Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:3333489 original size:109 final size:108
Alignment explanation
Indices: 3333189--3333558 Score: 398
Period size: 109 Copynumber: 3.4 Consensus size: 108
3333179 AGCATATTTT
*
3333189 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATG
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGAAAAT-
*
3333254 TTTCAAGTAATTAACCTATTTTATTATATAAGCGTTACCTATTAC
65 TTTC-AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTAC
* * ** * * **
3333299 ATTATATAAGCGATACCTAATATGTTAT-T--GTGCT---TGATAATGTT-TTAGTAATT-AACC
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAAT-ATGTTATT-GTGCTTGAA--
* * * * *
3333356 TATTTT-ATTATATAAACGCTACCTATTACATTATATAAACGCTACCTATTAC
62 AATTTTCAGTA-ATTAAC-CTA--T-TT-TATTATATAAGCGCTACCTATTAC
* *
3333408 ATTATATAAGCGCTATCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGAAAATT
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGAAAATT
3333473 TTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTAC
66 TT-CAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTAC
*
3333517 ATTATATAAGCGCTACCTATTACATTATATAAGTGCTACCTA
1 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTA
3333559 TTACATCATA
Statistics
Matches: 207, Mismatches: 33, Indels: 41
0.74 0.12 0.15
Matches are distributed among these distances:
103 3 0.01
104 11 0.05
105 15 0.07
106 2 0.01
107 5 0.02
108 2 0.01
109 106 0.51
110 27 0.13
111 1 0.00
112 3 0.01
113 8 0.04
114 14 0.07
115 10 0.05
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (108 bp):
ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGAAAATT
TTCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTAC
Found at i:3333508 original size:132 final size:132
Alignment explanation
Indices: 3333267--3333569 Score: 491
Period size: 132 Copynumber: 2.3 Consensus size: 132
3333257 CAAGTAATTA
** *
3333267 ACCTATTTTATTATATAAGCGTTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
* *
3333332 TTGATAATGTTTTAGTAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAACG
66 TTGAAAATGTTTCAGTAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAACG
3333397 CT
131 CT
* *
3333399 ACCTATTACATTATATAAGCGCTATCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGC
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
* *
3333464 TTGAAAAT-TTTCCAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGC
66 TTGAAAATGTTT-CAGTAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAAC
3333528 GCT
130 GCT
* *
3333531 ACCTATTACATTATATAAGTGCTACCTATTACATCATAT
1 ACCTATTACATTATATAAGCGCTACCTATTACATTATAT
3333570 TTTTACATGT
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 3 0.02
132 155 0.98
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (132 bp):
ACCTATTACATTATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTGC
TTGAAAATGTTTCAGTAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAACG
CT
Found at i:3333520 original size:23 final size:23
Alignment explanation
Indices: 3333485--3333569 Score: 134
Period size: 23 Copynumber: 3.7 Consensus size: 23
3333475 CCAGTAATTA
**
3333485 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
3333508 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
3333531 ACCTATTACATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
*
3333554 ACCTATTACATCATAT
1 ACCTATTACATTATAT
3333570 TTTTACATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:3340039 original size:41 final size:41
Alignment explanation
Indices: 3339967--3340044 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
3339957 TTAAAGGGTT
* *
3339967 AGTATCGATACTCATTTATAGAGTATCGATACCAGGGCAAG
1 AGTATCGATACTCATATATAGAGTATAGATACCAGGGCAAG
* *
3340008 AGTATCGATACTCCCTATATAG-GTATAGATACTAGGG
1 AGTATCGATACT-CATATATAGAGTATAGATACCAGGG
3340045 TATTTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 25 0.78
42 7 0.22
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (41 bp):
AGTATCGATACTCATATATAGAGTATAGATACCAGGGCAAG
Found at i:3353492 original size:20 final size:19
Alignment explanation
Indices: 3353467--3353552 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
3353457 TTTTGGTGCA
*
3353467 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
3353487 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
*
3353508 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATACCCCCT
*
3353529 -AGGGGAATCGATACCCCCT
1 GA-GGGAACCGATACCCCCT
3353548 GAGGG
1 GAGGG
3353553 TTCTGGTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.35
20 17 0.30
21 3 0.05
22 1 0.02
23 16 0.28
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:3353534 original size:19 final size:20
Alignment explanation
Indices: 3353469--3353552 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
3353459 TTGGTGCAGA
* *
3353469 GGGAATCGATACCCCCATGA-
1 GGGAACCGATTCCCCC-TGAG
3353489 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TG-AG
3353512 GGGAACCGATTCCCCCT-AG
1 GGGAACCGATTCCCCCTGAG
* *
3353531 GGGAATCGATACCCCCTGAG
1 GGGAACCGATTCCCCCTGAG
3353551 GG
1 GG
3353553 TTCTGGTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
19 17 0.31
20 18 0.33
21 3 0.05
22 1 0.02
23 16 0.29
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCTGAG
Found at i:3372841 original size:211 final size:212
Alignment explanation
Indices: 3372477--3372901 Score: 843
Period size: 211 Copynumber: 2.0 Consensus size: 212
3372467 AAGGTACGTC
3372477 CTTGAATAAGAGCCATTAAAAGCAATGAAGACAAATTGAAGACCATCCTCAAGTTCCTTCACAAG
1 CTTGAATAAGAGCCATTAAAAGCAATGAAGACAAATTGAAGACCATCCTCAAGTTCCTTCACAAG
3372542 AACATCTTCATACGATTTGGAGCACCTAGAGCCATTAAAAGAAATGAAGACACCCATTTTGAAAA
66 AACATCTTCATACGATTTGGAGCACCTAGAGCCATTAAAAGAAATGAAGACACCCATTTTGAAAA
3372607 CAAATTGATTGCTAAGGCTTTGCAAAGGTATGTGGTGTGACAT-AAATTGCTACAGCATATCACC
131 CAAATTGATTGCTAAGGCTTTGCAAAGGTATGTGGTGTGACATAAAATTGCTACAGCATATCACC
3372671 CTAGACCAATGGGTAGG
196 CTAGACCAATGGGTAGG
3372688 CTTGAATAAGAGCCATTAAAAGCAATGAAGACAAATTGAAGACCATCCTCAAGTTCCTTCACAAG
1 CTTGAATAAGAGCCATTAAAAGCAATGAAGACAAATTGAAGACCATCCTCAAGTTCCTTCACAAG
3372753 AACATCTTCATACGATTTGGAGCACCTAGAGCCATTAAAAGAAATGAAGACACCCATTTTGAAAA
66 AACATCTTCATACGATTTGGAGCACCTAGAGCCATTAAAAGAAATGAAGACACCCATTTTGAAAA
3372818 CAAATTGATTGCTAAGGCTTTGCAAAGGTATGTGGTGTGACATAAAATTGCTACAGCATATCACC
131 CAAATTGATTGCTAAGGCTTTGCAAAGGTATGTGGTGTGACATAAAATTGCTACAGCATATCACC
3372883 CTAGACCAATGGGTAGG
196 CTAGACCAATGGGTAGG
3372900 CT
1 CT
3372902 GAGGTGTCTA
Statistics
Matches: 213, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
211 173 0.81
212 40 0.19
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (212 bp):
CTTGAATAAGAGCCATTAAAAGCAATGAAGACAAATTGAAGACCATCCTCAAGTTCCTTCACAAG
AACATCTTCATACGATTTGGAGCACCTAGAGCCATTAAAAGAAATGAAGACACCCATTTTGAAAA
CAAATTGATTGCTAAGGCTTTGCAAAGGTATGTGGTGTGACATAAAATTGCTACAGCATATCACC
CTAGACCAATGGGTAGG
Found at i:3379501 original size:20 final size:20
Alignment explanation
Indices: 3379472--3379509 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3379462 CCCCTTCAAA
*
3379472 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
3379492 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3379510 TGCACAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:3387661 original size:48 final size:48
Alignment explanation
Indices: 3387556--3387702 Score: 203
Period size: 48 Copynumber: 3.1 Consensus size: 48
3387546 CATACTTTGT
**
3387556 GTATGATGGCTATCGATCG-ATTTGGTTTAATGCATAAGTTGCATTTT-
1 GTATGATGATTATCGATCGAATTT-GTTTAATGCATAAGTTGCATTTTC
*
3387603 GCATGATGATTATCGATCGAATTTGTTTAATGCATAAGTTGCATTTTC
1 GTATGATGATTATCGATCGAATTTGTTTAATGCATAAGTTGCATTTTC
*
3387651 GTATGATGATTATCGATCGATTTTGTTTAATGTCGAT--GTTGCATTTTC
1 GTATGATGATTATCGATCGAATTTGTTTAATG-C-ATAAGTTGCATTTTC
3387699 GTAT
1 GTAT
3387703 CAGTACTACA
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
47 39 0.43
48 49 0.54
49 1 0.01
50 2 0.02
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.44
Consensus pattern (48 bp):
GTATGATGATTATCGATCGAATTTGTTTAATGCATAAGTTGCATTTTC
Found at i:3394291 original size:48 final size:48
Alignment explanation
Indices: 3394150--3394276 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 48
3394140 ATACTTTGTT
* **
3394150 TATGATGGTTATTGATC-GATTTGTTTAATGCATAAGTTGCATTTTTG
1 TATGATGGTTATCGATCGGATTTGTTTAATGCATAAGTTGCATTTTCA
* *
3394197 TATGATGATTATCGATCGAATTTGTTTAATGCATAAGTTGCATTTTCA
1 TATGATGGTTATCGATCGGATTTGTTTAATGCATAAGTTGCATTTTCA
*
3394245 TATGATGGTTATCGATCGGTTTTGTTTAATGC
1 TATGATGGTTATCGATCGGATTTGTTTAATGC
3394277 CTATATTTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
47 15 0.21
48 56 0.79
ACGTcount: A:0.24, C:0.09, G:0.20, T:0.46
Consensus pattern (48 bp):
TATGATGGTTATCGATCGGATTTGTTTAATGCATAAGTTGCATTTTCA
Found at i:3402751 original size:45 final size:46
Alignment explanation
Indices: 3402662--3402752 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
3402652 TTTGAAAAAC
* *
3402662 CTGAGTGCATCGATGCATGGTCTTATGCATCAATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCAATGCATAAAATGCA
* *
3402708 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATGGTCATATGCATCAATGCATAAAATGCA
3402753 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 20 0.49
46 21 0.51
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATGGTCATATGCATCAATGCATAAAATGCA
