA
1 AAATAAAAAACCAGCAAAGAA
1333351 AAATAAAAAACCAGCAAAGAA
1 AAATAAAAAACCAGCAAAGAA
* *
1333372 AATTACAAAA-CAGTCAAAGAA
1 AAATAAAAAACCAG-CAAAGAA
*
1333393 TAAACAAAA
1 -AAATAAAA
1333402 GGAAAGAGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.07
21 34 0.81
22 5 0.12
ACGTcount: A:0.71, C:0.12, G:0.07, T:0.10
Consensus pattern (21 bp):
AAATAAAAAACCAGCAAAGAA
Found at i:1366528 original size:7 final size:7
Alignment explanation
Indices: 1366512--1366554 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
1366502 TGTAAGAGTC
1366512 TTTTCTTT
1 TTTTC-TT
1366520 TTTTCTT
1 TTTTCTT
1366527 TTTTC-T
1 TTTTCTT
1366533 TTTTCTT
1 TTTTCTT
*
1366540 ATTTCTT
1 TTTTCTT
1366547 TTTT-TT
1 TTTTCTT
1366553 TT
1 TT
1366555 GTTTCAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 10 0.31
7 17 0.53
8 5 0.16
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:1366528 original size:13 final size:13
Alignment explanation
Indices: 1366510--1366551 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
1366500 GATGTAAGAG
1366510 TCTTTTCTTTTTT
1 TCTTTTCTTTTTT
1366523 TCTTTT-TTCTTTT
1 TCTTTTCTT-TTTT
1366536 TCTTATTTCTTTTTT
1 TC-T-TTTCTTTTTT
1366551 T
1 T
1366552 TTTGTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 1 0.04
15 8 0.32
16 2 0.08
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TCTTTTCTTTTTT
Found at i:1366559 original size:15 final size:14
Alignment explanation
Indices: 1366512--1366559 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1366502 TGTAAGAGTC
1366512 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTT-TT
*
1366527 TTTTC-TTTTTCTT
1 TTTTCTTTTTTTTT
*
1366540 ATTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
1366554 TGTTTC
1 T-TTTC
1366560 AGCACTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 6 0.22
14 12 0.44
15 9 0.33
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:1368190 original size:13 final size:13
Alignment explanation
Indices: 1368168--1368199 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1368158 CCTTTACTTC
1368168 TTCTTAAATTCAT
1 TTCTTAAATTCAT
*
1368181 TTCTTTAATTCAT
1 TTCTTAAATTCAT
1368194 TTCTTA
1 TTCTTA
1368200 TTCCATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (13 bp):
TTCTTAAATTCAT
Found at i:1369747 original size:20 final size:20
Alignment explanation
Indices: 1369710--1369748 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1369700 ATGTTCTACA
* *
1369710 TATGTTTTAATTTTATTTAT
1 TATGTTTTAATATCATTTAT
*
1369730 TATGTTTTCATATCATTTA
1 TATGTTTTAATATCATTTA
1369749 CATATCATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TATGTTTTAATATCATTTAT
Found at i:1376707 original size:6 final size:6
Alignment explanation
Indices: 1376696--1376736 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
1376686 GTGTTGCAAC
1376696 AAAAAG AAAAAG -AAAAG AGAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAAAA
1376737 AAACTCCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1394752 original size:20 final size:20
Alignment explanation
Indices: 1394727--1394765 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1394717 ATGTTATACA
*
1394727 TATGTTTTAATTTCATTTAT
1 TATGTTTTAATATCATTTAT
*
1394747 TATGTTTTCATATCATTTA
1 TATGTTTTAATATCATTTA
1394766 CATATCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (20 bp):
TATGTTTTAATATCATTTAT
Found at i:1409850 original size:19 final size:19
Alignment explanation
Indices: 1409814--1409851 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1409804 CAACAAAAGC
