Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007978.1 Hibiscus syriacus cultivar Beakdansim tig00110415_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: 1479011
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 5 of 7
Found at i:982783 original size:18 final size:18
Alignment explanation
Indices: 982760--982806 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
982750 TCAGGACGAC
*
982760 GACGACGATGACGATGGT
1 GACGACGATGACGATGAT
* *
982778 GACGACGACGATGATGAT
1 GACGACGATGACGATGAT
*
982796 GACGGCGATGA
1 GACGACGATGA
982807 GTCAAAACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.38, T:0.15
Consensus pattern (18 bp):
GACGACGATGACGATGAT
Found at i:982783 original size:21 final size:21
Alignment explanation
Indices: 982757--982796 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
982747 TGCTCAGGAC
982757 GACGACGACGATGACGATGGT
1 GACGACGACGATGACGATGGT
*
982778 GACGACGACGATGATGATG
1 GACGACGACGATGACGATG
982797 ACGGCGATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.38, T:0.15
Consensus pattern (21 bp):
GACGACGACGATGACGATGGT
Found at i:982799 original size:15 final size:15
Alignment explanation
Indices: 982763--982806 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
982753 GGACGACGAC
* *
982763 GACGATGACGATGGT
1 GACGACGACGATGAT
982778 GACGACGACGATGAT
1 GACGACGACGATGAT
* *
982793 GATGACGGCGATGA
1 GACGACGACGATGA
982807 GTCAAAACCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.39, T:0.16
Consensus pattern (15 bp):
GACGACGACGATGAT
Found at i:983052 original size:35 final size:33
Alignment explanation
Indices: 983012--983096 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
983002 ATATTTCAGT
983012 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
983047 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
983082 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
983097 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:986879 original size:15 final size:15
Alignment explanation
Indices: 986859--986907 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
986849 AAAAATAATA
986859 ATAATTAGATATCAC
1 ATAATTAGATATCAC
* *
986874 ATAATT--AT-TAAA
1 ATAATTAGATATCAC
986886 ATAATTAGATATCAC
1 ATAATTAGATATCAC
986901 ATAATTA
1 ATAATTA
986908 TTAAAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.30
13 2 0.07
14 2 0.07
15 15 0.56
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (15 bp):
ATAATTAGATATCAC
Found at i:986896 original size:27 final size:27
Alignment explanation
Indices: 986858--986918 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
986848 CAAAAATAAT
986858 AATAATTAGATATCACATAATTATTAA
1 AATAATTAGATATCACATAATTATTAA
986885 AATAATTAGATATCACATAATTATTAA
1 AATAATTAGATATCACATAATTATTAA
986912 AATAATT
1 AATAATT
986919 TAATAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (27 bp):
AATAATTAGATATCACATAATTATTAA
Found at i:1002603 original size:19 final size:19
Alignment explanation
Indices: 1002566--1002603 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1002556 CCGAAACAAA
*
1002566 TTTTTATAAATTAATGTTT
1 TTTTTATAAATTAAAGTTT
1002585 TTTTTA-AAATTACAAGTTT
1 TTTTTATAAATTA-AAGTTT
1002604 AATTCGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTATAAATTAAAGTTT
Found at i:1010234 original size:24 final size:25
Alignment explanation
Indices: 1010187--1010239 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
1010177 TATTACCATC
* *
1010187 TAATTTCGTATCTCTTAAAATTTTA
1 TAATTTCGCACCTCTTAAAATTTTA
*
1010212 TAATTTCGCACCTC-TAAAATTTTT
1 TAATTTCGCACCTCTTAAAATTTTA
1010236 TAAT
1 TAAT
1010240 ACAACCTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49
Consensus pattern (25 bp):
TAATTTCGCACCTCTTAAAATTTTA
Found at i:1012935 original size:14 final size:14
Alignment explanation
Indices: 1012916--1012945 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1012906 AGATTTGTTT
1012916 CTAATTCATTCTTG
1 CTAATTCATTCTTG
1012930 CTAATTCATTCTTG
1 CTAATTCATTCTTG
1012944 CT
1 CT
1012946 TACATGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.07, T:0.50
Consensus pattern (14 bp):
CTAATTCATTCTTG
Found at i:1022112 original size:48 final size:48
Alignment explanation
Indices: 1022060--1022154 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
1022050 TTACTTTATT
* * * **
1022060 GGTTTATTATATTTTGGTCATTAAATTGTTAATTTCTGTTAATTTGAC
1 GGTTTAATATATCTTGATCATTAAACCGTTAATTTCTGTTAATTTGAC
* * *
1022108 GGTTTAATATATCTTGATCATTAGACCGTTAATTTTTGTTAGTTTGA
1 GGTTTAATATATCTTGATCATTAAACCGTTAATTTCTGTTAATTTGA
1022155 TGACAACTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (48 bp):
GGTTTAATATATCTTGATCATTAAACCGTTAATTTCTGTTAATTTGAC
Found at i:1022249 original size:16 final size:16
Alignment explanation
Indices: 1022221--1022261 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1022211 GTACATATGT
1022221 ATTGT-AAATATATCA
1 ATTGTCAAATATATCA
1022236 GATTGTCAAA-ATATCA
1 -ATTGTCAAATATATCA
1022252 ATTGTACAAA
1 ATTGT-CAAA
1022262 GAATTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 3 0.13
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (16 bp):
ATTGTCAAATATATCA
Found at i:1025750 original size:21 final size:21
Alignment explanation
Indices: 1025721--1025768 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1025711 GTCCTCATCC
*
1025721 GAGTAGGACTGACTACC-CTTG
1 GAGTTGGACTGAC-ACCTCTTG
1025742 GAGTTGGACTGACACCTCTTG
1 GAGTTGGACTGACACCTCTTG
*
1025763 AAGTTG
1 GAGTTG
1025769 AACTAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (21 bp):
GAGTTGGACTGACACCTCTTG
Found at i:1025864 original size:105 final size:105
Alignment explanation
Indices: 1025671--1025899 Score: 347
Period size: 105 Copynumber: 2.2 Consensus size: 105
1025661 CAAAACTGAG
* *
1025671 AACTGACA-TTGAGCTATGGGATTGACTCGATGAGGTGGATGTCCTCATCCGAGTAGGACTGACT
1 AACTGA-AGTTGAGCTATGGAACTGACTCGATGAGGTGGATGTCCTCATCCGAGTAGGACTGACT
* *
1025735 ACCCTTGGAGTTGGACTGACACCTCTTGAAGTTGAA-CTAA
65 ACCCTTGGAGTTGGACTGAAACCTCTTGAAGTTGAACCGAA
1025775 AACCTGAAGTTGAGCTATGGAACTGACTCGATGAGGTGGATG-CTCTCATCCGAGTAGGACTGAC
1 AA-CTGAAGTTGAGCTATGGAACTGACTCGATGAGGTGGATGTC-CTCATCCGAGTAGGACTGAC
* *
1025839 TACCCTTGGAGTTGGACTGAAACCTCTTGAATTTGAACCGAG
64 TACCCTTGGAGTTGGACTGAAACCTCTTGAAGTTGAACCGAA
*
1025881 AACTGAAGATGAGCTATGG
1 AACTGAAGTTGAGCTATGG
1025900 GATCGACTAT
Statistics
Matches: 114, Mismatches: 7, Indels: 7
0.89 0.05 0.05
Matches are distributed among these distances:
104 4 0.04
105 106 0.93
106 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (105 bp):
AACTGAAGTTGAGCTATGGAACTGACTCGATGAGGTGGATGTCCTCATCCGAGTAGGACTGACTA
CCCTTGGAGTTGGACTGAAACCTCTTGAAGTTGAACCGAA
Found at i:1025867 original size:21 final size:21
Alignment explanation
Indices: 1025826--1025867 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1025816 GCTCTCATCC
*
1025826 GAGTAGGACTGACTACCCTTG
1 GAGTAGGACTGACAACCCTTG
*
1025847 GAGTTGGACTGA-AACCTCTTG
1 GAGTAGGACTGACAACC-CTTG
1025868 AATTTGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
GAGTAGGACTGACAACCCTTG
Found at i:1026049 original size:84 final size:84
Alignment explanation
Indices: 1025922--1026101 Score: 245
Period size: 84 Copynumber: 2.1 Consensus size: 84
1025912 GTTTTTCTTA
** * * *
1025922 ATGAGGTGGATGTCCTCGTCCGAGTTGGACTAAGTACTCTTGGAGTTGAGCTGAGG-ACTGAAGT
1 ATGAGGTGGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGTTGAACTG-GGAACTGAAGT
** **
1025986 TGAGCTATGGGATTGACTTG
65 TGAGAGATGGGATTGACAAG
* *
1026006 ATGAGGTGGATGTCCTCACCCGAATTGGACTAACTACTTTTGGAGTTGAACTGGGAATTGAAGTT
1 ATGAGGTGGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGTTGAACTGGGAACTGAAGTT
1026071 GAGAGATGGGATTGACAAG
66 GAGAGATGGGATTGACAAG
1026090 ATGAGGTGGATG
1 ATGAGGTGGATG
1026102 ATGAGGCGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
83 2 0.02
84 82 0.98
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.28
Consensus pattern (84 bp):
ATGAGGTGGATGTCCTCACCCGAATTGGACTAACTACTCTTGGAGTTGAACTGGGAACTGAAGTT
GAGAGATGGGATTGACAAG
Found at i:1026300 original size:33 final size:33
Alignment explanation
Indices: 1026263--1026330 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
1026253 GAGAATTGAA
*
1026263 GTTGAGTTATGGGATTGACTGAAAGAGGTGGAT
1 GTTGAGCTATGGGATTGACTGAAAGAGGTGGAT
* * *
1026296 GTTGAGCTATGGGATTGATTGGATGAGGTGGAT
1 GTTGAGCTATGGGATTGACTGAAAGAGGTGGAT
1026329 GT
1 GT
1026331 CCTCATCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.41, T:0.32
Consensus pattern (33 bp):
GTTGAGCTATGGGATTGACTGAAAGAGGTGGAT
Found at i:1026414 original size:117 final size:117
Alignment explanation
Indices: 1026179--1026399 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 117
1026169 TAACTTTGTA
** * *
1026179 GTTGAGCTATGGGATTGACTTTCTGAGCTGGATGCCCTCATCCGAGTAGGACTGACTACTATTGG
1 GTTGAGCTATGGGATTGACTTGATGAGCTGGATGCCCTCATCCGAGTAGGACTGACAACCATTGG
* * * *
1026244 AGTTGAACTGAGAATTGAAGTTGAGTTATGGGATTGACTGAAAGAGGTGGAT