Found at i:3403909 original size:10 final size:11
Alignment explanation
Indices: 3403893--3403918 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3403883 TTATCCGGAT
3403893 TTTTTTTTTTG
1 TTTTTTTTTTG
3403904 TTTTTTTTTTG
1 TTTTTTTTTTG
3403915 TTTT
1 TTTT
3403919 ATATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:3403976 original size:27 final size:27
Alignment explanation
Indices: 3403927--3403984 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 27
3403917 TTATATATAT
**
3403927 ATATATATTAATATGGTATTTTTTTTAAA
1 ATATATATTAATAT-G-ATAGTTTTTAAA
3403956 ATATATA-TAATAT-ATAGTTTTTAAA
1 ATATATATTAATATGATAGTTTTTAAA
3403981 ATAT
1 ATAT
3403985 TTTGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (27 bp):
ATATATATTAATATGATAGTTTTTAAA
Found at i:3403995 original size:25 final size:25
Alignment explanation
Indices: 3403948--3404009 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
3403938 TATGGTATTT
*
3403948 TTTTTAAAATATATATAATATATAG
1 TTTTTAAAATATATATAAAATATAG
*
3403973 TTTTTAAAATAT-TTTGAAAATATA-
1 TTTTTAAAATATATAT-AAAATATAG
* *
3403997 TATTTAATATATA
1 TTTTTAAAATATA
3404010 GTTTTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
TTTTTAAAATATATATAAAATATAG
Found at i:3404036 original size:2 final size:2
Alignment explanation
Indices: 3404029--3404060 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3404019 AACATTTTGA
3404029 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3404061 GTTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3404062 original size:51 final size:46
Alignment explanation
Indices: 3403992--3404096 Score: 140
Period size: 50 Copynumber: 2.2 Consensus size: 46
3403982 TATTTTGAAA
*
3403992 ATATATATTTAATATATAGTTTTTGAAAACATTTTGAATATATATATAT
1 ATATATATATAATATATAGTTTTTG-AAACATTTTGAA-ATAT-TATAT
*
3404041 ATATATATATATATAATATAGTTTTTGAAACATTTTGAAATCTTATAT
1 ATATATATATA-AT-ATATAGTTTTTGAAACATTTTGAAATATTATAT
3404089 A-ATATATA
1 ATATATATA
3404097 GTTTTTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
47 7 0.13
48 6 0.12
49 13 0.25
50 14 0.27
51 12 0.23
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (46 bp):
ATATATATATAATATATAGTTTTTGAAACATTTTGAAATATTATAT
Found at i:3404111 original size:87 final size:86
Alignment explanation
Indices: 3403956--3404131 Score: 248
Period size: 87 Copynumber: 2.0 Consensus size: 86
3403946 TTTTTTTAAA
* * *
3403956 ATATATATAATATATAGTTTTTAAAATATTTTGAAAATATATATTTAATATATAGTTTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAGTTTTTAAAAA
*
3404021 CATTTTGAATATATATATATAT
66 CATTTTGAAAATATATATA-AT
* *
3404043 ATATATATATATAATATAGTTTTTGAAACATTTTG-AAATCT-TATATAATATATAGTTTTTAAA
1 ATATATATA-AT-ATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAGTTTTTAAA
*
3404106 AACATTTTGAAAATGTATATAAT
64 AACATTTTGAAAATATATATAAT
3404129 ATA
1 ATA
3404132 ATTTTGAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
86 5 0.06
87 48 0.60
88 7 0.09
89 20 0.25
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (86 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATAATATATAGTTTTTAAAAA
CATTTTGAAAATATATATAAT
Found at i:3404115 original size:37 final size:36
Alignment explanation
Indices: 3404046--3404160 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 36
3404036 TATATATATA
* *
3404046 TATATATATAATATAGTTTTTGAAACATTTTG-AAATCT
1 TATATA-AT-ATATAGTTTTTAAAACATTTTGAAAAT-G
3404084 TATATAATATATAGTTTTTAAAAACATTTTGAAAATG
1 TATATAATATATAGTTTTT-AAAACATTTTGAAAATG
* * *
3404121 TATATAATATA-A-TTTTGAAAATATTTCTGAAAATA
1 TATATAATATATAGTTTTTAAAACATTT-TGAAAATG
3404156 TATAT
1 TATAT
3404161 TAGTTTTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.12
35 16 0.23
36 12 0.17
37 23 0.33
38 10 0.14
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATG
Found at i:3404152 original size:35 final size:35
Alignment explanation
Indices: 3404047--3404160 Score: 117
Period size: 35 Copynumber: 3.2 Consensus size: 35
3404037 ATATATATAT
*
3404047 ATATATATAATATAGTTTTTG-AAACATTTTG-AA
1 ATATATATAATATAGATTTTGAAAACATTTTGAAA
* * *
3404080 ATCTTATATAATATATAGTTTTTAAAAACATTTTGAAA
1 AT-ATATAT-A-ATATAGATTTTGAAAACATTTTGAAA
* *
3404118 ATGTATATAATATA-ATTTTGAAAATATTTCTGAAA
1 ATATATATAATATAGATTTTGAAAACATTT-TGAAA
3404153 ATATATAT
1 ATATATAT
3404161 TAGTTTTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
33 2 0.03
34 17 0.25
35 18 0.26
36 12 0.18
37 15 0.22
38 4 0.06
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATATATAATATAGATTTTGAAAACATTTTGAAA
Found at i:3404260 original size:7 final size:7
Alignment explanation
Indices: 3404248--3404290 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
3404238 TTTTAAAATG
3404248 TTTTTTA
1 TTTTTTA
3404255 TTTTTTA
1 TTTTTTA
3404262 TTTATTTCA
1 TTT-TTT-A
*
3404271 TTTGTTA
1 TTTTTTA
*
3404278 TTTGTTA
1 TTTTTTA
3404285 TTTTTT
1 TTTTTT
3404291 TCTTTTTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 23 0.72
8 5 0.16
9 4 0.12
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (7 bp):
TTTTTTA
Found at i:3405383 original size:14 final size:13
Alignment explanation
Indices: 3405355--3405397 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
3405345 TAATTTAACA
* *
3405355 TTTTTGTTTACTT
1 TTTTTCTTTAATT
3405368 TTTTT-TTTAATT
1 TTTTTCTTTAATT
3405380 TTTTTCTTTAATT
1 TTTTTCTTTAATT
3405393 TTTTT
1 TTTTT
3405398 TATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTAATT
Found at i:3405398 original size:14 final size:12
Alignment explanation
Indices: 3405355--3405407 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
3405345 TAATTTAACA
* *
3405355 TTTTTGTTTACT
1 TTTTTTTTTAAT
3405367 TTTTTTTTTAAT
1 TTTTTTTTTAAT
3405379 TTTTTTCTTTAAT
1 TTTTTT-TTTAAT
*
3405392 TTTTTTTAT-AT
1 TTTTTTTTTAAT
3405403 TTTTT
1 TTTTT
3405408 ATATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 7 0.19
12 18 0.49
13 12 0.32
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:3405418 original size:24 final size:23
Alignment explanation
Indices: 3405367--3405418 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
3405357 TTTGTTTACT
*
3405367 TTTTTTTTTAATTTTTTTCTTTA
1 TTTTTTTTTAATTTTTTTCATTA
*
3405390 ATTTTTTTTATATTTTTTAT-ATTA
1 TTTTTTTTTA-ATTTTTT-TCATTA
3405414 TTTTT
1 TTTTT
3405419 CCCTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.38
24 14 0.58
25 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTTTAATTTTTTTCATTA
Found at i:3405442 original size:11 final size:11
Alignment explanation
Indices: 3405369--3405468 Score: 55
Period size: 11 Copynumber: 8.5 Consensus size: 11
3405359 TGTTTACTTT
*
3405369 TTTTTTTAATTT
1 TTTTTTT-ATTA
*
3405381 TTTTCTTTAAT-
1 TTTT-TTTATTA
3405392 TTTTTTTA-TA
1 TTTTTTTATTA
3405402 TTTTTTATATTA
1 TTTTTT-TATTA
3405414 TTTTTCCCTTCAATTA
1 TTTTT---TT--ATTA
3405430 TTTTTTTATTA
1 TTTTTTTATTA
*
3405441 TTATTTTATT-
1 TTTTTTTATTA
3405451 TTTATGTTT-TTA
1 TTT-T-TTTATTA
3405463 TTTTTT
1 TTTTTT
3405469 ATCTAGAATT
Statistics
Matches: 73, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
9 1 0.01
10 14 0.19
11 23 0.32
12 19 0.26
13 5 0.07
14 1 0.01
15 1 0.01
16 9 0.12
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:3405455 original size:14 final size:14
Alignment explanation
Indices: 3405426--3405467 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
3405416 TTTCCCTTCA
3405426 ATTATTTT-TTTATT
1 ATTATTTTATTT-TT
3405440 ATTATTTTATTTTT
1 ATTATTTTATTTTT
3405454 ATGT-TTTTATTTTT
1 AT-TATTTTATTTTT
3405468 TATCTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (14 bp):
ATTATTTTATTTTT
Found at i:3405463 original size:19 final size:19
Alignment explanation
Indices: 3405427--3405466 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3405417 TTCCCTTCAA
*
3405427 TTATTTTTTTATTATTATT
1 TTATTTTTATATTATTATT
* *
3405446 TTATTTTTATGTTTTTATT
1 TTATTTTTATATTATTATT
3405465 TT
1 TT
3405467 TTATCTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (19 bp):
TTATTTTTATATTATTATT
Found at i:3405551 original size:13 final size:13
Alignment explanation
Indices: 3405533--3405562 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3405523 GAATCGGGTT
3405533 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
3405546 TTTTAATTTTTAA
1 TTTTAAATTTTAA
3405559 TTTT
1 TTTT
3405563 TTCAAAATTA
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:3406033 original size:2 final size:2
Alignment explanation
Indices: 3406026--3406106 Score: 128
Period size: 2 Copynumber: 40.5 Consensus size: 2
3406016 GGATTTCCTG
3406026 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
* *
3406068 AT A- AA AGG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3406107 AAAGGATTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.01
2 73 0.97
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3406175 original size:22 final size:22
Alignment explanation
Indices: 3406136--3406178 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3406126 TTATAATTTT
* * *
3406136 ATTTTATTTTTTAGATTATATA
1 ATTTTAATTTATAAATTATATA
3406158 ATTTTAATTTATAAATTATAT
1 ATTTTAATTTATAAATTATAT
3406179 TTCTATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTAATTTATAAATTATATA
Found at i:3408365 original size:65 final size:61
Alignment explanation
Indices: 3408276--3408396 Score: 156