*
1409814 AACAAGAAAGAAGAAAAAA
1 AACAAGAAAGAAAAAAAAA
1409833 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
1409852 TACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AACAAGAAAGAAAAAAAAA
Found at i:1427600 original size:12 final size:12
Alignment explanation
Indices: 1427576--1427616 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
1427566 GGAATATGAT
1427576 TAATAAA-GGAA
1 TAATAAATGGAA
1427587 TAATAAATGGAA
1 TAATAAATGGAA
1427599 TAAT-AAT-G-A
1 TAATAAATGGAA
1427608 TAATAAATG
1 TAATAAATG
1427617 AATTGAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 10 0.37
12 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.27
Consensus pattern (12 bp):
TAATAAATGGAA
Found at i:1430276 original size:16 final size:15
Alignment explanation
Indices: 1430247--1430299 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1430237 GCAAAAAGAA
1430247 AAGAAAAGACAAAAAG
1 AAGAAAAGA-AAAAAG
**
1430263 AAGAATAAGAAAAATT
1 AAGAA-AAGAAAAAAG
*
1430279 CAGAAAAGAAGAAAAG
1 AAGAAAAGAA-AAAAG
1430295 AAGAA
1 AAGAA
1430300 GAAAAGTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.69
17 4 0.14
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.06
Consensus pattern (15 bp):
AAGAAAAGAAAAAAG
Found at i:1432527 original size:19 final size:19
Alignment explanation
Indices: 1432471--1432529 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 19
1432461 ATAATGGACT
*
1432471 TAATAAATGGAATAATAAT-A
1 TAAT-AATGAAATAA-AATAA
1432491 TAAGTAATGAAA-ATAAATAA
1 TAA-TAATGAAATA-AAATAA
1432511 TAATAATGAAATAAAATAA
1 TAATAATGAAATAAAATAA
1432530 AGAAAGGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 18 0.53
20 15 0.44
21 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.27
Consensus pattern (19 bp):
TAATAATGAAATAAAATAA
Found at i:1432968 original size:20 final size:19
Alignment explanation
Indices: 1432943--1432985 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1432933 AAACCCCTTT
1432943 TGAAAACACA-AGATTTTTAA
1 TGAAAACACATA-A-TTTTAA
*
1432963 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
1432982 TGAA
1 TGAA
1432986 GATAAATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 10 0.48
21 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:1433936 original size:30 final size:31
Alignment explanation
Indices: 1433895--1433953 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1433885 ACATGCTGTC
**
1433895 ATGATATCTAAATGATATGCAAACATAATGA
1 ATGATATCTAAAACATATGCAAACATAATGA
*
1433926 ATGA-ATCTAAAACATATGTAAACATAAT
1 ATGATATCTAAAACATATGCAAACATAAT
1433954 ATAAGGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATGA
Found at i:1436221 original size:8 final size:8
Alignment explanation
Indices: 1436205--1436263 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
1436195 CTTTTTGAAC
*
1436205 TTCTCTTT
1 TTCTTTTT
1436213 TTC-TTTT
1 TTCTTTTT
*
1436220 TT-TTTTC
1 TTCTTTTT
*
1436227 TTCTTTTC
1 TTCTTTTT
*
1436235 TTATTTTT
1 TTCTTTTT
1436243 TTCTTATTT
1 TTCTT-TTT
1436252 TGTCTTTTT
1 T-TCTTTTT
1436261 TTC
1 TTC
1436264 GTTCTTTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
7 10 0.24
8 20 0.48
9 8 0.19
10 4 0.10
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (8 bp):
TTCTTTTT
Found at i:1436227 original size:19 final size:18
Alignment explanation
Indices: 1436205--1436272 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 18
1436195 CTTTTTGAAC
1436205 TTCTCTTTTTCTTTTTTTT
1 TTCT-TTTTTCTTTTTTTT
*