66 AGTTGAACTGAGAACTGAAGTTGAGCTATAGGATAGACTGAAAGAGGTGGAT
* * * *
1026296 GTTGAGCTATGGGATTGA-TTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCTTG
1 GTTGAGCTATGGGATTGACTT-GATGAGCTGGATGCCCTCATCCGAGTAGGACTGACAACCATTG
* * *
1026360 GAGTTGAATTGATAACTGATGTTGAGCTATAGGATAGACT
65 GAGTTGAACTGAGAACTGAAGTTGAGCTATAGGATAGACT
1026400 TGATGTGGTG
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 2 0.02
117 86 0.98
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.30
Consensus pattern (117 bp):
GTTGAGCTATGGGATTGACTTGATGAGCTGGATGCCCTCATCCGAGTAGGACTGACAACCATTGG
AGTTGAACTGAGAACTGAAGTTGAGCTATAGGATAGACTGAAAGAGGTGGAT
Found at i:1026434 original size:84 final size:84
Alignment explanation
Indices: 1026293--1026449 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
1026283 GAAAGAGGTG
* *
1026293 GATGTTGAGCTATGGGATTGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCT
1 GATGTTGAGCTATAGGATAGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCT
1026358 TGGAGTTGAATTGATAACT
66 TGGAGTTGAATTGATAACT
* *
1026377 GATGTTGAGCTATAGGATAGACTT-GATGTGGTGGATGTCC-CA-CTCGTAGTTGGACTGACTAC
1 GATGTTGAGCTATAGGATAGA-TTGGATGAGGTGGATGTCCTCATC-CG-AGTTGGACTGACAAC
1026439 CCTTGGAGTTG
63 CCTTGGAGTTG
1026450 GACTGACTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
82 1 0.02
83 4 0.06
84 59 0.89
85 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.31
Consensus pattern (84 bp):
GATGTTGAGCTATAGGATAGATTGGATGAGGTGGATGTCCTCATCCGAGTTGGACTGACAACCCT
TGGAGTTGAATTGATAACT
Found at i:1026474 original size:21 final size:21
Alignment explanation
Indices: 1026424--1026493 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
1026414 TCCCACTCGT
* *
1026424 AGTTGGACTGACTACCCTTGG
1 AGTTGGACTGACTCCCCTTGA
1026445 AGTTGGACTGACTCCCCTTGA
1 AGTTGGACTGACTCCCCTTGA
* * *
1026466 AGTAT-GACTGGCTCCTCTTGC
1 AGT-TGGACTGACTCCCCTTGA
1026487 AGTTGGA
1 AGTTGGA
1026494 GTTGGACTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (21 bp):
AGTTGGACTGACTCCCCTTGA
Found at i:1026509 original size:27 final size:27
Alignment explanation
Indices: 1026471--1026710 Score: 176
Period size: 27 Copynumber: 9.6 Consensus size: 27
1026461 CTTGAAGTAT
1026471 GACTGGCTCCTCTTGCAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
1026498 GACTGGCTCCTCTTGCAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* * *
1026525 GACTGACTCCCCTTGAAG-T--A--T-
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
*
1026546 GACCGGCTCCTCTTGCAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* * * *
1026573 GACTGACTCCCCTTGAAG-T--A-CT-
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* *
1026595 -ACTGACTTCTCTTGCAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* *
1026621 GACTGAG-TCCCCTTGAAG-T--A--T-
1 GACTG-GCTCCTCTTGCAGTTGGAGTTG
*
1026642 GACTGGATCCTCTTGCAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* * *
1026669 GACTGGATTCTCTTACAGTTGGAGTTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTG
* *
1026696 GACTGACTCCCCTTG
1 GACTGGCTCCTCTTG
1026711 AAGTAAGACT
Statistics
Matches: 164, Mismatches: 29, Indels: 40
0.70 0.12 0.17
Matches are distributed among these distances:
20 1 0.01
21 42 0.26
22 5 0.03
23 1 0.01
24 6 0.04
25 1 0.01
26 5 0.03
27 103 0.63
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (27 bp):
GACTGGCTCCTCTTGCAGTTGGAGTTG
Found at i:1026541 original size:75 final size:75
Alignment explanation
Indices: 1026441--1026587 Score: 267
Period size: 75 Copynumber: 2.0 Consensus size: 75
1026431 CTGACTACCC
* *
1026441 TTGGAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTGGAGTTGGACTGGCT
1 TTGGAGTTGGACTGACTCCCCTTGAAGTATGACCGGCTCCTCTTGCAGTTGGAGTTGGACTGACT
*
1026506 CCTCTTGCAG
66 CCCCTTGCAG
1026516 TTGGAGTTGGACTGACTCCCCTTGAAGTATGACCGGCTCCTCTTGCAGTTGGAGTTGGACTGACT
1 TTGGAGTTGGACTGACTCCCCTTGAAGTATGACCGGCTCCTCTTGCAGTTGGAGTTGGACTGACT
1026581 CCCCTTG
66 CCCCTTG
1026588 AAGTACTACT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (75 bp):
TTGGAGTTGGACTGACTCCCCTTGAAGTATGACCGGCTCCTCTTGCAGTTGGAGTTGGACTGACT
CCCCTTGCAG
Found at i:1026573 original size:48 final size:48
Alignment explanation
Indices: 1026498--1026673 Score: 291
Period size: 48 Copynumber: 3.7 Consensus size: 48
1026488 GTTGGAGTTG
1026498 GACTGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTAT
1 GACTGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTAT
*
1026546 GACCGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTACT
1 GACTGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTA-T
* * *
1026595 -ACTGACTTCTCTTGCAGTTGGAGTTGGACTGAGTCCCCTTGAAGTAT
1 GACTGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTAT
*
1026642 GACTGGATCCTCTTGCAGTTGGAGTTGGACTG
1 GACTGGCTCCTCTTGCAGTTGGAGTTGGACTG
1026674 GATTCTCTTA
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 116 0.98
49 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (48 bp):
GACTGGCTCCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTAT
Found at i:1026682 original size:123 final size:121
Alignment explanation
Indices: 1026441--1026736 Score: 341
Period size: 123 Copynumber: 2.4 Consensus size: 121
1026431 CTGACTACCC
1026441 TTGGAGTTGGACTGACTCCCCTTGAAGTATGACTGGCTCCTCTTGCAGTTGGAGTTGGACTGGCT
1 TTGGAGTTGGACTGACTCCCCTTGAAGTAT-ACTGGCTCCTCTTGCAGTTGGAGTTGGACTGGCT
* * * * * *
1026506 CCTCTTGCAGTTGGAGTTGGACTGACTCCCCTTGAAGTATGACCGGCTCCTCTTGCAG
65 CCCCTTGAAGTTGGAGCTGGACT-ACTCCACTTGAAGTATGACCGGATCCTCTTACAG
* *
1026564 TTGGAGTTGGACTGACTCCCCTTGAAGTACTACTGACTTCTCTTGCAGTTGGAGTTGGACTGAG-
1 TTGGAGTTGGACTGACTCCCCTTGAAGTA-TACTGGCTCCTCTTGCAGTTGGAGTTGGACTG-GC
* * * * *
1026628 TCCCCTTGAAGTAT-GA-CTGGATCCT-CTTGCAGTTGGAGT-TGGACTGGATTCTCTTACAG
64 TCCCCTTGAAGT-TGGAGCTGGA--CTAC-TCCACTTGAAGTAT-GACCGGATCCTCTTACAG
*
1026687 TTGGAGTTGGACTGACTCCCCTTGAAGTAAGACTGGCTCCTCTTGCAGTT
1 TTGGAGTTGGACTGACTCCCCTTGAAGT-ATACTGGCTCCTCTTGCAGTT
1026737 TTAGTGGAAG
Statistics
Matches: 149, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
122 6 0.04
123 137 0.92
124 6 0.04
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.32
Consensus pattern (121 bp):
TTGGAGTTGGACTGACTCCCCTTGAAGTATACTGGCTCCTCTTGCAGTTGGAGTTGGACTGGCTC
CCCTTGAAGTTGGAGCTGGACTACTCCACTTGAAGTATGACCGGATCCTCTTACAG
Found at i:1031315 original size:23 final size:22
Alignment explanation
Indices: 1031285--1031359 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
1031275 ACTAATGGAT
1031285 GTAAACGAACATAATAAACGAAC
1 GTAAACGAACA-AATAAACGAAC
* *
1031308 GTAAACGAATACAAATGAACGAAT
1 GTAAACG-A-ACAAATAAACGAAC
* *
1031332 GTAAACAAACACAATAAATGAAC
1 GTAAACGAACA-AATAAACGAAC
*
1031355 ATAAA
1 GTAAA
1031360 TAAACGTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 3 0.07
23 20 0.48
24 16 0.38
25 3 0.07
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (22 bp):
GTAAACGAACAAATAAACGAAC
Found at i:1031335 original size:24 final size:23
Alignment explanation
Indices: 1031283--1031349 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
1031273 AAACTAATGG
1031283 ATGTAAACGAACATAATAAACGA
1 ATGTAAACGAACATAATAAACGA
* *
1031306 ACGTAAACGAATACA-AATGAACGA
1 ATGTAAACG-A-ACATAATAAACGA
* *
1031330 ATGTAAACAAACACAATAAA
1 ATGTAAACGAACATAATAAA
1031350 TGAACATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 3 0.08
23 14 0.39
24 16 0.44
25 3 0.08
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (23 bp):
ATGTAAACGAACATAATAAACGA
Found at i:1031593 original size:20 final size:20
Alignment explanation
Indices: 1031570--1031608 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1031560 ATGAATGCAT
1031570 ATAAACGAACATAAACAAAC
1 ATAAACGAACATAAACAAAC
* *
1031590 ATAAATGAATATAAACAAA
1 ATAAACGAACATAAACAAA
1031609 ATTATTACTG
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:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAACGAACATAAACAAAC
Found at i:1036670 original size:6 final size:6
Alignment explanation
Indices: 1036655--1036915 Score: 504
Period size: 6 Copynumber: 43.5 Consensus size: 6
1036645 ACACACCCAG
* *
1036655 GTGTAT GTGTAC GTGTAT GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1036703 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1036751 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1036799 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1036847 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1 GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC GTGTAC
1036895 GTGTAC GTGTAC GTGTAC GTG
1 GTGTAC GTGTAC GTGTAC GTG
1036916 CATGAAGCTA
Statistics
Matches: 252, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 252 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (6 bp):
GTGTAC
Found at i:1038196 original size:126 final size:126
Alignment explanation
Indices: 1038027--1038259 Score: 303
Period size: 128 Copynumber: 1.8 Consensus size: 126
1038017 AAAGGAAAAA
* * * *
1038027 AAGCAATTGAGCGTTGGAAAGAGAAATAAACAGCCAATAACTCTTCC-AAAGCTGTTAA-AGAAC
1 AAGCAAATGAGCGTTGGAAAGAGAAATAAACAGCCAACAACTCTTCCAAAAACCGTTAACAGAAC