Period size: 65 Copynumber: 1.9 Consensus size: 61
3408266 ATCACAATAT
*
3408276 TTTCTCAAAATAATAAATTATGACAAAT-TTATTTAGTTATAATAAAAATTTATAAAAAATATTA
1 TTTCTCAAAATAATAAATTATGACAAATAATATTT--TTATAAT--AAA-TTATAAAAAATATTA
3408340 A
61 A
*
3408341 TTTCTCAATATAA-AAATTTATGACAAATAATATTTTTATAATAAATTATAAAAAAT
1 TTTCTCAAAATAATAAA-TTATGACAAATAATATTTTTATAATAAATTATAAAAAAT
3408397 TTATTTAGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
61 11 0.21
62 3 0.06
64 10 0.19
65 23 0.44
66 5 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (61 bp):
TTTCTCAAAATAATAAATTATGACAAATAATATTTTTATAATAAATTATAAAAAATATTAA
Found at i:3408369 original size:33 final size:32
Alignment explanation
Indices: 3408276--3408375 Score: 89
Period size: 33 Copynumber: 3.1 Consensus size: 32
3408266 ATCACAATAT
*
3408276 TTTCTCAAAATAATAAA-TTATGACAAAT-TTA
1 TTTCTCAATATAA-AAATTTATGACAAATATTA
* * * *
3408307 TTTAGT-TATAATAAAAATTTATAAAAAATATTAA
1 TTT-CTCAAT-ATAAAAATTTATGACAAATATT-A
*
3408341 TTTCTCAATATAAAAATTTATGACAAATAATA
1 TTTCTCAATATAAAAATTTATGACAAATATTA
3408373 TTT
1 TTT
3408376 TTATAATAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
31 7 0.13
32 18 0.34
33 22 0.42
34 6 0.11
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (32 bp):
TTTCTCAATATAAAAATTTATGACAAATATTA
Found at i:3408530 original size:193 final size:193
Alignment explanation
Indices: 3408201--3408549 Score: 529
Period size: 193 Copynumber: 1.8 Consensus size: 193
3408191 ATTTAATATT
* * * * *
3408201 AATTTATTTATTCCCAATAATATATTAAATCTAGTCAAAATAAAAAATTATGTCAAATTTATTTA
1 AATTTATTTAGTCACAATAAAATATTAAATCTAATCAAAATAAAAAATTATGTCAAATATATTTA
* * *
3408266 ATCACAATATTTTCTCAAAATAATAAATTATGACAAATTTATTTAGTTATAATAAAAATTTATAA
66 ATCACAATAGTTTCTCAAAATAATAAATTATGACAAATTTATTTAATCATAATAAAAATTTATAA
3408331 AAAATATT-AATTTCTCAATATAAAAATTTATGACAAATAATATTTTTATAATAAATTATAAAA
131 AAAATATTAAATTT-TCAATATAAAAATTTATGACAAATAATATTTTTATAATAAATTATAAAA
* * *
3408394 AATTTATTTAGTCATAATAAAATATTAAATTTAATCAAAATTAAAAATTATGTCAAATATATTTA
1 AATTTATTTAGTCACAATAAAATATTAAATCTAATCAAAATAAAAAATTATGTCAAATATATTTA
* * *** *
3408459 GTCATAATAGTTTCTTGGAATAATAAATTATGACAAATTTATTTAATCATAATAACAATTTATAA
66 ATCACAATAGTTTCTCAAAATAATAAATTATGACAAATTTATTTAATCATAATAAAAATTTATAA
3408524 AAAATATTAAATTTTCAATATAAAAA
131 AAAATATTAAATTTTCAATATAAAAA
3408550 AATCATGACA
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
193 133 0.96
194 5 0.04
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (193 bp):
AATTTATTTAGTCACAATAAAATATTAAATCTAATCAAAATAAAAAATTATGTCAAATATATTTA
ATCACAATAGTTTCTCAAAATAATAAATTATGACAAATTTATTTAATCATAATAAAAATTTATAA
AAAATATTAAATTTTCAATATAAAAATTTATGACAAATAATATTTTTATAATAAATTATAAAA
Found at i:3418447 original size:20 final size:20
Alignment explanation
Indices: 3418422--3418466 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3418412 TGAGACCAAT
3418422 TGGTCTCCATA-CAGAAGGAA
1 TGGTCTCCATATC-GAAGGAA
* *
3418442 TGGTCTTCATATCGTAGGAA
1 TGGTCTCCATATCGAAGGAA
3418462 TGGTC
1 TGGTC
3418467 CCCACAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
TGGTCTCCATATCGAAGGAA
Found at i:3420368 original size:2 final size:2
Alignment explanation
Indices: 3420361--3420392 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3420351 AATTATGCTG
*
3420361 AT AT AT AT AT AT GT 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
3420393 CAAAGAGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3423184 original size:26 final size:23
Alignment explanation
Indices: 3423155--3423228 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
3423145 ATTAGCCTAT
3423155 ATATTTTTATATGATATTTTCTGAAA
1 ATATTTTTA-ATGA-ATTTTCT-AAA
*
3423181 ATATATTTGAATGAATTTTCTAAA
1 ATAT-TTTTAATGAATTTTCTAAA
* *
3423205 ATGATTTTTAAAGAATTATCTAAA
1 AT-ATTTTTAATGAATTTTCTAAA
3423229 TTTTAATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 21 0.50
25 9 0.21
26 8 0.19
27 4 0.10
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (23 bp):
ATATTTTTAATGAATTTTCTAAA
Found at i:3430649 original size:14 final size:14
Alignment explanation
Indices: 3430630--3430656 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3430620 TCAACGTCGG
3430630 TCAACGGTCAATGA
1 TCAACGGTCAATGA
3430644 TCAACGGTCAATG
1 TCAACGGTCAATG
3430657 GCTCGGCTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (14 bp):
TCAACGGTCAATGA
Found at i:3431712 original size:59 final size:59
Alignment explanation
Indices: 3431348--3431693 Score: 525
Period size: 59 Copynumber: 5.9 Consensus size: 59
3431338 ATTCAATAGA
* * * *
3431348 AAATTCATACAATTATTATGATTTCCATATCATTTTAGCACACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATATGG
* *
3431407 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTTCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATATGG
* *
3431466 AAATTCATACACTTAGTATGATTTCCTTA-CAATTTTAGCACACAAAGTGCCCTATTTGG
1 AAATTCATACACTTAGTATGATTTCCCTATC-ATTTTAGCACACAAAGTGCCCTATATGG
* *
3431525 AAATTCATACATTTAGTATGATTTCCCAATCATTTTAGCACACAAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATATGG
* * * *
3431584 AAATTCACACATTTAGTATGATTTCCTTA-CGATTTTAGCACACAAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATGATTTCCCTATC-ATTTTAGCACACAAAGTGCCCTATATGG
*
3431643 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGTACACAAAGTGCC
1 AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCC
3431694 ATTTGGTAAT
Statistics
Matches: 262, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
58 2 0.01
59 258 0.98
60 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATATGG
Found at i:3432052 original size:22 final size:20
Alignment explanation
Indices: 3432014--3432085 Score: 94
Period size: 22 Copynumber: 3.5 Consensus size: 20
3432004 TGGCCCTTCA
3432014 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
3432034 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
*
3432056 GTATCGATACCCCCTTCTA--
1 GTATCGATA-CCCCTACTATG
3432075 GTATCGATACC
1 GTATCGATACC
3432086 TAAATTAGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 2 0.04
19 9 0.19
20 10 0.21
21 7 0.15
22 19 0.40
23 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:3432159 original size:95 final size:95
Alignment explanation
Indices: 3432014--3432232 Score: 244
Period size: 95 Copynumber: 2.3 Consensus size: 95
3432004 TGGCCCTTCA
* * *
3432014 GTATCGATACCC-CTACTATGGTATCGATACTACCCTACTATGGTATCGATA-CCCCCTTCTAGT
1 GTATCGATACCCTC-ACCATGGTATCGATACTACCATACTATGGTACCGATATCCCCC-TCTAGT
* *
3432077 ATCGATACCTAAATTAGCTTCGATGTAGCCTG
64 ATCGATACCAAAATTAGCTCCGATGTAGCCTG
* * * * * *
3432109 GTATCGATACCCTCACCATAGTATTGATACTACTATGCTATGGTACCGATATCTCCCTCTGGTAT
1 GTATCGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATATCCCCCTCTAGTAT
* * ** *
3432174 TGATACCAAAATTAGGTCCGATGTTTCTTG
66 CGATACCAAAATTAGCTCCGATGTAGCCTG
* *
3432204 GTATCGATACTCTTACCATGGTATCGATA
1 GTATCGATACCCTCACCATGGTATCGATA
3432233 TTACATCATT
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 97 0.95
96 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (95 bp):
GTATCGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATATCCCCCTCTAGTAT
CGATACCAAAATTAGCTCCGATGTAGCCTG
Found at i:3438409 original size:59 final size:59
Alignment explanation
Indices: 3438316--3438650 Score: 490
Period size: 59 Copynumber: 5.7 Consensus size: 59
3438306 AAATTCAATA
* * * * *
3438316 GGAAATTCATACAATTATTATGATTTCCTTATCATTTTAGCATACGAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
* * * *
3438375 AGAAATTCACACACTTAATATGATTTCCCTATCATTTTAGCACACAAAATGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
* * * * *
3438434 GGAAATTCATACACATAGTATGATTTCCTTACCAGTTTAGCACACAAAGTGCCCTATTT
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
* *
3438493 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTATCACACAAGGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
* *
3438552 GGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCT
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
**
3438611 ATAAATTCATACACTTAGTATGATTTCCCTATCATTTTAG
1 GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAG
3438651 TACATACAGT
Statistics
Matches: 244, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 244 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGATTTCCCTATCATTTTAGCACACAAAGTGCCCTATCT
Found at i:3439028 original size:18 final size:20
Alignment explanation
Indices: 3438984--3439033 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3438974 CTGGCCCTTC
3438984 AGTATCGATACCCCTACTATG
1 AGTATCGATACCCCTA-TATG
3439005 -GTATCGATACCCCT-T-TG
1 AGTATCGATACCCCTATATG
*
3439022 AGTATCGTTACC
1 AGTATCGATACC
3439034 AAAATTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
20 14 0.52
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (20 bp):
AGTATCGATACCCCTATATG
Found at i:3448793 original size:21 final size:22
Alignment explanation
Indices: 3448755--3448795 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3448745 TTAAATATTA
**
3448755 TAAAGGTAGTACTGATACTCAC
1 TAAAGGTAGTACCAATACTCAC
3448777 TAAAGG-AGTACCAATACTC
1 TAAAGGTAGTACCAATACTC
3448796 TGGGGAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TAAAGGTAGTACCAATACTCAC
Found at i:3460171 original size:82 final size:82
Alignment explanation
Indices: 3460034--3460197 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