1436224 TTCTTCTTTTCTTATTTTT
1 TTCTT-TTTTCTTTTTTTT
*
1436243 TTCTTATTTTGTCTTTTTTTCG
1 TTC-T-TTTT-TCTTTTTTT-T
1436265 TTCTTTTT
1 TTCTTTTT
1436273 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.02
19 19 0.46
20 8 0.20
21 10 0.24
22 3 0.07
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (18 bp):
TTCTTTTTTCTTTTTTTT
Found at i:1436573 original size:19 final size:20
Alignment explanation
Indices: 1436527--1436575 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1436517 TAATAAAGGG
1436527 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
1436547 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
1436566 AATAAAATAA
1 AATAAAATAA
1436576 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:1438685 original size:15 final size:16
Alignment explanation
Indices: 1438665--1438707 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1438655 AGTTATCATC
1438665 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
1438680 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
1438696 AAAATAACTATA
1 ATAATAACTATA
1438708 TTAAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:1444001 original size:6 final size:6
Alignment explanation
Indices: 1443992--1444017 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1443982 GATATAGTAT
1443992 ATGAAA ATGAAA ATGAAA ATGAAA AT
1 ATGAAA ATGAAA ATGAAA ATGAAA AT
1444018 AAATATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
ATGAAA
Found at i:1446963 original size:20 final size:19
Alignment explanation
Indices: 1446923--1446986 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1446913 CTTGGCTTGC
* * *
1446923 TTTCTCTTTGAAATTTCTT
1 TTTCTTTTTGAATTTTTTT
1446942 TTTCTTTTCTGAATTTTTTT
1 TTTCTTTT-TGAATTTTTTT
**
1446962 TTTCTTTTTGTCTTTTTTT
1 TTTCTTTTTGAATTTTTTT
1446981 TTTCTT
1 TTTCTT
1446987 AATGCACTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.08, C:0.12, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTCTTTTTGAATTTTTTT
Found at i:1448495 original size:12 final size:12
Alignment explanation
Indices: 1448478--1448502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1448468 CAGGTAGAAT
1448478 AGAAAAAGGTTA
1 AGAAAAAGGTTA
1448490 AGAAAAAGGTTA
1 AGAAAAAGGTTA
1448502 A
1 A
1448503 AGTAATGAAA
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AGAAAAAGGTTA
Found at i:1448542 original size:16 final size:16
Alignment explanation
Indices: 1448512--1448560 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1448502 AAGTAATGAA
1448512 AATAAGAAAAGATGAAAG
1 AATAAG-AAA-ATGAAAG
*
1448530 AATAAGAAAATGAAAT
1 AATAAGAAAATGAAAG
*
1448546 AGTAAGAAAACTGAA
1 AATAAGAAAA-TGAA
1448561 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 15 0.54
17 7 0.25
18 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.18, T:0.14
Consensus pattern (16 bp):
AATAAGAAAATGAAAG
Found at i:1448764 original size:20 final size:20
Alignment explanation
Indices: 1448735--1448777 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1448725 ATGTAGGGGT
*
1448735 CTTTTTC-T-TTTCTTTTTG
1 CTTTTTCTTCTTTCTTGTTG
1448753 -TTTTTCTTCTTTCTTGTTG
1 CTTTTTCTTCTTTCTTGTTG
1448772 CTTTTT
1 CTTTTT
1448778 TTTGTAGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 1 0.05
19 9 0.43
20 5 0.24
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTCTTCTTTCTTGTTG
Found at i:1451994 original size:17 final size:17
Alignment explanation
Indices: 1451972--1452024 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1451962 AATTAAGAGT
*