* * *
1038090 TA-CGATTTAGACATGCATCATGTATCTCGATGTCTGTGTTTACATAGGTGAGAATGTCTTC
66 -AGCGATTTAGACATGCATAATGTAGCTCAATGTCTGTGTTTACATAGGTGAGAATGTCTTC
*
1038151 AAGCAAATGAG-GATTGGAAAGAAAGAAATGAACAGCCAACAACTCTTCCAAAAACCGTTAACAG
1 AAGCAAATGAGCG-TTGGAAAG--AGAAATAAACAGCCAACAACTCTTCCAAAAACCGTTAACAG
* * *
1038215 AACAGTGTTTTAGACATGCATAATGTGGCTCAATGTCTGTGTTTA
63 AACAGCGATTTAGACATGCATAATGTAGCTCAATGTCTGTGTTTA
1038260 ATCCAACAAC
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
123 1 0.01
124 18 0.20
126 24 0.26
127 10 0.11
128 39 0.42
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (126 bp):
AAGCAAATGAGCGTTGGAAAGAGAAATAAACAGCCAACAACTCTTCCAAAAACCGTTAACAGAAC
AGCGATTTAGACATGCATAATGTAGCTCAATGTCTGTGTTTACATAGGTGAGAATGTCTTC
Found at i:1038315 original size:75 final size:75
Alignment explanation
Indices: 1038186--1038335 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
1038176 AAATGAACAG
*
1038186 CCAACAACTCTTCCAAAAACCGTTAACAGAACAGTGTTTTAGACATGCATAATGTGGCTCAATGT
1 CCAACAACTCTTCCAAAAACCGTTAACAGAACAGTGTTTTAGACATGCAAAATGTGG-TCAATGT
1038251 CTGTGTTTAAT
65 CTGTGTTTAAT
*
1038262 CCAACAACTCTTCC-AAAACCGTTAACAGCACAGTGTTTTAGACATGCAAAATGTGGTCAATGTC
1 CCAACAACTCTTCCAAAAACCGTTAACAGAACAGTGTTTTAGACATGCAAAATGTGGTCAATGTC
1038326 TGTGTTTAAT
66 TGTGTTTAAT
1038336 TATCATTAGA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 18 0.25
75 40 0.56
76 14 0.19
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (75 bp):
CCAACAACTCTTCCAAAAACCGTTAACAGAACAGTGTTTTAGACATGCAAAATGTGGTCAATGTC
TGTGTTTAAT
Found at i:1044835 original size:30 final size:30
Alignment explanation
Indices: 1044799--1044866 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1044789 TGAGTCATGT
1044799 GTTGATGGAG-AAGCACATGGTGGAACACAC
1 GTTGATGGAGCAAGCAC-TGGTGGAACACAC
* *
1044829 GTTGATGGAGCAGGCACTGGTGGAACGCAC
1 GTTGATGGAGCAAGCACTGGTGGAACACAC
1044859 GTTGATGG
1 GTTGATGG
1044867 GACTTGCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.26, C:0.16, G:0.38, T:0.19
Consensus pattern (30 bp):
GTTGATGGAGCAAGCACTGGTGGAACACAC
Found at i:1055629 original size:2 final size:2
Alignment explanation
Indices: 1055622--1055667 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1055612 CCTGATCAAG
1055622 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
1055664 AT AT
1 AT AT
1055668 TCATACTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1056975 original size:22 final size:21
Alignment explanation
Indices: 1056950--1057008 Score: 59
Period size: 25 Copynumber: 2.7 Consensus size: 21
1056940 ATTAAATACA
1056950 ATAAATAATATTATTATTTATC
1 ATAAATAATATTATTATTT-TC
*
1056972 ATAAAACTTAATATTATTATTTTT
1 AT-AAA--TAATATTATTATTTTC
1056996 A-AAATAAT-TTATT
1 ATAAATAATATTATT
1057009 TATTATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
22 5 0.15
23 3 0.09
24 2 0.06
25 14 0.42
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAATAATATTATTATTTTC
Found at i:1057011 original size:20 final size:20
Alignment explanation
Indices: 1056988--1057031 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1056978 CTTAATATTA
*
1056988 TTATTTTTAAAATAATTTAT
1 TTATTATTAAAATAATTTAT
* *
1057008 TTATTATTAAAATATTTTTT
1 TTATTATTAAAATAATTTAT
1057028 TTAT
1 TTAT
1057032 AATTTTATTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTAAAATAATTTAT
Found at i:1057096 original size:31 final size:29
Alignment explanation
Indices: 1057028--1057097 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
1057018 AATATTTTTT
*
1057028 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
1057058 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
1057091 TTATATT
1 TTATATT
1057098 AATTATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:1057172 original size:23 final size:21
Alignment explanation
Indices: 1057124--1057172 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1057114 AATAGTGTTA
1057124 TATTATATTTTTAAAAATATT
1 TATTATATTTTTAAAAATATT
* * *
1057145 AATTAGTATATTTTAAATATCTT
1 TATTA-TAT-TTTTAAAAATATT
1057168 TATTA
1 TATTA
1057173 AAATATTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATATTTTTAAAAATATT
Found at i:1057385 original size:22 final size:23
Alignment explanation
Indices: 1057357--1057403 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1057347 TTGATTATTT
1057357 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1057379 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1057402 TA
1 TA
1057404 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1057408 original size:22 final size:22
Alignment explanation
Indices: 1057365--1057408 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1057355 TTTATTATAA
*
1057365 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1057387 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1057409 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1057433 original size:53 final size:53
Alignment explanation
Indices: 1057325--1057474 Score: 134
Period size: 53 Copynumber: 2.9 Consensus size: 53
1057315 ATAAGATCTT
* ** *
1057325 ATATTATATTATTATAATATAATTGATTATTTTATTATAATATTAAAAATATA
1 ATATTATATTATTAAAATATAATAAATTATTTTATAATAATATTAAAAATATA
* *
1057378 ATATTATATTATTAGAAATATTAATAAATATATTTTA-AAT-ATTTTAATAAT-TA
1 ATATTATATTATTA-AAATA-TAATAAAT-TATTTTATAATAATATTAAAAATATA
* * *
1057431 ATATT-T-TGATTAAAATGATATTAAAATATTTTAT--TAATATTAAA
1 ATATTATATTATTAAAAT-ATAATAAATTATTTTATAATAATATTAAA
1057475 TTTATAAAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
48 1 0.01
49 13 0.16
50 10 0.12
51 6 0.08
52 1 0.01
53 21 0.26
54 13 0.16
55 8 0.10
56 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (53 bp):
ATATTATATTATTAAAATATAATAAATTATTTTATAATAATATTAAAAATATA
Found at i:1057898 original size:2 final size:2
Alignment explanation
Indices: 1057891--1057923 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1057881 GATTTTTGCT
*
1057891 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1057924 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1066122 original size:65 final size:63
Alignment explanation
Indices: 1066003--1066212 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
1065993 TTTTTCAGAG
* * *
1066003 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGT
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
1066065 ATT
61 ATT
* *
1066068 TCATGCATCGATGCACATACCATGCA-CTGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACA-ACCATGCATC-GATGCACTCAGGATATTT-TG-AAACATCGAATGCA
1066131 TT
62 TT
* * * * *
1066133 TGATTCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
1066197 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1066213 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.37
65 66 0.54
66 6 0.05
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1066227 original size:19 final size:19
Alignment explanation
Indices: 1066200--1066270 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
1066190 ATGCACTTGA
*
1066200 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1066219 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1066238 TGCACCGATGCACTCTTAG
1 TGCACCGATGCACTCTTAG
1066257 TGCACCGATGCACT
1 TGCACCGATGCACT
1066271 AAGGATCCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (19 bp):
TGCACCGATGCACTCTTAG
Found at i:1074871 original size:315 final size:312
Alignment explanation
Indices: 1074230--1074879 Score: 930
Period size: 316 Copynumber: 2.1 Consensus size: 312
1074220 GGGATGACAA
* * * * *
1074230 ATATAAAATAGGATATAAAATATTAAAATAAAGGCTTTTCTAAGTCAAAACTGAGTGTGATTTTT
1 ATATAAAATAGGGTATAAAATAATAAAATAAAGGCTTTTCTAAGTCAAAACTGAGTGAGATATTC
* *
1074295 TTTTTAATAATTTGGGTAAGTACATGACGTTATTATCTGTTTAAAGATAGTTCTCAAATTTTAAT
66 TTTTTAATAATATGGGTAAGTACATGACGTTATTATCTGTTTAAAGATAGCTCTCAAATTTTAAT
* * * * **
1074360 ATTGATCGCACACCTCATTAATATTTATAGTGTTCGAATCTGAATCTTTAAGAAATAATAACAAT
131 ATTGATCGCACACATCACTAATATCTATAATGTTCGAATCTGAATCTCAAAGAAATAATAACAAT
* ** * * *
1074425 TCATTTACTACAGAAATCACTTTGATTTGTGCGAGTGTGGAAATAGTTTAAATATATAAAATAGG
196 TCATTTACTACAGAAATCACTTTAATTCATGCGACTGTAGAAATAGTTCAAATATATAAAATAGG
1074490 TATAAAATAAAGACTTTTCTAAGTCAAAACTGAGTGTGGAAATAATTTAAAT
261 TATAAAATAAAGACTTTTCTAAGTCAAAACTGAGTGTGGAAATAATTTAAAT
* *
1074542 ATATAAAGTAGGGTATAAAATAATAAAGTAAAAGGCTTTTCTAAGTCAAAACTGAGTGAGAAATA
1 ATATAAAATAGGGTATAAAATAATAAAAT-AAAGGCTTTTCTAAGTCAAAACTGAGTGAG--ATA
* * *
1074607 TTCTTTTTAATAATATGGGTAATTACATGATGTTATTATCTGTTTAAAGATAGCTCTTAATATTT
63 TTCTTTTTAATAATATGGGTAAGTACATGACGTTATTATCTGTTTAAAGATAGCTCTCAA-ATTT
* * ** * *
1074672 TGATATTGATTGTTCACATCACT-GTCATCTATAATGTTTGAATCTGAACTCTCAAAG-AATAAT
127 TAATATTGATCGCACACATCACTAAT-ATCTATAATGTTCGAATCTGAA-TCTCAAAGAAATAAT
1074735 AACAATTCATTTACTAC-GAAAGTCACTTTAATTCATGCGACTGTAGAAATAGTTCAAATATATA
190 AACAATTCATTTACTACAGAAA-TCACTTTAATTCATGCGACTGTAGAAATAGTTCAAATATATA
*
1074799 AAATAGGTATAAAATAAAGACTTTT-TAAGTCAAAACTGAGTGTGGAAATAGTTTAAAT