3460024 ATGGTCACAT
3460034 GGAACTTACTTGTCCTATAAAGAAAGGAAAACTTTGTAGAATTAGACAAGTATGAGTTCATAAAA
1 GGAACTTACTTGTCCTATAAAGAAAGGAAAACTTTGTAGAATTAGACAAGTATGAGTTCATAAAA
3460099 GAACAAGGGGTATTGAA
66 GAACAAGGGGTATTGAA
3460116 GGAACTTACTTGTCCTATAAAGAAAGGAAAACTTTGTAGAATTAGACAAGTATGAGTTCATAAAA
1 GGAACTTACTTGTCCTATAAAGAAAGGAAAACTTTGTAGAATTAGACAAGTATGAGTTCATAAAA
3460181 GAACAAGGGGTATTGAA
66 GAACAAGGGGTATTGAA
3460198 ACTAATTTTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.26
Consensus pattern (82 bp):
GGAACTTACTTGTCCTATAAAGAAAGGAAAACTTTGTAGAATTAGACAAGTATGAGTTCATAAAA
GAACAAGGGGTATTGAA
Found at i:3462276 original size:36 final size:36
Alignment explanation
Indices: 3462234--3462304 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3462224 CAAAACATTG
*
3462234 TAATTTGAGAATACGAGCAATAAAAGAACTTTTGAA
1 TAATTTGAGAATACAAGCAATAAAAGAACTTTTGAA
*
3462270 TAATTTGATAATACAAGCAATAAAAGAACTTTTGA
1 TAATTTGAGAATACAAGCAATAAAAGAACTTTTGA
3462305 CTAGAGGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (36 bp):
TAATTTGAGAATACAAGCAATAAAAGAACTTTTGAA
Found at i:3470765 original size:77 final size:76
Alignment explanation
Indices: 3470566--3470770 Score: 261
Period size: 75 Copynumber: 2.7 Consensus size: 76
3470556 GACCGTTGAA
* ** * *
3470566 CAGGGGGGAATCGGTACC-CCTGGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
**
3470630 ACAAAAATGTT
66 ACAAAAACATT
*
3470641 TAGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
1 CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
* * *
3470705 GCCAAACCATT
66 ACAAAAACATT
* * *
3470716 CAGGGGGGGAATTGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 CA-GGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTG
3470771 TAATTTTTGG
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
75 61 0.54
76 24 0.21
77 27 0.24
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (76 bp):
CAGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGA
ACAAAAACATT
Found at i:3475494 original size:23 final size:23
Alignment explanation
Indices: 3475464--3475516 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3475454 AATTAAATTG
3475464 CAATTAAGCT-TCTATAACGACTA
1 CAATTAAGCTGT-TATAACGACTA
* *
3475487 CAATTAAGCTGTTATAATGACTG
1 CAATTAAGCTGTTATAACGACTA
3475510 CAATTAA
1 CAATTAA
3475517 ACAAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (23 bp):
CAATTAAGCTGTTATAACGACTA
Found at i:3476320 original size:2 final size:2
Alignment explanation
Indices: 3476313--3476388 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
3476303 GTATCCCCTC
3476313 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
3476355 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
3476389 TAAAAAATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3480205 original size:19 final size:19
Alignment explanation
Indices: 3480181--3480246 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
3480171 TATGCATTGG
* * *
3480181 GCTATGAATTTGAAGTTTA
1 GCTATGAATATGAAATTAA
*
3480200 GCTATGAATCTGAAATTAA
1 GCTATGAATATGAAATTAA
*
3480219 GCTATGAATATGAAAATAA
1 GCTATGAATATGAAATTAA
*
3480238 GTTATGAAT
1 GCTATGAAT
3480247 CTCAGAATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (19 bp):
GCTATGAATATGAAATTAA
Found at i:3480299 original size:13 final size:13
Alignment explanation
Indices: 3480282--3480344 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
3480272 AATATTGGTT
*
3480282 ATGAAAATGAAAT
1 ATGAAAATGAAAA
* *
3480295 ATGAAAACG-AAC
1 ATGAAAATGAAAA
*
3480307 ATGAAAGTGAAAA
1 ATGAAAATGAAAA
3480320 ATGAAAATGAAAA
1 ATGAAAATGAAAA
3480333 ATGAAATATGAA
1 ATGAAA-ATGAA
3480345 CGTTCTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.21
13 28 0.67
14 5 0.12
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (13 bp):
ATGAAAATGAAAA
Found at i:3480300 original size:7 final size:6
Alignment explanation
Indices: 3480282--3480344 Score: 63
Period size: 6 Copynumber: 9.8 Consensus size: 6
3480272 AATATTGGTT
* * *
3480282 ATGAAA ATGAAA TATGAAA ACGAAC ATGAAA GTGAAAA ATGAAA ATGAAAA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATG-AAA ATGAAA ATG-AAA
3480333 ATGAAA TATGAA
1 ATGAAA -ATGAA
3480345 CGTTCTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
6 25 0.53
7 22 0.47
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAA
Found at i:3483942 original size:21 final size:21
Alignment explanation
Indices: 3483916--3483968 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3483906 AAATGCCTCA
* * *
3483916 GTATCAATACTGACCGTCCGG
1 GTATCAATACTAACCATCCAG
*
3483937 GTATCAACACTAACCATCCAG
1 GTATCAATACTAACCATCCAG
*
3483958 GTATCGATACT
1 GTATCAATACT
3483969 CCTTAAAGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
GTATCAATACTAACCATCCAG
Found at i:3488355 original size:2 final size:2
Alignment explanation
Indices: 3488348--3488385 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3488338 TATATCACCA
3488348 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
3488386 CCGCTTCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3495435 original size:2 final size:2
Alignment explanation
Indices: 3495428--3495456 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3495418 CATATCACCG
3495428 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3495457 GAGATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3495465 original size:2 final size:2
Alignment explanation
Indices: 3495460--3495533 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
3495450 ACACACAGAG
3495460 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
3495502 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
3495534 TCTGTTTCTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3500320 original size:45 final size:45
Alignment explanation
Indices: 3500213--3500321 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
3500203 AGATCGGTTT
**
3500213 CGCTGTCACTCA-GGAAATATCAGATCTAGGGATGAGTGATCTGTTC
1 CGCTGTCACTCATGG-AATATCAGATCTA-GGATGAGTGATCCATTC
* *
3500259 CGCT-TCTTCTGAATGGAATATCAGATCT-GGATGAGTTGATCCATTC
1 CGCTGTC-ACT-CATGGAATATCAGATCTAGGATGAG-TGATCCATTC
3500305 CGCTGTCACTCATGGAA
1 CGCTGTCACTCATGGAA
3500322 GATTGAATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
45 15 0.29
46 20 0.38
47 15 0.29
48 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (45 bp):
CGCTGTCACTCATGGAATATCAGATCTAGGATGAGTGATCCATTC
Found at i:3500686 original size:134 final size:134
Alignment explanation
Indices: 3500249--3500683 Score: 690
Period size: 134 Copynumber: 3.2 Consensus size: 134
3500239 TAGGGATGAG
* * *
3500249 TGATCTGTTCCGCTTCTTCTGAATGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAC
1 TGATTTGTTCCACTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAC
* *
3500314 TCATGGAAGATTGAATCATGGTAGACTTGTTTCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
66 TCAGGGAAGATTGAATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
3500379 AGAA
131 AGAA
* * *
3500383 TGATTTGTTCCGCATCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCTGCTGTCAC
1 TGATTTGTTCCACTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAC
* *
3500448 TCAGGGAAGATTGAATCCTGGTATACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
66 TCAGGGAAGATTGAATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
3500513 AGAA
131 AGAA
* * * *
3500517 TGATATGTTCCACTTCTTCTGAAGGGAATATCATATCTGGATGAGTTGATCCATTCCACTATCAC
1 TGATTTGTTCCACTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAC
* * * *
3500582 TCAGGGAAGATTGAATCATGGTAGATTTGTTCCGCTGTCACTCAGGGAACATCAAATCTTGAAAA
66 TCAGGGAAGATTGAATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
*
3500647 AGAG
131 AGAA
*
3500651 TGATTTGTTCCACTTCTTCTGAAGGAAATATCA
1 TGATTTGTTCCACTTCTTCTGAAGGGAATATCA
3500684 TATAGATGGA
Statistics
Matches: 277, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 277 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (134 bp):
TGATTTGTTCCACTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAC
TCAGGGAAGATTGAATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAG
AGAA
Found at i:3500818 original size:37 final size:37
Alignment explanation
Indices: 3500768--3500845 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
3500758 AGGCTTACTG
*
3500768 ATGGATTTGCTTCACAACTCTTCGGTGAAGGCTTAAA
1 ATGGATTTGCTTCACAACTCTTCAGTGAAGGCTTAAA
* * *
3500805 ATGGATTTTCTTCACTACTCTTCATTGAAGGCTTAAA
1 ATGGATTTGCTTCACAACTCTTCAGTGAAGGCTTAAA
3500842 ATGG
1 ATGG
3500846 CCCGGAGGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (37 bp):
ATGGATTTGCTTCACAACTCTTCAGTGAAGGCTTAAA
Found at i:3500893 original size:116 final size:116
Alignment explanation
Indices: 3500689--3500924 Score: 377
Period size: 116 Copynumber: 2.0 Consensus size: 116
3500679 TATCATATAG
* * *
3500689 ATGGATTTGCTTCACTATTCTTCTGTGAAGGCTTAAGATGGCCCGGAGGACTTCATCGTCATGCT
1 ATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATGCT
*
3500754 CGGAAGGCTTACTGATGGATTTGCTTCACAACT-CTTCGGTGAAGGCTTAAA
66 CGAAAGGCTTACTGATGGATTTGCTTCACAA-TACTTCGGTGAAGGCTTAAA
*
3500805 ATGGATTTTCTTCACTACTCTTCAT-TGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATGC
1 ATGGATTTGCTTCACTACTCTTC-TGTGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATGC
* *
3500869 TCGAAAGGCTTACTGATGGATTTGCTTCACTATACTTCGGTGAAGGCTTAAG