1451972 TAGTTTCATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
1451989 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
1452006 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
1452023 TA
1 TA
1452025 ACATTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1455134 original size:19 final size:20
Alignment explanation
Indices: 1455094--1455142 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1455084 AACCCTTTTA
* *
1455094 AAAATACATTATTTTTAATG
1 AAAATACATGATTTTAAATG
1455114 AAAATACATGA-TTTAAATG
1 AAAATACATGATTTTAAATG
*
1455133 AAGATACATG
1 AAAATACATG
1455143 CTCTTAGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTAAATG
Found at i:1460754 original size:25 final size:24
Alignment explanation
Indices: 1460712--1460760 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1460702 TTTTTCTTAT
*
1460712 TTTTGAGTGCTGGATTTTTTTTTC
1 TTTTGAGTGCTGCATTTTTTTTTC
* *
1460736 TTTTGAGTGCTTCACTTTTTTTTC
1 TTTTGAGTGCTGCATTTTTTTTTC
1460760 T
1 T
1460761 GATTTTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.08, C:0.12, G:0.16, T:0.63
Consensus pattern (24 bp):
TTTTGAGTGCTGCATTTTTTTTTC
Found at i:1464668 original size:27 final size:28
Alignment explanation
Indices: 1464616--1464680 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
1464606 AAAGAAAATC
*
1464616 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
1464644 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
1464671 AGAAAAGAAA
1 AGAAAAGAAA
1464681 AGAAAAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.62, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:1464680 original size:5 final size:5
Alignment explanation
Indices: 1464670--1464704 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1464660 ATTCAAAAAG
*
1464670 AAGAA AAGAA AAGAA AAGAA GAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1464705 GTTGAAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1470805 original size:19 final size:20
Alignment explanation
Indices: 1470765--1470814 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1470755 GAAACCCCTT
**
1470765 TGAAAATA-ATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1470784 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1470803 TGAAGATACATG
1 TGAAAATACATG
1470815 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1470923 original size:22 final size:22
Alignment explanation
Indices: 1470893--1470946 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1470883 GGTGCCAAAA
*
1470893 TGAAGAGGAAAGAGTCTTTGGC
1 TGAATAGGAAAGAGTCTTTGGC
1470915 TGAATAGGAAAGAGTCTTTGGC
1 TGAATAGGAAAGAGTCTTTGGC
1470937 TGAATAGGAA
1 TGAATAGGAA
1470947 GTATCCCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.24
Consensus pattern (22 bp):
TGAATAGGAAAGAGTCTTTGGC
Found at i:1475467 original size:24 final size:24
Alignment explanation
Indices: 1475433--1475485 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1475423 TCAAAACATT
* *
1475433 AAGAGATATGTCTTGTGAATCAGA
1 AAGAGACATGTCTTGTGAATCACA
*
1475457 AAGAGACATGTCTTGTGGATCACA
1 AAGAGACATGTCTTGTGAATCACA
1475481 AAGAG
1 AAGAG
1475486 TCACACCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTGAATCACA
Found at i:1483534 original size:34 final size:34
Alignment explanation
Indices: 1483496--1483578 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
1483486 CTAACTTTAT
* * *
1483496 TAAATGAACTAGATGCATGAATGGAGTAGCTT-CC
1 TAAATGAACTAGATGCATAAATGAACTA-CTTCCC
* * *
1483530 TAAATGATCTAAAGGCATAAATGAACTACTTCCC