254 AAATAGGTATAAAATAAAGACTTTTCTAAGTCAAAACTGAGTGTGGAAATAATTTAAAT
1074857 ATATAAAATAGGGTATAAAATAA
1 ATATAAAATAGGGTATAAAATAA
1074880 AGAGAAAATC
Statistics
Matches: 299, Mismatches: 32, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
312 25 0.08
313 29 0.10
315 115 0.38
316 124 0.41
317 6 0.02
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (312 bp):
ATATAAAATAGGGTATAAAATAATAAAATAAAGGCTTTTCTAAGTCAAAACTGAGTGAGATATTC
TTTTTAATAATATGGGTAAGTACATGACGTTATTATCTGTTTAAAGATAGCTCTCAAATTTTAAT
ATTGATCGCACACATCACTAATATCTATAATGTTCGAATCTGAATCTCAAAGAAATAATAACAAT
TCATTTACTACAGAAATCACTTTAATTCATGCGACTGTAGAAATAGTTCAAATATATAAAATAGG
TATAAAATAAAGACTTTTCTAAGTCAAAACTGAGTGTGGAAATAATTTAAAT
Found at i:1075047 original size:21 final size:20
Alignment explanation
Indices: 1075021--1075118 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1075011 ATCAGTTTCC
1075021 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
1075042 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
1075061 ACAAATTCGCATTGCGATTTTA
1 A-AAA-TCGCAACGCGATTTTG
* *
1075083 AATAATCGCAACGCGAATATG
1 AA-AATCGCAACGCGATTTTG
1075104 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1075119 ACACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 17 0.28
21 39 0.65
22 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:1075111 original size:20 final size:20
Alignment explanation
Indices: 1075086--1075396 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
1075076 GATTTTAAAT
* *
1075086 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1075106 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1075126 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1075146 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
1075166 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
1075186 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1075206 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1075226 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1075247 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1075267 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1075287 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1075307 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
1075327 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1075347 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
1075367 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1075387 AATCGCAACG
1 AATCGCAACG
1075397 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1075131 original size:40 final size:40
Alignment explanation
Indices: 1075086--1075475 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
1075076 GATTTTAAAT
* ** * * *
1075086 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
1075126 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
1075166 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1075206 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
1075247 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
1075287 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
1075327 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
1075367 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
1075407 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
1075447 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
1075476 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:1075403 original size:20 final size:19
Alignment explanation
Indices: 1075124--1075475 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
1075114 CGCGAACACA
1075124 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1075144 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
1075164 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
1075184 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1075204 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
1075224 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
1075244 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
1075265 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
1075285 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1075305 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
1075325 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1075345 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
1075365 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
1075385 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1075405 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1075425 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
1075445 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
1075465 TAAATCACAAC
1 TAAATCGCAAC
1075476 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:1076197 original size:24 final size:24
Alignment explanation
Indices: 1076158--1076204 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1076148 AAATTTGGTC
1076158 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1076182 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1076205 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1076396 original size:12 final size:12
Alignment explanation
Indices: 1076379--1076403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1076369 ATATAATCCT
1076379 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1076391 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1076403 G
1 G
1076404 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1078708 original size:19 final size:19
Alignment explanation
Indices: 1078686--1078959 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1078676 CGGAAAATAC
*
1078686 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078705 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1078719 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1078739 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1078753 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078772 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078791 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1078805 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078824 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078843 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
1078862 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078881 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078900 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1078914 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078933 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1078952 AATCGCAA
1 AATCGCAA
1078960 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 147 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1078888 original size:109 final size:105
Alignment explanation
Indices: 1078714--1078981 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
1078704 AAATCCCAAC
1078714 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
1078778 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1078819 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
1078884 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1078928 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
1078982 TATAAACGCA
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 32 0.21
105 16 0.10
106 4 0.03
107 5 0.03
108 1 0.01
109 97 0.63
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1078997 original size:52 final size:52
Alignment explanation
Indices: 1078714--1078981 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
1078704 AAATCCCAAC
1078714 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1078767 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1078819 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
1078876 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1078928 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1078980 AT
1 AT
1078982 TATAAACGCA
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 134 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 46 0.22
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1079078 original size:19 final size:19
Alignment explanation
Indices: 1078988--1079070 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
1078978 AAATTATAAA
1078988 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1079007 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1079027 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1079043 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1079060 CGCATTGCGAT
1 CGCATTGCGAT
1079071 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1079196 original size:14 final size:14
Alignment explanation
Indices: 1079177--1079213 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1079167 CATCAATTAC
1079177 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1079191 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1079205 ACAAATCAA