65 TCGAAAGGCTTACTGATGGATTTGCTTCACAATACTTCGGTGAAGGCTTAAA
3500921 ATGG
1 ATGG
3500925 CCCAAAAGAT
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
115 1 0.01
116 109 0.98
117 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (116 bp):
ATGGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATGCT
CGAAAGGCTTACTGATGGATTTGCTTCACAATACTTCGGTGAAGGCTTAAA
Found at i:3500946 original size:79 final size:79
Alignment explanation
Indices: 3500799--3500971 Score: 188
Period size: 79 Copynumber: 2.2 Consensus size: 79
3500789 TCGGTGAAGG
* * ** * * *
3500799 CTTA-AAATGGATTTTCTTCACTACTCTTCATTGAAGGCTTAAAATGGCCCGGAGGACTTAATCG
1 CTTACAAATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAAATGGCCCAAAAGACTTAAGCA
*
3500863 TCATGCTCGAAAGG
66 TCATGCTCGAAAGA
** * * * *
3500877 CTTACTGATGGATTTGCTTCACTA-TACTTCGGTGAAGGCTTAAGATGGCCCAAAAGATTTTAGC
1 CTTACAAATGGATTTGCTTCACTACT-CTTCAGTGAAGGCTTAAAATGGCCCAAAAGACTTAAGC
*
3500941 ATCATGCTCGAAATA
65 ATCATGCTCGAAAGA
3500956 CTTACAAATGGATTTG
1 CTTACAAATGGATTTG
3500972 ATCATCATGC
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
78 5 0.07
79 71 0.93
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (79 bp):
CTTACAAATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAAATGGCCCAAAAGACTTAAGCA
TCATGCTCGAAAGA
Found at i:3500978 original size:34 final size:34
Alignment explanation
Indices: 3500940--3501067 Score: 186
Period size: 34 Copynumber: 3.8 Consensus size: 34
3500930 AAGATTTTAG
* **
3500940 CATCATGCTCGAAATACTTACAAATGGATTTGAT
1 CATCATGCTCGAAAGACTTACTGATGGATTTGAT
*
3500974 CATCATGCTC-ATAAGACATACTGATGGATTTGAT
1 CATCATGCTCGA-AAGACTTACTGATGGATTTGAT
*
3501008 CATCATGCTCGGAAGACTTACTGATGGATTTGAT
1 CATCATGCTCGAAAGACTTACTGATGGATTTGAT
*
3501042 CATCATGCTCGGAAGACTTACTGATG
1 CATCATGCTCGAAAGACTTACTGATG
3501068 ACCTGAAGGA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
33 1 0.01
34 85 0.99
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (34 bp):
CATCATGCTCGAAAGACTTACTGATGGATTTGAT
Found at i:3501332 original size:174 final size:174
Alignment explanation
Indices: 3501033--3501387 Score: 622
Period size: 174 Copynumber: 2.0 Consensus size: 174
3501023 ACTTACTGAT
* * * *
3501033 GGATTTGATCATCATGCTCGGAAGACTTACTGATGACCTGAAGGATTTAATTTTGGAAATAGTTT
1 GGATTTAAGCATCATGCTCGGAAGACTTACTGATGACCCGAAGGATTTAATTTTGGAAATAATTT
3501098 ACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTAAATTTAAATGAGAAACCTTTC
66 ACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTAAATTTAAATGAGAAACCTTTC
*
3501163 TCATGTGAAAACATCCTGCCCGAAGGTCTTATTGATGACCAGAA
131 TCATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCAGAA
3501207 GGATTTAAGCATCATGCTCGGAAGACTTACTGATGACCCGAAGGATTTAATTTTGGAAATAATTT
1 GGATTTAAGCATCATGCTCGGAAGACTTACTGATGACCCGAAGGATTTAATTTTGGAAATAATTT
* *
3501272 ACTAGGTAAGAAACCTTTCTTACTTTTCAAAAAATTT-AATTTTATATTTAAATTAGAAACCTTT
66 ACTAGGTAAGAAACCTTTCTTACTTTTC-AAAAATTTCAATTTTAAATTTAAATGAGAAACCTTT
*
3501336 CTCATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAA
130 CTCATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCAGAA
3501381 GGATTTA
1 GGATTTA
3501388 TAAATTTTGG
Statistics
Matches: 172, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
174 164 0.95
175 8 0.05
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (174 bp):
GGATTTAAGCATCATGCTCGGAAGACTTACTGATGACCCGAAGGATTTAATTTTGGAAATAATTT
ACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTAAATTTAAATGAGAAACCTTTC
TCATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGACCAGAA
Found at i:3516829 original size:13 final size:13
Alignment explanation
Indices: 3516813--3516838 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3516803 TTTTCCGTTA
3516813 AATTTTTATTTTT
1 AATTTTTATTTTT
3516826 AATTTTTATTTTT
1 AATTTTTATTTTT
3516839 GTTCGACCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
AATTTTTATTTTT
Found at i:3518909 original size:19 final size:18
Alignment explanation
Indices: 3518884--3518933 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
3518874 AAAATGTTGA
3518884 AAAAAAAAAATAGCAGTTCG
1 AAAAAAAAAA-A-CAGTTCG
*
3518904 AAAAAAAAAAACTGTTCG
1 AAAAAAAAAAACAGTTCG
3518922 AAAGAAAAAAAA
1 AAA-AAAAAAAA
3518934 AAGACATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 9 0.32
20 10 0.36
ACGTcount: A:0.68, C:0.08, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAAAAAAAAACAGTTCG
Found at i:3528131 original size:6 final size:6
Alignment explanation
Indices: 3528120--3528174 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
3528110 ATTTACTTTG
*
3528120 ATTTTT ATTTTT A-TTTT ATTTTT ATTTGTT TTTGTTAT ATTTTT A-TTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT ATT-TT-T ATTTTT ATTTTT
3528169 ATTTTT
1 ATTTTT
3528175 CTTTGAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 21 0.50
7 7 0.17
8 4 0.10
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:3528138 original size:11 final size:11
Alignment explanation
Indices: 3528122--3528174 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
3528112 TTACTTTGAT
3528122 TTTTATTTTTA
1 TTTTATTTTTA
3528133 TTTTATTTTTA
1 TTTTATTTTTA
* *
3528144 -TTTGTTTTTG
1 TTTTATTTTTA
*
3528154 TTATATTTTTA
1 TTTTATTTTTA
3528165 TTTTATTTTT
1 TTTTATTTTT
3528175 CTTTGAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 8 0.23
11 27 0.77
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3528160 original size:21 final size:21
Alignment explanation
Indices: 3528127--3528167 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3528117 TTGATTTTTA
*
3528127 TTTTTATTTTATTTTTATTTG
1 TTTTTATTATATTTTTATTTG
*
3528148 TTTTTGTTATATTTTTATTT
1 TTTTTATTATATTTTTATTT
3528168 TATTTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTATTATATTTTTATTTG
Found at i:3529483 original size:17 final size:18
Alignment explanation
Indices: 3529453--3529486 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3529443 GTCGAACAAA
3529453 AAAACAAAGAAAGAAAGG
1 AAAACAAAGAAAGAAAGG
*
3529471 AAAA-AAAGGAAGAAAG
1 AAAACAAAGAAAGAAAG
3529487 ATTCGAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAACAAAGAAAGAAAGG
Found at i:3538105 original size:45 final size:45
Alignment explanation
Indices: 3537949--3538817 Score: 1193
Period size: 45 Copynumber: 19.2 Consensus size: 45
3537939 TAAAATCTCC
* ** ** * ** *
3537949 TTTGAAAACATCTTGCACTGAAGATCTTATGGATGGCTTGAAGGAC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
* * * **
3537995 TTTAAAAACATCCTGCACTGAAGGTCTTACAGATGACCTAAAGGCTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG--T
* * * **
3538042 TTTGAAAACAACCTGCACTGTAA-GTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTG-AAGGGCTTACAGATGACCCGAAGGT
* * **
3538087 TTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * * **
3538132 TTTGAAAACATCATACACCGTAGGTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
** *
3538177 TTTGAAAACATCATGCACTGAAGATCTTACAGATGACCCGAAAGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538222 TTTGAAAGCATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
3538267 TTTGAAAACAT-ATTGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCA-TGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538312 TTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCGAGGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538357 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538402 TTTGAAAACATCATGCGCTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538447 TTTGAAAACATCATGCACTAAAGGGATTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
3538492 TTTGAAAACATCATGTACTAAAGGGCTTACATATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538537 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538582 TTTGAAAACCTCATGCACTGAAGGGATTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538627 TTTGAAAATATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
3538672 TTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCTGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538717 TTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538762 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
3538807 TTTAAAAACAT
1 TTTGAAAACAT
3538818 AAAAAAGCTC
Statistics
Matches: 751, Mismatches: 67, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
44 2 0.00
45 675 0.90
46 37 0.05
47 35 0.05
48 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:3538560 original size:25 final size:25
Alignment explanation
Indices: 3538532--3538605 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
3538522 ATATGACCCA
3538532 AAGGTTTTGAAAACATCATGCACTG
1 AAGGTTTTGAAAACATCATGCACTG
* * *
3538557 AAGGTCTT----ACA-GATG-ACCCG
1 AAGGTTTTGAAAACATCATGCA-CTG
*
3538577 AAGGTTTTGAAAACCTCATGCACTG
1 AAGGTTTTGAAAACATCATGCACTG
3538602 AAGG
1 AAGG
3538606 GATTACAGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 14
0.62 0.12 0.25
Matches are distributed among these distances:
19 1 0.03
20 12 0.34
21 3 0.09
24 2 0.06
25 16 0.46
26 1 0.03
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (25 bp):
AAGGTTTTGAAAACATCATGCACTG
Found at i:3538900 original size:45 final size:45
Alignment explanation
Indices: 3538837--3538983 Score: 231
Period size: 45 Copynumber: 3.3 Consensus size: 45
3538827 CTTGAAGGTT
* *