1 TAAATGAACTAGATGCATAAATGAACTACTTCCC
1483564 TAAATGAACTAGATG
1 TAAATGAACTAGATG
1483579 ATTTAAATGC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 3 0.08
34 36 0.92
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (34 bp):
TAAATGAACTAGATGCATAAATGAACTACTTCCC
Found at i:1503159 original size:42 final size:42
Alignment explanation
Indices: 1503100--1503185 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1503090 AGAATCCAAG
*
1503100 ACCAAGCAATGATGAACTTTTAGTACCCAGGCGAGAACAACC
1 ACCAAACAATGATGAACTTTTAGTACCCAGGCGAGAACAACC
* * *
1503142 ACCAAACAATGCTGAACTTTTGGTACCCAGGTGAGAACAACC
1 ACCAAACAATGATGAACTTTTAGTACCCAGGCGAGAACAACC
1503184 AC
1 AC
1503186 GTTTCCAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (42 bp):
ACCAAACAATGATGAACTTTTAGTACCCAGGCGAGAACAACC
Found at i:1529718 original size:13 final size:13
Alignment explanation
Indices: 1529700--1529734 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1529690 TGATCTAGGG
1529700 AGCCTTGTGGTGC
1 AGCCTTGTGGTGC
*
1529713 AGCCTTGTGGTGT
1 AGCCTTGTGGTGC
1529726 AGCCTTGTG
1 AGCCTTGTG
1529735 CATGGGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.34
Consensus pattern (13 bp):
AGCCTTGTGGTGC
Found at i:1530026 original size:13 final size:13
Alignment explanation
Indices: 1530008--1530042 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1529998 TGATCTAGGG
1530008 AGCCTTGTGGTGC
1 AGCCTTGTGGTGC
*
1530021 AGCCTTGTGGTGT
1 AGCCTTGTGGTGC
*
1530034 ATCCTTGTG
1 AGCCTTGTG
1530043 CATGGGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.20, G:0.34, T:0.37
Consensus pattern (13 bp):
AGCCTTGTGGTGC
Found at i:1530135 original size:308 final size:308
Alignment explanation
Indices: 1529577--1530194 Score: 1173
Period size: 308 Copynumber: 2.0 Consensus size: 308
1529567 TGAAGAGAAA
* *
1529577 AGAGTCTTTGGCATAATAGGAAGCATCCCTTGGTATTTTGGTGCCAATTTGATGTCACATGGAGT
1 AGAGTCTTTGGAATAATAGGAAGCATCCCTTGGTATTTTGGCGCCAATTTGATGTCACATGGAGT
*
1529642 GCACATTCTTGAATGATGCACATAGCAGCCTACTTGAATGCACATGGGTGATCTAGGGAGCCTTG
66 GCACATGCTTGAATGATGCACATAGCAGCCTACTTGAATGCACATGGGTGATCTAGGGAGCCTTG
1529707 TGGTGCAGCCTTGTGGTGTAGCCTTGTGCATGGGATGATGGCTGGTCATGTGCTCCATCTTGGGC
131 TGGTGCAGCCTTGTGGTGTAGCCTTGTGCATGGGATGATGGCTGGTCATGTGCTCCATCTTGGGC
*
1529772 ATGCATGTGTCTCCTCTTAGCTAGCTTGAATGTGGAGCTAGCTTAGCAAGCATGGGGCTGTTTGT
196 ATGCATGCGTCTCCTCTTAGCTAGCTTGAATGTGGAGCTAGCTTAGCAAGCATGGGGCTGTTTGT
*
1529837 GAACAGGCTTCCTAGATGAGTCCTTGAGAGCTCCATAATAGCATGTTC
261 GAACAGGCTTCCTAGATGAGTCATTGAGAGCTCCATAATAGCATGTTC
1529885 AGAGTCTTTGGAATAATAGGAAGCATCCCTTGGTATTTTGGCGCCAATTTGATGTCACATGGAGT
1 AGAGTCTTTGGAATAATAGGAAGCATCCCTTGGTATTTTGGCGCCAATTTGATGTCACATGGAGT
1529950 GCACATGCTTGAATGATGCACATAGCAGCCTACTTGAATGCACATGGGTGATCTAGGGAGCCTTG
66 GCACATGCTTGAATGATGCACATAGCAGCCTACTTGAATGCACATGGGTGATCTAGGGAGCCTTG
*
1530015 TGGTGCAGCCTTGTGGTGTATCCTTGTGCATGGGATGATGGCTGGTCATGTGCTCCATCTTGGGC
131 TGGTGCAGCCTTGTGGTGTAGCCTTGTGCATGGGATGATGGCTGGTCATGTGCTCCATCTTGGGC
1530080 ATGCATGCGTCTCCTCTTAGCTAGCTTGAATGTGGAGCTAGCTTAGCAAGCATGGGGCTGTTTGT
196 ATGCATGCGTCTCCTCTTAGCTAGCTTGAATGTGGAGCTAGCTTAGCAAGCATGGGGCTGTTTGT
*
1530145 GAACAGGCTTCCTAGATGAGTCATTGTGAGCTCCATAATAGCATGTTC
261 GAACAGGCTTCCTAGATGAGTCATTGAGAGCTCCATAATAGCATGTTC
1530193 AG
1 AG
1530195 CTACATTTAG
Statistics
Matches: 303, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
308 303 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (308 bp):
AGAGTCTTTGGAATAATAGGAAGCATCCCTTGGTATTTTGGCGCCAATTTGATGTCACATGGAGT