1 ACAAATCAA
1079214 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1081149 original size:19 final size:19
Alignment explanation
Indices: 1081109--1081237 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1081099 TAGTTTACTT
* *
1081109 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1081129 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1081148 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1081167 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1081181 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1081200 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1081214 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1081233 TCGCA
1 TCGCA
1081238 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:1081188 original size:33 final size:32
Alignment explanation
Indices: 1081145--1081237 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1081135 CGCGAAACCA
**
1081145 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1081177 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1081210 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1081238 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:1081235 original size:52 final size:52
Alignment explanation
Indices: 1081109--1081237 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1081099 TAGTTTACTT
**
1081109 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1081161 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1081214 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1081238 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:1081255 original size:19 final size:19
Alignment explanation
Indices: 1081233--1081367 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1081223 GAAACCAAAA
*
1081233 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1081252 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1081268 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1081285 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1081301 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1081318 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1081337 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1081357 TCGTGTTGCGA
1 TCGCGTTGCGA
1081368 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1081274 original size:14 final size:14
Alignment explanation
Indices: 1081255--1081311 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1081245 TTTCATTTCG
1081255 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1081269 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1081286 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1081302 CGTTGCGATT
1 CGTTGCGATT
1081312 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1081280 original size:33 final size:33
Alignment explanation
Indices: 1081238--1081330 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1081228 CAAAATCGCA
*
1081238 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1081271 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1081304 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1081331 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1081581 original size:92 final size:93
Alignment explanation
Indices: 1081411--1081789 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
1081401 TTGAATGGAT
1081411 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1081476 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1081504 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1081568 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1081596 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1081660 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1081688 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1081753 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1081781 AAATTTACT
1 AAATTTACT
1081790 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1081740 original size:185 final size:185
Alignment explanation
Indices: 1081411--1081789 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
1081401 TTGAATGGAT
1081411 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1081476 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1081541 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1081596 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1081660 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1081725 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1081781 AAATTTACT
1 AAATTTACT
1081790 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1083513 original size:14 final size:14
Alignment explanation
Indices: 1083494--1083583 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1083484 TTGAAATGAA
1083494 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1083508 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1083525 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1083541 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1083560 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1083574 AATCGCAACG
1 AATCGCAACG
1083584 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1083531 original size:33 final size:33
Alignment explanation
Indices: 1083486--1083600 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1083476 TCTTTTGGTT
1083486 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1083519 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1083552 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1083585 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1083601 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1083532 original size:19 final size:18
Alignment explanation
Indices: 1083493--1083605 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1083483 GTTGAAATGA
1083493 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1083508 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1083525 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1083541 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1083558 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1083574 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1083591 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1083606 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1083649 original size:33 final size:33
Alignment explanation
Indices: 1083601--1083671 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1083591 AAAATCGCAA
** *
1083601 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTATCGT
1083634 TGCGATTTTCATTTCGCGTTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTATCGT
1083667 TGCGA
1 TGCGA
1083672 CAGTCATTCT
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:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTATCGT
Found at i:1083679 original size:33 final size:33
Alignment explanation
Indices: 1083612--1083693 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
1083602 GCGATTTTGG
* ***
1083612 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGACAGTCA
1083645 TTTCGCGTTGCGATTCTATCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTATCGTTGCGACAGTCA
*
1083678 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1083694 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTATCGTTGCGACAGTCA
Found at i:1083698 original size:20 final size:20
Alignment explanation
Indices: 1083624--1083712 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
1083614 TCGCGTTGCG
1083624 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1083644 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
* ***
1083657 ATTCTATCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1083677 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1083697 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1083713 CTCTTCTGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
13 3 0.06
14 8 0.15
19 9 0.17
20 20 0.38
21 13 0.25
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1083834 original size:33 final size:33
Alignment explanation
Indices: 1083792--1083862 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1083782 AATACTAACT
*
1083792 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1083825 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1083858 TGAAA
1 TGAAA
1083863 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1084096 original size:22 final size:22
Alignment explanation
Indices: 1084044--1084098 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1084034 TGGTTGTGAG
**
1084044 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1084066 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1084088 GGATTTCTTCG
1 GGATTTCTTCG
1084099 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1084270 original size:20 final size:20
Alignment explanation
Indices: 1084245--1084437 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1084235 CTTTAAATAT