3538837 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGATGG
1 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
3538882 TTTTGAAAACATCATGCACTGAATGGCTTACAGATAACCCGAAGG
1 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGG
3538927 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
3538972 CTTTAAAAACAT
1 TTTTGAAAACAT
3538984 TAAAAAGCTT
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (45 bp):
TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:3538930 original size:121 final size:121
Alignment explanation
Indices: 3538716--3538938 Score: 374
Period size: 121 Copynumber: 1.8 Consensus size: 121
3538706 GACCTGAAGG
3538716 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACT
*
3538781 GAAGGGCTTACAGATGACCCGAAAGTTTTAAAAACATAAAAAAGCTCTTGAAGGTT
66 GAAGGGCTTACAGATAACCCGAAAGTTTTAAAAACATAAAAAAGCTCTTGAAGGTT
* * * *
3538837 TTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGATGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACT
* * *
3538902 GAATGGCTTACAGATAACCCGAAGGTTTTGAAAACAT
66 GAAGGGCTTACAGATAACCCGAAAGTTTTAAAAACAT
3538939 CCTGCACTGA
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 94 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACT
GAAGGGCTTACAGATAACCCGAAAGTTTTAAAAACATAAAAAAGCTCTTGAAGGTT
Found at i:3538947 original size:166 final size:166
Alignment explanation
Indices: 3538664--3539038 Score: 603
Period size: 166 Copynumber: 2.3 Consensus size: 166
3538654 TACAGATGAC
* *
3538664 CCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAAATGACCTGAAGGTTTTGAAAACA
1 CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACA
*
3538727 TCATGCACTGAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTAC
66 TCATGCACTGAAGGGCTTACAAATAACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTAC
*
3538792 AGATGACCCGAAAGTTTTAAAAACATAAAAAAGC-T
131 AGATGACCCGAAAGCTTTAAAAACATAAAAAAGCTT
* * *
3538827 CTTGAAGGTTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGATGGTTTTGAAAAC
1 C-CGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAAC
* * *
3538892 ATCATGCACTGAATGGCTTACAGATAACCCGAAGGTTTTGAAAACATCCTGCACTGAAGGGCTTA
65 ATCATGCACTGAAGGGCTTACAAATAACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTA
* *
3538957 CAGATGACCCGAAGGCTTTAAAAACATTAAAAAGCTT
130 CAGATGACCCGAAAGCTTTAAAAACATAAAAAAGCTT
*
3538994 CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTATAGATG
1 CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATG
3539039 TGGGAAATAG
Statistics
Matches: 194, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
163 1 0.01
164 5 0.03
166 186 0.96
167 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (166 bp):
CCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACA
TCATGCACTGAAGGGCTTACAAATAACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTAC
AGATGACCCGAAAGCTTTAAAAACATAAAAAAGCTT
Found at i:3539766 original size:22 final size:22
Alignment explanation
Indices: 3539718--3539775 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
3539708 AATAAAGCTT
* *
3539718 TCATCTTT-GAAAGAGAATCTA
1 TCATCTTTGGAGAGTGAATCTA
* *
3539739 TTATCTTTGGAGAGTGAATTTA
1 TCATCTTTGGAGAGTGAATCTA
*
3539761 TCATCTTTGAAGAGT
1 TCATCTTTGGAGAGT
3539776 ATAGATGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (22 bp):
TCATCTTTGGAGAGTGAATCTA
Found at i:3540221 original size:55 final size:54
Alignment explanation
Indices: 3540141--3540303 Score: 204
Period size: 55 Copynumber: 3.0 Consensus size: 54
3540131 ATAATCACTG
*
3540141 GTTCGTAAAACATTTGACAATACATTCATCCTTTCTCGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCTGCACAGAT
* * * * *
3540195 GTTCGTAAAAACATTAGATAACACATTCATCCTTTCTTGTGGCTTCTGGC-CAAAT
1 GTTCGT-AAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCT-GCACAGAT
* * *
3540250 GTTTGTAAAGCATTTGACAACACATTCATCATTT-TCTGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTC-GTGGTTTCTGCACAGAT
3540304 TTCTGATCAA
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
53 3 0.03
54 42 0.46
55 44 0.48
56 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTCGTGGTTTCTGCACAGAT
Found at i:3541306 original size:74 final size:75
Alignment explanation
Indices: 3541174--3541345 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 75
3541164 GATATGGGTC
* * * * * *
3541174 TTCAACATGCCCTAACATTTGTTGATACAGACGTTCCAAATGCACCAACATTCCTGATTCTAATT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAACCAACATTCCTGATTCTAATT
3541239 -AAAAGGGCT
66 GAAAAGGGCT
* * * * * *
3541248 TTCAGCATGCCCCAACATTTGCTGATACAAATGTTCAAAAT-AAGTCAATATTCTTGATTTTGAT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAA-CCAACATTCCTGATTCTAAT
*
3541312 TGAAATGGGCT
65 TGAAAAGGGCT
*
3541323 TTCAGCATGCCCCATCATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
3541346 TTTTTTTAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
73 1 0.01
74 51 0.62
75 30 0.37
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAACCAACATTCCTGATTCTAATT
GAAAAGGGCT
Found at i:3543866 original size:32 final size:32
Alignment explanation
Indices: 3543825--3543887 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3543815 TGAAGAAATG
* *
3543825 ATTGTTATGCTTATCTGGTAGAGATACTTCTC
1 ATTGTTATGCTCATCTCGTAGAGATACTTCTC
3543857 ATTGTTATGCTCATCTCGTAGAGATACTTCT
1 ATTGTTATGCTCATCTCGTAGAGATACTTCT
3543888 TATTTCCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (32 bp):
ATTGTTATGCTCATCTCGTAGAGATACTTCTC
Found at i:3544382 original size:16 final size:15
Alignment explanation
Indices: 3544343--3544389 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
3544333 TTTGATTCAA
3544343 TTTTTTTTTCCTTCC
1 TTTTTTTTTCCTTCC
*
3544358 TTCTTTTTTTCCTTTTC
1 TT-TTTTTTTCC-TTCC
3544375 TTTTTTTTTCTCTTC
1 TTTTTTTTTC-CTTC
3544390 TTCAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.07
16 19 0.70
17 6 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTCCTTCC
Found at i:3547269 original size:21 final size:20
Alignment explanation
Indices: 3547230--3547273 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3547220 ATAAAAGTAT
3547230 AAATGAAAATGCAAATATGCA
1 AAATGAAAATGCAAATATG-A
* **
3547251 AAATGCAAATGCATGTATGA
1 AAATGAAAATGCAAATATGA
3547271 AAA
1 AAA
3547274 GGTGTTACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (20 bp):
AAATGAAAATGCAAATATGA
Found at i:3548835 original size:19 final size:17
Alignment explanation
Indices: 3548794--3548826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3548784 AATACTTGAA
3548794 AATAAAATAAAAATATT
1 AATAAAATAAAAATATT
3548811 AATAAAA-AAATAATAT
1 AATAAAATAAA-AATAT
3548827 ATATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAATAAAAATATT
Found at i:3548838 original size:29 final size:29
Alignment explanation
Indices: 3548803--3548874 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
3548793 AAATAAAATA
3548803 AAAATATTAATAAAAA-AATAA-TATATAT
1 AAAATATT-ATAAAAATAATAAGTATATAT
3548831 ATAAATATTATAAAAATAATAAGTATATAT
1 A-AAATATTATAAAAATAATAAGTATATAT
* *
3548861 AAAATTTTTTAAAA
1 AAAATATTATAAAA
3548875 GAAAGAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 8 0.21
29 23 0.59
30 8 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAATATTATAAAAATAATAAGTATATAT
Found at i:3550289 original size:10 final size:8
Alignment explanation
Indices: 3550258--3550283 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3550248 ATTCTCAAAA
3550258 TTCTTCAT
1 TTCTTCAT
3550266 TTCTTCAT
1 TTCTTCAT
3550274 TTCTTCAT
1 TTCTTCAT
3550282 TT
1 TT
3550284 TTCTTCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (8 bp):
TTCTTCAT
Found at i:3550855 original size:23 final size:23
Alignment explanation
Indices: 3550824--3550869 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3550814 GGGAACATGA
* *
3550824 CGGCGGAGCAGTTGGAGTAGAGG
1 CGGCAGAGCAATTGGAGTAGAGG
3550847 CGGCAGAGCAATTGGAGTAGAGG
1 CGGCAGAGCAATTGGAGTAGAGG
3550870 AACGGCTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.48, T:0.13
Consensus pattern (23 bp):
CGGCAGAGCAATTGGAGTAGAGG
Found at i:3551222 original size:19 final size:20
Alignment explanation
Indices: 3551170--3551223 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
3551160 AGCTTTGTTA
*
3551170 TTTGTTTTACTTTTTATAAAGT
1 TTTGTTTTACTTTTTAT--ACT
3551192 TTT-TTTT-C-TTTTAT-CT
1 TTTGTTTTACTTTTTATACT
3551208 TTTGTTTTACTTTTTA
1 TTTGTTTTACTTTTTA
3551224 AAGTTTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 4 0.14
17 4 0.14
18 1 0.04
19 11 0.39
20 1 0.04
21 4 0.14
22 3 0.11
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (20 bp):
TTTGTTTTACTTTTTATACT
Found at i:3553489 original size:21 final size:21
Alignment explanation
Indices: 3553463--3553512 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3553453 CGTCAAATAA
*
3553463 CACCCTGGTGCAGTTGGACAG
1 CACCCTGGTGCAGCTGGACAG
* *
3553484 CACCCTTGTGCAGCTGGGCAG
1 CACCCTGGTGCAGCTGGACAG
3553505 CACCCTGG
1 CACCCTGG
3553513 GCGGTCTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.18
Consensus pattern (21 bp):
CACCCTGGTGCAGCTGGACAG
Found at i:3554176 original size:15 final size:15
Alignment explanation
Indices: 3554158--3554226 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
3554148 TTAATATTAT
3554158 GATATGTGTTATTCG
1 GATATGTGTTATTCG
*
3554173 GATATGCGTTATTCG
1 GATATGTGTTATTCG
*
3554188 GATATAAATGTTATTCG