GCACATGCTTGAATGATGCACATAGCAGCCTACTTGAATGCACATGGGTGATCTAGGGAGCCTTG
TGGTGCAGCCTTGTGGTGTAGCCTTGTGCATGGGATGATGGCTGGTCATGTGCTCCATCTTGGGC
ATGCATGCGTCTCCTCTTAGCTAGCTTGAATGTGGAGCTAGCTTAGCAAGCATGGGGCTGTTTGT
GAACAGGCTTCCTAGATGAGTCATTGAGAGCTCCATAATAGCATGTTC
Found at i:1531919 original size:24 final size:21
Alignment explanation
Indices: 1531885--1531927 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1531875 CCCACAAGAC
*
1531885 ATGTCCTTTGACATTTCAAAGT
1 ATGTCCTTTGA-AGTTCAAAGT
1531907 ATGTACCTCTTGAAGTTCAAA
1 ATGT-CCT-TTGAAGTTCAAA
1531928 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAGTTCAAAGT
Found at i:1550443 original size:22 final size:22
Alignment explanation
Indices: 1550415--1550468 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1550405 CTCATAGCTG
1550415 GATTAAGCTACAAGATGACTTC
1 GATTAAGCTACAAGATGACTTC
1550437 GATTAAGCTACAAGATGACTTC
1 GATTAAGCTACAAGATGACTTC
* *
1550459 AATTCAGCTA
1 GATTAAGCTA
1550469 GGGAGCTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (22 bp):
GATTAAGCTACAAGATGACTTC
Found at i:1553916 original size:17 final size:17
Alignment explanation
Indices: 1553894--1553994 Score: 94
Period size: 17 Copynumber: 5.9 Consensus size: 17
1553884 AATTAATAGT
1553894 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
1553911 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
1553928 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
1553945 TAAATTTATTGAATGAAC
1 T-AGTTTAATAAATGAAC
* * * *
1553963 TAGGTGAATGAATGAAA
1 TAGTTTAATAAATGAAC
* *
1553980 TAGCTTACTAAATGA
1 TAGTTTAATAAATGA
1553995 TCTAAAGGCA
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
17 53 0.79
18 14 0.21
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1553933 original size:34 final size:35
Alignment explanation
Indices: 1553894--1553965 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 35
1553884 AATTAATAGT
*
1553894 TAGTTTAATAAATGAACT-AGTTTGA-TGAATGAAC
1 TAGTTTAATAAATGAACTAAATTT-ATTGAATGAAC
1553928 TAGTTTAATAAATGAACTAAATTTATTGAATGAAC
1 TAGTTTAATAAATGAACTAAATTTATTGAATGAAC
1553963 TAG
1 TAG
1553966 GTGAATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
34 19 0.54
35 16 0.46
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (35 bp):
TAGTTTAATAAATGAACTAAATTTATTGAATGAAC
Found at i:1569921 original size:3 final size:3
Alignment explanation
Indices: 1569915--1569975 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
1569905 TTATTTCTTT
** *
1569915 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1569960 TTA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
1569976 TAATAAATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1571465 original size:2 final size:2
Alignment explanation
Indices: 1571458--1571494 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1571448 ATAAAAACAA
1571458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1571495 GTTATTCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1571584 original size:27 final size:29
Alignment explanation
Indices: 1571540--1571595 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
1571530 AATTTTAGTC
* *
1571540 ATAATAATATATATTATTTGATTAATTTT
1 ATAATAATATATAATATTTAATTAATTTT
*
1571569 ATAA-AATA-ATAATATTTAATTATTTTT
1 ATAATAATATATAATATTTAATTAATTTT
1571596 GATATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 16 0.67
28 4 0.17
29 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
ATAATAATATATAATATTTAATTAATTTT