1084245 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1084265 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1084287 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1084306 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1084326 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1084346 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1084366 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1084386 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1084406 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1084426 CGCGTTGCGATT
1 CGCGTTGCGATT
1084438 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1084432 original size:60 final size:60
Alignment explanation
Indices: 1084245--1084437 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1084235 CTTTAAATAT
**
1084245 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1084306 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1084366 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1084426 CGCGTTGCGATT
1 CGCGTTGCGATT
1084438 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1085227 original size:18 final size:20
Alignment explanation
Indices: 1085188--1085227 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1085178 AACTTTGGTT
*
1085188 ATCGGTTAATTTAGTTCGAA
1 ATCGGTTAATTTAGTCCGAA
1085208 ATCGGTTAA-TTAG-CCGAA
1 ATCGGTTAATTTAGTCCGAA
1085226 AT
1 AT
1085228 TATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
ATCGGTTAATTTAGTCCGAA
Found at i:1086176 original size:2 final size:2
Alignment explanation
Indices: 1086169--1086198 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1086159 TTTGATATTA
1086169 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
1086199 TTATTTAACT
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:1086947 original size:15 final size:15
Alignment explanation
Indices: 1086925--1086974 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1086915 CTTTATTTAG
1086925 TCGTATATTAAACTA
1 TCGTATATTAAACTA
* *
1086940 TTGTATATTAAACTG
1 TCGTATATTAAACTA
* *
1086955 TCCTATATTAAACTG
1 TCGTATATTAAACTA
1086970 TCGTA
1 TCGTA
1086975 AGAACTACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (15 bp):
TCGTATATTAAACTA
Found at i:1087085 original size:3 final size:3
Alignment explanation
Indices: 1087077--1087126 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1087067 CAACATAAAC
1087077 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1087125 TA
1 TA
1087127 AATAATGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1087715 original size:31 final size:32
Alignment explanation
Indices: 1087674--1087757 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 32
1087664 CATATCTAAA
* *
1087674 GTTTACTTTTTGTTTCATTTTAATACC-CGGT
1 GTTTAATTTTTGTTTCATTTTAATACCTCAGT
* *
1087705 GTTTATTTTTTGTTTCA-TTTAATACCTCATT
1 GTTTAATTTTTGTTTCATTTTAATACCTCAGT
* *
1087736 GTTAAATTTTTGTTTTATTTTA
1 GTTTAATTTTTGTTTCATTTTA
1087758 GTATCTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.20
31 32 0.71
32 4 0.09
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.61
Consensus pattern (32 bp):
GTTTAATTTTTGTTTCATTTTAATACCTCAGT
Found at i:1087935 original size:20 final size:21
Alignment explanation
Indices: 1087863--1087924 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
1087853 GAACCGAATC
* *
1087863 AAACACATTTCACCCGAGACA
1 AAACAAATGTCACCCGAGACA
1087884 AAACAAATGTCACCCGAGACA
1 AAACAAATGTCACCCGAGACA
1087905 AAACAAATGTCACCCGAGAC
1 AAACAAATGTCACCCGAGAC
1087925 GAACACATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.45, C:0.31, G:0.13, T:0.11
Consensus pattern (21 bp):
AAACAAATGTCACCCGAGACA
Found at i:1097277 original size:13 final size:13
Alignment explanation
Indices: 1097259--1097285 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1097249 GCAAGACTGG
1097259 TGGTCAAAGGATA
1 TGGTCAAAGGATA
1097272 TGGTCAAAGGATA
1 TGGTCAAAGGATA
1097285 T
1 T
1097286 ACTTAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (13 bp):
TGGTCAAAGGATA
Found at i:1102349 original size:65 final size:63
Alignment explanation
Indices: 1102233--1102439 Score: 229
Period size: 65 Copynumber: 3.2 Consensus size: 63
1102223 ATTTGAGGTG
* * * * *
1102233 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
1102297 C
63 C
* *
1102298 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
1102363 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
1102427 ATGCATCGATGCA
1 ATGCACCGATGCA
1102440 CACTTGGTGC
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 37 0.30
65 84 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:1102458 original size:64 final size:65
Alignment explanation
Indices: 1102280--1102443 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
1102270 GAATTAATTG
* * ** *
1102280 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
1102345 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
1102409 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
1102444 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:1108251 original size:20 final size:21
Alignment explanation
Indices: 1108222--1108277 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1108212 TTTGTGCTTC
*
1108222 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1108242 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1108264 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1108278 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1109846 original size:21 final size:21
Alignment explanation
Indices: 1109804--1109847 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1109794 ACCCTGGGAG
*
1109804 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1109825 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1109846 CT
1 CT
1109848 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1110774 original size:65 final size:64
Alignment explanation
Indices: 1110705--1110886 Score: 172
Period size: 65 Copynumber: 2.8 Consensus size: 64
1110695 TGCATCAACC
* * * ****
1110705 ATGCATTAGTGAATTAATTGAAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCG
1 ATGCATTAGTGAATT-ATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCG
* * * *
1110770 ATGCACT-CTGAATATTTTCAAAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATC
1 ATGCATTAGTGAAT-TATT-AAAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATC
1110834 G
64 G
* * *
1110835 ATGCACTCAG-GCTATT-TTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 ATGCA-TTAGTG-AATTATTAAAACATCGAATGCATTTCATGCATCGATGCACA
1110887 CTTGGTGCAC
Statistics
Matches: 95, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
64 39 0.41
65 52 0.55
66 2 0.02
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
ATGCATTAGTGAATTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCG
Found at i:1110903 original size:64 final size:65
Alignment explanation
Indices: 1110725--1110888 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 65
1110715 GAATTAATTG
* * ** *
1110725 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* ** **
1110790 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
1110854 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
1110889 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:1125009 original size:12 final size:14
Alignment explanation
Indices: 1124992--1125023 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1124982 TACTAAAATT
1124992 TATTTTA-TC-TTA
1 TATTTTATTCATTA
1125004 TATTTTATTCATTA
1 TATTTTATTCATTA
1125018 TATTTT
1 TATTTT
1125024 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 2 0.11
14 9 0.50
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTTTATTCATTA
Found at i:1130827 original size:21 final size:21
Alignment explanation
Indices: 1130801--1130868 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
1130791 CTTGAAATTT
*
1130801 TTTAAAATTTGAATTTTCTTC
1 TTTAAAATTAGAATTTTCTTC
*
1130822 TTTAAAA-TCGAAATTTTCTTC
1 TTTAAAATTAG-AATTTTCTTC
* *
1130843 TTTAAAATCAAAATTTTCTTC
1 TTTAAAATTAGAATTTTCTTC
*
1130864 ATTAA
1 TTTAA
1130869 TGTATGTGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.95
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTAAAATTAGAATTTTCTTC
Found at i:1130901 original size:22 final size:23
Alignment explanation
Indices: 1130871--1130914 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1130861 TTCATTAATG
*
1130871 TATGTGTGTCTACCCTGAAATTC
1 TATGTGTGTCCACCCTGAAATTC
*
1130894 TATG-GTGTCCGCCCTGAAATT
1 TATGTGTGTCCACCCTGAAATT
1130915 TTATTGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (23 bp):
TATGTGTGTCCACCCTGAAATTC
Found at i:1132439 original size:34 final size:35
Alignment explanation
Indices: 1132372--1132454 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
1132362 ATTTTTAATA
* * *
1132372 TATATATTTAATTTTTTGGTAATTTTATTTAATTT
1 TATATTTTTAATTTTTTGGTAATTTGATATAATTT