1 GATAT--GTGTTATTCG
* * *
3554205 GATATATGCTATTGG
1 GATATGTGTTATTCG
3554220 GATATGT
1 GATATGT
3554227 ATGTCATTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 33 0.72
17 13 0.28
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (15 bp):
GATATGTGTTATTCG
Found at i:3554223 original size:32 final size:32
Alignment explanation
Indices: 3554164--3554224 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
3554154 TTATGATATG
* *
3554164 TGTTATTCGGATATGCGTTATTCGGATATAAA
1 TGTTATTCGGATATACGCTATTCGGATATAAA
* *
3554196 TGTTATTCGGATATATGCTATTGGGATAT
1 TGTTATTCGGATATACGCTATTCGGATAT
3554225 GTATGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (32 bp):
TGTTATTCGGATATACGCTATTCGGATATAAA
Found at i:3554932 original size:40 final size:40
Alignment explanation
Indices: 3554881--3554962 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
3554871 AAGTTTTAAA
* *
3554881 TCAAAAGTGGTTACGTGAGGGATAAGTTTTAATACGACTT
1 TCAAAAATGGTTACGTGAGGGATAAGTCTTAATACGACTT
3554921 TCAAAAATGGTTACGTGAGGGATAAGTCTTAATACGACTT
1 TCAAAAATGGTTACGTGAGGGATAAGTCTTAATACGACTT
3554961 TC
1 TC
3554963 CAAATTCGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (40 bp):
TCAAAAATGGTTACGTGAGGGATAAGTCTTAATACGACTT
Found at i:3561952 original size:18 final size:18
Alignment explanation
Indices: 3561929--3561974 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
3561919 GAATCAGCCA
*
3561929 CATTATCTTCTATCTCAT
1 CATTATCCTCTATCTCAT
3561947 CATTATCCTCTATCTCAT
1 CATTATCCTCTATCTCAT
3561965 CATTATCCTC
1 CATTATCCTC
3561975 GGCATCAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (18 bp):
CATTATCCTCTATCTCAT
Found at i:3571909 original size:7 final size:7
Alignment explanation
Indices: 3571897--3571937 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
3571887 ATTTTTTTTA
3571897 TATATTT
1 TATATTT
3571904 TATATTT
1 TATATTT
3571911 TAT-TTAT
1 TATATT-T
3571918 T-TATTT
1 TATATTT
3571924 T-TATTT
1 TATATTT
3571930 TATATTT
1 TATATTT
3571937 T
1 T
3571938 CGGTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TATATTT
Found at i:3571927 original size:21 final size:21
Alignment explanation
Indices: 3571868--3571936 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
3571858 TACTTGTATG
*
3571868 TATTTATATATTTATTGCTATTT
1 TATTTATATATTT-TT-ATATTT
*
3571891 TTTTTATATA-TTTTATATTT
1 TATTTATATATTTTTATATTT
*
3571911 TATTTATTTATTTTTAT-TTT
1 TATTTATATATTTTTATATTT
3571931 ATATTT
1 -TATTT
3571937 TCGGTTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.40
21 13 0.32
22 2 0.05
23 9 0.22
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (21 bp):
TATTTATATATTTTTATATTT
Found at i:3571931 original size:19 final size:19
Alignment explanation
Indices: 3571870--3571932 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
3571860 CTTGTATGTA
* **
3571870 TTTATATATTTATTGCTAT
1 TTTATTTATTTATTTTTAT
* *
3571889 TTTTTTTATATATTTTATAT
1 TTTATTTATTTATTTT-TAT
3571909 TTTATTTATTTATTTTTAT
1 TTTATTTATTTATTTTTAT
3571928 TTTAT
1 TTTAT
3571933 ATTTTCGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTATTTATTTTTAT
Found at i:3571932 original size:15 final size:15
Alignment explanation
Indices: 3571868--3571929 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
3571858 TACTTGTATG
3571868 TATTTATATATTTATT
1 TATTTATAT-TTTATT
*
3571884 GCTATTT-T-TTTTATA
1 --TATTTATATTTTATT
3571899 TATTTTATATTTTATT
1 TA-TTTATATTTTATT
3571915 TATTTAT-TTTTATT
1 TATTTATATTTTATT
3571929 T
1 T
3571930 TATATTTTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.05
14 11 0.28
15 11 0.28
16 9 0.23
17 1 0.03
18 5 0.13
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (15 bp):
TATTTATATTTTATT
Found at i:3582430 original size:59 final size:59
Alignment explanation
Indices: 3582324--3582438 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 59
3582314 AATACTTCGC
* * * *
3582324 TTAGGATGAAAACCCGAAAGGGTGTCCTAAGTCAAAAAAAAATAAAAAGGGAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAATAAAAAGAGAAAAACGT
* ** *
3582383 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAAT-TGAAAAAATTGAAAAAGAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAAT-AAAAAGAGAAAAA
3582439 AGAACAAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 7 0.15
59 40 0.85
ACGTcount: A:0.50, C:0.12, G:0.23, T:0.15
Consensus pattern (59 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATCAAAAAAAAATAAAAAGAGAAAAACGT
Found at i:3582438 original size:9 final size:8
Alignment explanation
Indices: 3582426--3582459 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3582416 GAAAAAATTG
3582426 AAAAAGAGA
1 AAAAAGA-A
3582435 AAAAAGAA
1 AAAAAGAA
*
3582443 CAAAAGAA
1 AAAAAGAA
3582451 AAAAAGAA
1 AAAAAGAA
3582459 A
1 A
3582460 GAACAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3582453 original size:16 final size:17
Alignment explanation
Indices: 3582427--3582458 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3582417 AAAAAATTGA
3582427 AAAAGAGAAAAAAGAAC
1 AAAAGAGAAAAAAGAAC
3582444 AAAAGA-AAAAAAGAA
1 AAAAGAGAAAAAAGAA
3582459 AGAACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAAAGAAC
Found at i:3583042 original size:14 final size:14
Alignment explanation
Indices: 3583023--3583049 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3583013 GATCGAAACT
3583023 TCAAGATTCCAGAA
1 TCAAGATTCCAGAA
3583037 TCAAGATTCCAGA
1 TCAAGATTCCAGA
3583050 CAAGAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAA
Found at i:3583782 original size:106 final size:106
Alignment explanation
Indices: 3583486--3583839 Score: 406
Period size: 106 Copynumber: 3.3 Consensus size: 106
3583476 AAACAATTTC
* * * * ** *
3583486 CCAATTTTAAATTCACAACGACGGATATTGGACTTAAGACAACACAATCTCAACTTCACAATGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAATGAA
* * * *
3583551 GGGGTGGCT-CGTTGTCATCAAACAACTTCCCAATTTTAGAG
66 GGGGCGGCTGC-TTGTCAACAAATAATTTCCCAATTTTAGAG
* *
3583592 TCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAATGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAATGAA
* * * *
3583657 GGGACGACTGGTTGTCAACAAATAATTTCCTAATTTTAGAG
66 GGGGCGGCTGCTTGTCAACAAATAATTTCCCAATTTTAGAG
* * * *
3583698 CCAATTTCAATTTCCCAGCGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAATGAA
* * ** * *
3583763 GGGGCGGCTGACTT-ACAACAAATAATTTCCCAGTTCCATAA
66 GGGGCGGCTG-CTTGTCAACAAATAATTTCCCAATTTTAGAG
* * *
3583804 CCAATTTCAACTTCACGGTGGAGGATATTGGACTCG
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
3583840 GAACAATACA
Statistics
Matches: 207, Mismatches: 39, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
106 205 0.99
107 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (106 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAATGAA
GGGGCGGCTGCTTGTCAACAAATAATTTCCCAATTTTAGAG
Found at i:3584433 original size:2 final size:2
Alignment explanation
Indices: 3584416--3584462 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
3584406 AAATAAATAA
* *
3584416 AT AT AT TT AT AT -T AT AT AT AT AT CAT AT AT AT CAT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT AT AT AT
3584459 AT AT
1 AT AT
3584463 TGTATAGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 1 0.03
2 33 0.87
3 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3584437 original size:11 final size:11
Alignment explanation
Indices: 3584417--3584475 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
3584407 AATAAATAAA
*
3584417 TATATTTATAT
1 TATATATATAT
3584428 TATATATATAT
1 TATATATATAT
*
3584439 CATATATATCAT
1 TATATATAT-AT
*
3584451 ATGTATATATAT
1 -TATATATATAT
* *
3584463 TGTATAGATAT
1 TATATATATAT
3584474 TA
1 TA
3584476 CTATTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 29 0.73
12 4 0.10
13 7 0.17
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (11 bp):
TATATATATAT
Found at i:3585645 original size:16 final size:16
Alignment explanation
Indices: 3585626--3585669 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3585616 TATTTTCCTT
*
3585626 TTTTTTTTTTTATTAC
1 TTTTTTTTTATATTAC
* *
3585642 TTTTATATTATATTAC
1 TTTTTTTTTATATTAC
3585658 TTTTTTTATTAT
1 TTTTTTT-TTAT
3585670 GGTGTTTTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTTTATATTAC
Found at i:3585730 original size:8 final size:8
Alignment explanation
Indices: 3585717--3585743 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3585707 CTACTACTTG
3585717 TATATATT
1 TATATATT
3585725 TATATATT
1 TATATATT
3585733 TATATATT
1 TATATATT
3585741 TAT
1 TAT
3585744 TGCTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATATATT
Found at i:3585759 original size:19 final size:19
Alignment explanation
Indices: 3585735--3585780 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3585725 TATATATTTA
3585735 TATATTTATTGCTATTT-TT
1 TATATTT-TTGCTATTTATT
*
3585754 TATATTTTTGTTATTTATT
1 TATATTTTTGCTATTTATT
*
3585773 TTTATTTT
1 TATATTTT
3585781 ATTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (19 bp):
TATATTTTTGCTATTTATT
Found at i:3585770 original size:15 final size:17
Alignment explanation
Indices: 3585751--3585793 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
3585741 TATTGCTATT
3585751 TTTTATATTTT-TGTTA
1 TTTTATATTTTATGTTA
*
3585767 -TTTAT-TTTTATTTTA
1 TTTTATATTTTATGTTA
3585782 TTTTATATTTTA
1 TTTTATATTTTA