Found at i:1574206 original size:21 final size:22
Alignment explanation
Indices: 1574180--1574223 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1574170 TACATTTACA
1574180 TTTGCATTTGTAT-TTTGCATT
1 TTTGCATTTGTATGTTTGCATT
* *
1574201 TTTGCATTTTTATGTTTGTATT
1 TTTGCATTTGTATGTTTGCATT
1574223 T
1 T
1574224 ATATTTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.66
Consensus pattern (22 bp):
TTTGCATTTGTATGTTTGCATT
Found at i:1576947 original size:10 final size:10
Alignment explanation
Indices: 1576927--1576963 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1576917 TATTATACTT
1576927 GAAAAACAAAA
1 GAAAAA-AAAA
1576938 GAAAAAAAAA
1 GAAAAAAAAA
1576948 G-AAAAAAAA
1 GAAAAAAAAA
1576957 GAAAAAA
1 GAAAAAA
1576964 TTGAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 10 0.40
11 6 0.24
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:1576952 original size:9 final size:9
Alignment explanation
Indices: 1576929--1576963 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
1576919 TTATACTTGA
1576929 AAAACAAAAG
1 AAAA-AAAAG
1576939 AAAAAAAAAG
1 -AAAAAAAAG
1576949 AAAAAAAAG
1 AAAAAAAAG
1576958 AAAAAA
1 AAAAAA
1576964 TTGAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 5 0.21
11 4 0.17
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1577458 original size:32 final size:32
Alignment explanation
Indices: 1577418--1577479 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1577408 TTTGGAAACA
* *
1577418 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATAAGCATAACAACG
1577450 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
1577480 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACG
Found at i:1581452 original size:54 final size:54
Alignment explanation
Indices: 1581377--1581527 Score: 144
Period size: 54 Copynumber: 2.8 Consensus size: 54
1581367 TAAATCTGCA
* * *
1581377 CAGAAATCAC-AGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTG-G
1 CAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTACAAAAATCCGTG
* * ***
1581430 CCAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAACCTTTACAAAAATCCGTG
1 -CAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAAATCCGTG
** * ** *
1581485 CAGAAACCATGAGAAACGATGAATGAATTGTCACATGTTTTAC
1 CAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1581528 GAACCAGTGA
Statistics
Matches: 76, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
54 73 0.96
55 3 0.04
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (54 bp):
CAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAAAATCCGTG
Found at i:1582822 original size:76 final size:74
Alignment explanation
Indices: 1582626--1582838 Score: 320
Period size: 75 Copynumber: 2.9 Consensus size: 74
1582616 GTGCATGTTG
*
1582626 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTTAAAAACCCTTCGGGA
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAA-CCTTCGGGA
1582691 GCTTTTGATA
65 GCTTTTGATA
* *
1582701 TTTTCAAAACCTTCGGGTTATCCATAAGACCTGCAGTCCAGGATGTTTTCAAAAAGCCTTCGGGA
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAA-CCTTCGGGA
1582766 GCTTTTTGATA
65 GC-TTTTGATA
** * * *
1582777 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAACCTTCGGG
1582839 TCATCCATAA
Statistics
Matches: 126, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
74 8 0.06
75 67 0.53
76 51 0.40
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (74 bp):
TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAACCTTCGGGAG
CTTTTGATA
Done.