1132407 T-TAATTTTTAATTTTTTGG-ATATTTGA-ATAATTT
1 TAT-ATTTTTAATTTTTTGGTA-ATTTGATATAATTT
*
1132441 TATATTTATAATTT
1 TATATTTTTAATTT
1132455 AAATAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
34 19 0.46
35 22 0.54
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (35 bp):
TATATTTTTAATTTTTTGGTAATTTGATATAATTT
Found at i:1138665 original size:23 final size:23
Alignment explanation
Indices: 1138611--1138665 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1138601 TAAGCTACCA
1138611 AAAGGCAAAGATAAACGTAACAC
1 AAAGGCAAAGATAAACGTAACAC
** *
1138634 AAAAACAAAGATAAACG-AGACAT
1 AAAGGCAAAGATAAACGTA-ACAC
1138657 AAAGGCAAA
1 AAAGGCAAA
1138666 AAAATGTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.62, C:0.15, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAGGCAAAGATAAACGTAACAC
Found at i:1139178 original size:21 final size:21
Alignment explanation
Indices: 1139152--1139199 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1139142 CCGATCTCGA
*
1139152 AACATCAGTCGGGATGATTAG
1 AACATCAGTCGAGATGATTAG
1139173 AACATCAGTCGAGATGATTAG
1 AACATCAGTCGAGATGATTAG
1139194 AACATC
1 AACATC
1139200 CGGTGAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
AACATCAGTCGAGATGATTAG
Found at i:1140394 original size:2 final size:2
Alignment explanation
Indices: 1140389--1140417 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1140379 TAAAAAATGA
1140389 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 A
1140418 ACAAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1142771 original size:39 final size:39
Alignment explanation
Indices: 1142692--1142774 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
1142682 ATTTGATAAA
** ** *
1142692 TAATTTTAACGGTAAAGTGACATATTATGTTTTTTTTTT
1 TAATTTTAACGGTAAAGTGACATATTATGAATAATATTT
*
1142731 TAATTTTAACGGTAAAGTGATATATTTAT-AATAATATTT
1 TAATTTTAACGGTAAAGTGACATA-TTATGAATAATATTT
1142770 TAATT
1 TAATT
1142775 AAATATTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 33 0.89
40 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (39 bp):
TAATTTTAACGGTAAAGTGACATATTATGAATAATATTT
Found at i:1143118 original size:23 final size:23
Alignment explanation
Indices: 1143092--1143135 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1143082 AGCTCCTCAA
1143092 CATCATGTTCC-CGCTCTTTTTGT
1 CATCATGTTCCTCG-TCTTTTTGT
* *
1143115 CATCCTTTTCCTCGTCTTTTT
1 CATCATGTTCCTCGTCTTTTT
1143136 CTTGCCACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.07, C:0.32, G:0.09, T:0.52
Consensus pattern (23 bp):
CATCATGTTCCTCGTCTTTTTGT
Found at i:1162426 original size:33 final size:34
Alignment explanation
Indices: 1162367--1162463 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1162357 AAATGTTTTT
*
1162367 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1162401 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1162434 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1162464 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1162470 original size:34 final size:33
Alignment explanation
Indices: 1162365--1162470 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1162355 ATAAATGTTT
*
1162365 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1162399 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1162431 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1162466 TTAAA
1 TTAAA
1162471 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1163155 original size:125 final size:126
Alignment explanation
Indices: 1162848--1163199 Score: 679
Period size: 125 Copynumber: 2.8 Consensus size: 126
1162838 TTTAAGTTAT
1162848 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1162913 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1162974 TCCCCGAGGGACATGAGTGACATAATAGGGCAATAATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1163039 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATA-GTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
1163099 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1163164 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
1163200 CCGATTATAG
Statistics
Matches: 223, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
125 117 0.52
126 106 0.48
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (126 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:1163280 original size:8 final size:8
Alignment explanation
Indices: 1163267--1163307 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1163257 TCACAATCTT
1163267 TCAAATTC
1 TCAAATTC
1163275 TCAAATTC
1 TCAAATTC
* *
1163283 CCAAACTC
1 TCAAATTC
1163291 T-AAATTC
1 TCAAATTC
1163298 TCAAATTC
1 TCAAATTC
1163306 TC
1 TC
1163308 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1166311 original size:13 final size:12
Alignment explanation
Indices: 1166293--1166331 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1166283 TACATAAATA
1166293 TATTTAATATAAT
1 TATTTAATAT-AT
1166306 TATTTAATATA-
1 TATTTAATATAT
1166317 TATTTAATATTAT
1 TATTTAATA-TAT
1166330 TA
1 TA
1166332 GTTATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 3 0.12
13 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:1166322 original size:11 final size:11
Alignment explanation
Indices: 1166290--1166330 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1166280 AAATACATAA
1166290 ATATATTTAAT
1 ATATATTTAAT
1166301 ATAATTATTTAAT
1 AT-A-TATTTAAT
1166314 ATATATTTAAT
1 ATATATTTAAT
1166325 AT-TATT
1 ATATATT
1166331 AGTTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 12 0.43
12 2 0.07
13 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:1168063 original size:61 final size:61
Alignment explanation
Indices: 1167941--1168072 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
1167931 GGATGACTAC
* * *
1167941 TTTGTAACTTTTAATATTTGAGGGACTTAACAAAGTAATATTCTATAGTCGAAGAATCATT
1 TTTGTAACTTTTAATATATGAGGGACTTAACAAAGTAATACTCTATAGTCGAAGAACCATT
* * *
1168002 TTTGTAACTTTTAATAGTATGA-GGACTTAATAAA-TCATTACTCTATAGTTG-AGAGACCATT
1 TTTGTAACTTTTAATA-TATGAGGGACTTAACAAAGT-AATACTCTATAGTCGAAGA-ACCATT
*
1168063 TATGT-ACTTT
1 TTTGTAACTTT
1168073 ACCCTATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
60 9 0.15
61 48 0.79
62 4 0.07
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (61 bp):
TTTGTAACTTTTAATATATGAGGGACTTAACAAAGTAATACTCTATAGTCGAAGAACCATT
Found at i:1169245 original size:23 final size:24
Alignment explanation
Indices: 1169219--1169263 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1169209 CATTCTTAAC
*
1169219 TTAAATTCACATATT-ATATTATA
1 TTAAATTAACATATTAATATTATA
* *
1169242 TTAAGTTAACATCTTAATATTA
1 TTAAATTAACATATTAATATTA
1169264 AAAATATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (24 bp):
TTAAATTAACATATTAATATTATA
Found at i:1169371 original size:43 final size:43
Alignment explanation
Indices: 1169264--1169437 Score: 233
Period size: 43 Copynumber: 4.0 Consensus size: 43
1169254 CTTAATATTA
** * *
1169264 AAAATATATATATTATTTTTATCTTAATTTTAAAAT-ATTATAAGAA
1 AAAATATAT-T-TTATTTTTATCTTAATTTTAATTTAACT-TAA-AT
* *
1169310 AAAATATGTTTTATTTTTATCTTAATTTTGATTTAACTTAAAT
1 AAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAAAT
*
1169353 AAAATATATTTTATTTTTATCTTAATTTTGATTTAACTTAAAT
1 AAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAAAT
*
1169396 AAAATACATTTTATTTTTATCTTAATTTTAATTTAACTTAAA
1 AAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAAA
1169438 AATATAATTT
Statistics
Matches: 118, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
43 83 0.70
44 24 0.20
45 3 0.03
46 8 0.07
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (43 bp):
AAAATATATTTTATTTTTATCTTAATTTTAATTTAACTTAAAT
Found at i:1169568 original size:38 final size:38
Alignment explanation
Indices: 1169474--1169739 Score: 172
Period size: 46 Copynumber: 6.7 Consensus size: 38
1169464 AAATATTTAT
*
1169474 TTTTAATCTTATAATATTTTAAAA-TAAAAATAAATATA
1 TTTTATTCTTATAATA-TTTAAAATTAAAAATAAATATA
** * * *
1169512 TTTT-TAAATTA-AATTATTTAAAATTTAAGATAAATGTA
1 TTTTAT-TCTTATAA-TATTTAAAATTAAAAATAAATATA
***
1169550 TTTTATTCTTATAATATTTAAAATTGCTAATAAA-ATA
1 TTTTATTCTTATAATATTTAAAATTAAAAATAAATATA
** **
1169587 -AATATAT-TTA-AAT-TTTAGGA-TAAAAATAAAATATA
1 TTTTAT-TCTTATAATATTTAAAATTAAAAAT-AAATATA
1169622 TTTTATTCTTATAATATTTTAAAATTTAGGATAAAAATAAAATATA
1 TTTTATTCTTATAATA-TTTAAAA--T----TAAAAAT-AAATATA
1169668 TTTTATTCTTATAATATTTTAAAATTTAGGATAAAAATAAATATA
1 TTTTATTCTTATAATA-TTTAAAA--T----TAAAAATAAATATA
1169713 TTTTATTCTTATAATATTTAAAATTAA
1 TTTTATTCTTATAATATTTAAAATTAA
1169740 TATAAAAATA
Statistics
Matches: 184, Mismatches: 24, Indels: 40
0.74 0.10 0.16
Matches are distributed among these distances:
33 4 0.02
34 8 0.04
35 7 0.04
36 12 0.07
37 15 0.08
38 46 0.25
39 8 0.04
42 1 0.01
44 7 0.04
45 23 0.12
46 53 0.29
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (38 bp):
TTTTATTCTTATAATATTTAAAATTAAAAATAAATATA
Found at i:1169625 original size:23 final size:23