3585794 GTTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 5 0.22
17 5 0.22
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATATTTTATGTTA
Found at i:3585802 original size:17 final size:17
Alignment explanation
Indices: 3585751--3585807 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
3585741 TATTGCTATT
*
3585751 TTTTATATTTTTG-TTA
1 TTTTATATTTTAGTTTA
*
3585767 -TTTAT-TTTTATTTTA
1 TTTTATATTTTAGTTTA
*
3585782 TTTTATATTTTAGTTTC
1 TTTTATATTTTAGTTTA
*
3585799 TTTTCTATT
1 TTTTATATT
3585808 AATATTGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 4 0.12
15 8 0.24
16 5 0.15
17 16 0.48
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTATATTTTAGTTTA
Found at i:3591636 original size:17 final size:20
Alignment explanation
Indices: 3591614--3591650 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
3591604 CATTATCATT
3591614 CACAAG-AA-CAATA-TACA
1 CACAAGCAACCAATACTACA
3591631 CACAAGCAACCAATACTACA
1 CACAAGCAACCAATACTACA
3591651 GTATCACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 5 0.29
20 4 0.24
ACGTcount: A:0.54, C:0.30, G:0.05, T:0.11
Consensus pattern (20 bp):
CACAAGCAACCAATACTACA
Found at i:3607783 original size:32 final size:32
Alignment explanation
Indices: 3607747--3607818 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
3607737 TTACACACCT
* * *
3607747 AAGGTACT-TCATTGGGTAGGTTCTTAGGCCCC
1 AAGGTACTATC-TTGGATAGGCTCTAAGGCCCC
*
3607779 AAGGTACTATCTTGGATAGGCTCTAAGGTCCC
1 AAGGTACTATCTTGGATAGGCTCTAAGGCCCC
*
3607811 GAGGTACT
1 AAGGTACT
3607819 CCCTTATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (32 bp):
AAGGTACTATCTTGGATAGGCTCTAAGGCCCC
Found at i:3614366 original size:42 final size:41
Alignment explanation
Indices: 3614271--3614374 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
3614261 TTTTCTCACG
**
3614271 TCTTTTTTTCTTTTTTTTTCTTTCTAACAACTTTTGTTATT
1 TCTTTTTTTCTTTTTTTTTCTTTCTAACAACTGATGTTATT
**
3614312 TCCTTTTTTTCTTTTTTTTCTCTTT-TTTCGAACTGATGTT-TT
1 T-CTTTTTTTCTTTTTTTT-TCTTTCTAAC-AACTGATGTTATT
3614354 TCTTTTTCTTCTTCTTTTTTT
1 TCTTTTT-TTCTT-TTTTTTT
3614375 TCGATGGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
41 7 0.13
42 28 0.52
43 19 0.35
ACGTcount: A:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (41 bp):
TCTTTTTTTCTTTTTTTTTCTTTCTAACAACTGATGTTATT
Found at i:3619619 original size:11 final size:12
Alignment explanation
Indices: 3619603--3619643 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
3619593 AACAAAGCTT
3619603 GAAAAAT-AAAA
1 GAAAAATGAAAA
3619614 GAAAAATGAAAA
1 GAAAAATGAAAA
*
3619626 G-AACATGAAAA
1 GAAAAATGAAAA
3619637 GTAAAAA
1 G-AAAAA
3619644 GAGAAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 17 0.68
12 5 0.20
13 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (12 bp):
GAAAAATGAAAA
Found at i:3629904 original size:25 final size:25
Alignment explanation
Indices: 3629870--3629918 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3629860 AAGTGATTTA
3629870 TTAAGGATTTAATAAAAT-GGGTTT
1 TTAAGGATTTAATAAAATAGGGTTT
* *
3629894 TTAAGTGATTTGATGAAATAGGGTT
1 TTAAG-GATTTAATAAAATAGGGTT
3629919 AGTTATTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 11 0.52
26 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (25 bp):
TTAAGGATTTAATAAAATAGGGTTT
Found at i:3630174 original size:54 final size:54
Alignment explanation
Indices: 3630095--3630352 Score: 327
Period size: 54 Copynumber: 4.8 Consensus size: 54
3630085 TGGATAAGTG
* * *
3630095 ATAATGAATTTTTAAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
1 ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
* * * * *
3630149 ATATTGAGTTTGTGAATTATCGTATTGGAACTATGTATGAAACCTAAGTAATTC
1 ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
* * * *
3630203 ATAATGAGTCTGGGAATTACCATATTGGCACTATATGTGCAACCTAAGTAATTC
1 ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
* * * *
3630257 ATAATGAGTTTGTGAATTAGCGTATTGGCATTACGTGTGCAACCTACGTAATTC
1 ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
* ** * *
3630311 ACAATGAGTTTGTGAATTACTATATCGACACTATGTGTGCAA
1 ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAA
3630353 AACCACATAA
Statistics
Matches: 171, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 171 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (54 bp):
ATAATGAGTTTGTGAATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTC
Found at i:3632391 original size:32 final size:32
Alignment explanation
Indices: 3632283--3632404 Score: 108
Period size: 32 Copynumber: 3.8 Consensus size: 32
3632273 TAAAAAATGC
* **
3632283 CTCGGGGTCTTAGAGCCTACCCAA-GGAATGT
1 CTCGGGGCCTTAGAGCCTACCCAAGGGAACAT
* * *
3632314 CTTGGGGCCTTAGAGCCCACCCAAGTGAGTACAT
1 CTCGGGGCCTTAGAGCCTACCCAAG-G-GAACAT
* *
3632348 -T-AGGGCCTAAGAGCCTACCCAAGGGAACAT
1 CTCGGGGCCTTAGAGCCTACCCAAGGGAACAT
*
3632378 CTCGGGG-CTTAAGAGCCTACCCGAGGG
1 CTCGGGGCCTT-AGAGCCTACCCAAGGG
3632405 TCACCTTAGG
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
30 5 0.07
31 25 0.35
32 37 0.51
33 2 0.03
34 3 0.04
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.18
Consensus pattern (32 bp):
CTCGGGGCCTTAGAGCCTACCCAAGGGAACAT
Found at i:3636628 original size:2 final size:2
Alignment explanation
Indices: 3636616--3636647 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3636606 TAAATTGTTT
3636616 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3636648 TACATTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3637161 original size:19 final size:19
Alignment explanation
Indices: 3637137--3637173 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3637127 ACGTTGGGCT
*
3637137 AATTAAACCAATGGATATC
1 AATTAAACAAATGGATATC
*
3637156 AATTAAACAAATTGATAT
1 AATTAAACAAATGGATAT
3637174 ATATTGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (19 bp):
AATTAAACAAATGGATATC
Found at i:3638785 original size:20 final size:22
Alignment explanation
Indices: 3638757--3638809 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
3638747 TTTTGCAAAT
*
3638757 GATCAATCCCTTTTC-A-AAAG
1 GATCGATCCCTTTTCAAGAAAG
*
3638777 GATTGATCCC-TTTCAAGAAAG
1 GATCGATCCCTTTTCAAGAAAG
3638798 GATCGATCCCTT
1 GATCGATCCCTT
3638810 CACTGTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 9 0.33
21 13 0.48
22 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (22 bp):
GATCGATCCCTTTTCAAGAAAG
Found at i:3654373 original size:42 final size:43
Alignment explanation
Indices: 3654295--3654377 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
3654285 ATATATGTTG
3654295 ATTTATAAGATATCATGTCAACTCCAACTGAACAAATCCCAGT
1 ATTTATAAGATATCATGTCAACTCCAACTGAACAAATCCCAGT
* *
3654338 ATTTATAAGATATCA-GTCAACTCGAACTGAGCAAATCCCA
1 ATTTATAAGATATCATGTCAACTCCAACTGAACAAATCCCA
3654378 ACACTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 23 0.61
43 15 0.39
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.27
Consensus pattern (43 bp):
ATTTATAAGATATCATGTCAACTCCAACTGAACAAATCCCAGT
Found at i:3658711 original size:20 final size:21
Alignment explanation
Indices: 3658686--3658726 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3658676 ATTGATTGAA
3658686 AATTA-TTAAAAAATTAATAT
1 AATTATTTAAAAAATTAATAT
3658706 AATTATTTTTAAAAAATTAAT
1 AATTA--TTTAAAAAATTAAT
3658727 TTTTGCTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
23 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATTTAAAAAATTAATAT
Found at i:3659070 original size:30 final size:30
Alignment explanation
Indices: 3659034--3659115 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
3659024 CTTACCATAG
* * *
3659034 CACTAAGTTTCATTACACACTACAATGCTA
1 CACTAAGTATCCTTACACACTACAATGATA
* * *
3659064 CACTAAGTGTCCTTCCACACTACAATGATG
1 CACTAAGTATCCTTACACACTACAATGATA
3659094 CACTAAGTATCCTTACACACTA
1 CACTAAGTATCCTTACACACTA
3659116 TGGTGCCAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.28
Consensus pattern (30 bp):
CACTAAGTATCCTTACACACTACAATGATA
Found at i:3659781 original size:20 final size:21
Alignment explanation
Indices: 3659756--3659796 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3659746 ATTGACTGAA
3659756 AATTA-TTAAAAAATTAATAT
1 AATTATTTAAAAAATTAATAT
3659776 AATTATTTTTAAAAAATTAAT
1 AATTA--TTTAAAAAATTAAT
3659797 TTTTGCTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
23 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATTTAAAAAATTAATAT
Found at i:3660152 original size:30 final size:30
Alignment explanation
Indices: 3660103--3660184 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
3660093 CTTACCATAG
* * **
3660103 CACTGAGTGTCATTACACACTACAATTCTA
1 CACTAAGTGTCCTTACACACTACAATGATA
* *
3660133 CACTAAGTGTCCTTCCACACTACAATGATG
1 CACTAAGTGTCCTTACACACTACAATGATA
*
3660163 CACTAAGTATCCTTACACACTA
1 CACTAAGTGTCCTTACACACTA
3660185 TAGTGCCAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (30 bp):
CACTAAGTGTCCTTACACACTACAATGATA
Found at i:3660847 original size:20 final size:21
Alignment explanation
Indices: 3660822--3660862 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3660812 ATTGATTGAA
3660822 AATTA-TTAAAAAATTAATAT
1 AATTATTTAAAAAATTAATAT
3660842 AATTATTTTTAAAAAATTAAT
1 AATTA--TTTAAAAAATTAAT
3660863 TTTAGCTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
23 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTATTTAAAAAATTAATAT
Done.