Alignment explanation
Indices: 1169598--1169672 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
1169588 ATATATTTAA
1169598 ATTTTAGGATAAAAATAAAATAT
1 ATTTTAGGATAAAAATAAAATAT
*** * * *** *
1169621 ATTTTATTCTTATAATATTTTAA
1 ATTTTAGGATAAAAATAAAATAT
*
1169644 AATTTAGGATAAAAATAAAATAT
1 ATTTTAGGATAAAAATAAAATAT
1169667 ATTTTA
1 ATTTTA
1169673 TTCTTATAAT
Statistics
Matches: 32, Mismatches: 20, Indels: 0
0.62 0.38 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (23 bp):
ATTTTAGGATAAAAATAAAATAT
Found at i:1169683 original size:23 final size:23
Alignment explanation
Indices: 1169611--1169683 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
1169601 TTAGGATAAA
1169611 AATAAAATATATTTTATTCTTAT
1 AATAAAATATATTTTATTCTTAT
*** * * *** * *
1169634 AATATTTTAAAATTTAGGATAAA
1 AATAAAATATATTTTATTCTTAT
1169657 AATAAAATATATTTTATTCTTAT
1 AATAAAATATATTTTATTCTTAT
1169680 AATA
1 AATA
1169684 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 20, Indels: 0
0.60 0.40 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (23 bp):
AATAAAATATATTTTATTCTTAT
Found at i:1169685 original size:91 final size:89
Alignment explanation
Indices: 1169587--1169760 Score: 285
Period size: 89 Copynumber: 1.9 Consensus size: 89
1169577 TAATAAAATA
* *
1169587 AATATATTTAAATTTTAGGATAAAAATAAAATATATTTTATTCTTATAATATTTTAAAATTTAGG
1 AATAT-TTTAAAATTTAGGATAAAAAT-AAATATATTTTATTCTTATAATA-TTTAAAA-TTAAG
1169652 ATAAAAATAAAATATATTTTATTCTTAT
62 ATAAAAATAAAATATATTTTATTCTTAT
*
1169680 AATATTTTAAAATTTAGGATAAAAATAAATATATTTTATTCTTATAATATTTAAAATTAATATAA
1 AATATTTTAAAATTTAGGATAAAAATAAATATATTTTATTCTTATAATATTTAAAATTAAGATAA
1169745 AAATAAAATATATTTT
66 AAATAAAATATATTTT
1169761 TAATGTTAAG
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
89 23 0.29
90 7 0.09
91 23 0.29
92 20 0.26
93 5 0.06
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (89 bp):
AATATTTTAAAATTTAGGATAAAAATAAATATATTTTATTCTTATAATATTTAAAATTAAGATAA
AAATAAAATATATTTTATTCTTAT
Found at i:1169695 original size:23 final size:23
Alignment explanation
Indices: 1169623--1169695 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
1169613 TAAAATATAT
1169623 TTTATTCTTATAATATTTTAAAA
1 TTTATTCTTATAATATTTTAAAA
*** * * *** * *
1169646 TTTAGGATAAAAATAAAATATAT
1 TTTATTCTTATAATATTTTAAAA
1169669 TTTATTCTTATAATATTTTAAAA
1 TTTATTCTTATAATATTTTAAAA
1169692 TTTA
1 TTTA
1169696 GGATAAAAAT
Statistics
Matches: 30, Mismatches: 20, Indels: 0
0.60 0.40 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTATTCTTATAATATTTTAAAA
Found at i:1169706 original size:23 final size:23
Alignment explanation
Indices: 1169634--1169706 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
1169624 TTATTCTTAT
1169634 AATATTTTAAAATTTAGGATAAA
1 AATATTTTAAAATTTAGGATAAA
*** * * *** * *
1169657 AATAAAATATATTTTATTCTTAT
1 AATATTTTAAAATTTAGGATAAA
1169680 AATATTTTAAAATTTAGGATAAA
1 AATATTTTAAAATTTAGGATAAA
1169703 AATA
1 AATA
1169707 AATATATTTT
Statistics
Matches: 30, Mismatches: 20, Indels: 0
0.60 0.40 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.42
Consensus pattern (23 bp):
AATATTTTAAAATTTAGGATAAA
Found at i:1169762 original size:45 final size:46
Alignment explanation
Indices: 1169587--1169760 Score: 291
Period size: 46 Copynumber: 3.8 Consensus size: 46
1169577 TAATAAAATA
*
1169587 AATATATTTAAATTTTAGGATAAAAATAAAATATATTTTATTCTTAT
1 AATAT-TTTAAAATTTAGGATAAAAATAAAATATATTTTATTCTTAT
1169634 AATATTTTAAAATTTAGGATAAAAATAAAATATATTTTATTCTTAT
1 AATATTTTAAAATTTAGGATAAAAATAAAATATATTTTATTCTTAT
1169680 AATATTTTAAAATTTAGGATAAAAAT-AAATATATTTTATTCTTAT
1 AATATTTTAAAATTTAGGATAAAAATAAAATATATTTTATTCTTAT
**
1169725 AATA-TTTAAAA-TTAATATAAAAATAAAATATATTTT
1 AATATTTTAAAATTTAGGATAAAAATAAAATATATTTT
1169761 TAATGTTAAG
Statistics
Matches: 123, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
43 11 0.09
44 18 0.15
45 23 0.19
46 66 0.54
47 5 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (46 bp):
AATATTTTAAAATTTAGGATAAAAATAAAATATATTTTATTCTTAT
Found at i:1172383 original size:29 final size:29
Alignment explanation
Indices: 1172341--1172399 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1172331 ATTTTCACCT
1172341 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
*
1172370 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
1172399 A
1 A
1172400 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:1177021 original size:29 final size:29
Alignment explanation
Indices: 1176979--1177037 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1176969 ATTTTCACCT
1176979 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1177008 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1177037 A
1 A
1177038 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1179506 original size:17 final size:17
Alignment explanation
Indices: 1179484--1179524 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1179474 TATTTTTTTT
*
1179484 AGACCCTTACTATTCCG
1 AGACCCTTACTATTACG
*
1179501 AGACCCTTACTATTATG
1 AGACCCTTACTATTACG
1179518 AGACCCT
1 AGACCCT
1179525 GTTCCATCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (17 bp):
AGACCCTTACTATTACG
Found at i:1216429 original size:31 final size:31
Alignment explanation
Indices: 1216391--1216546 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
1216381 CCCGAAGGAC
* * *
1216391 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1216422 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1216453 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1216484 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1216515 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1216546 C
1 C
1216547 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1217348 original size:21 final size:21
Alignment explanation
Indices: 1217318--1217362 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1217308 ATTCTGTCGT
* *
1217318 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1217339 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1217360 TTG
1 TTG
1217363 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1220400 original size:31 final size:31
Alignment explanation
Indices: 1220362--1220517 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
1220352 CCCGAAGGAC
* * *
1220362 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1220393 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1220424 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1220455 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1220486 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1220517 C
1 C
1220518 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1221319 original size:21 final size:21
Alignment explanation
Indices: 1221289--1221333 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1221279 ATTCTGTCGT
* *
1221289 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1221310 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1221331 TTG
1 TTG
1221334 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1233162 original size:35 final size:35
Alignment explanation
Indices: 1233116--1233189 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
1233106 CCAGAAAGTA
1233116 TGCTACTATCTATTAGGTCTACTTTCTTCTTTTTC
1 TGCTACTATCTATTAGGTCTACTTTCTTCTTTTTC
1233151 TGCTACTATCTATTAGGTCTACTTTCTTCTTTTTC
1 TGCTACTATCTATTAGGTCTACTTTCTTCTTTTTC
1233186 TGCT
1 TGCT
1233190 CTTTAATGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.14, C:0.23, G:0.09, T:0.54
Consensus pattern (35 bp):
TGCTACTATCTATTAGGTCTACTTTCTTCTTTTTC
Found at i:1238676 original size:24 final size:23
Alignment explanation
Indices: 1238627--1238677 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1238617 TATTCAACAC
*
1238627 ATAAATTTAATGTATAATGATAT
1 ATAAATTTAATGTATAATAATAT
1238650 ATAATATTATAATGTA-AATAATAT
1 ATAA-ATT-TAATGTATAATAATAT
1238674 ATAA
1 ATAA
1238678 CATATTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
ATAAATTTAATGTATAATAATAT
Found at i:1240745 original size:20 final size:20
Alignment explanation
Indices: 1240722--1240773 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1240712 AACGCGATCC
1240722 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1240742 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1240762 CCAAAATCGCAA
1 CCAGAATCGCAA
1240774 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:1240790 original size:21 final size:20
Alignment explanation
Indices: 1240763--1240861 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1240753 AATCAGTTTC
1240763 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1240784 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1240805 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1240825 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1240846 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1240862 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
Done.