Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 135 of 279
Found at i:43599786 original size:3 final size:3
Alignment explanation
Indices: 43599778--43599809 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43599768 TACCCCACAA
43599778 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
43599810 AAGGGAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43612168 original size:50 final size:50
Alignment explanation
Indices: 43612091--43612322 Score: 230
Period size: 47 Copynumber: 4.8 Consensus size: 50
43612081 GACCTCAGCA
* * *
43612091 TGCTCTCTGAT-TATTAGCACGCTAGTGCTCTCTAATTATTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGCCAGTGCTCTCTGATTATTAGCACGTCAG
* * * **
43612141 TGCTCTCTAAT-TATTAGCACGCCAGTGCTTTCTG---ATTAGCACATTTG
1 TGCTCTCTGATAT-TTAGCACGCCAGTGCTCTCTGATTATTAGCACGTCAG
* * *
43612188 TGCTCTCTGATATTTAGCACGTCAATGCTCTCTGA-TATTTAGCATGTCAG
1 TGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATTA-TTAGCACGTCAG
* * **
43612238 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG---ATTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATTATTAGCACGTCAG
*
43612285 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTA
1 TGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATTA
43612323 GCACATTTGT
Statistics
Matches: 154, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
47 79 0.51
48 2 0.01
49 1 0.01
50 72 0.47
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (50 bp):
TGCTCTCTGATATTTAGCACGCCAGTGCTCTCTGATTATTAGCACGTCAG
Found at i:43612205 original size:47 final size:47
Alignment explanation
Indices: 43612140--43612340 Score: 287
Period size: 47 Copynumber: 4.2 Consensus size: 47
43612130 TAGCACGCCA
* * *
43612140 GTGCTCTCTAAT-TATTAGCACGCCAGTGCTTTCTGATTAGCACATTT
1 GTGCTCTCTGATAT-TTAGCACGTCAGTGCTCTCTGATTAGCACATTT
* ** **
43612187 GTGCTCTCTGATATTTAGCACGTCAATGCTCTCTGATATTTAGCATGTCA
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTG--A-TTAGCACATTT
43612237 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
43612284 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
1 GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
43612331 GTGCTCTCTG
1 GTGCTCTCTG
43612341 TTCATTAGTG
Statistics
Matches: 137, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
47 93 0.68
48 2 0.01
49 1 0.01
50 41 0.30
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (47 bp):
GTGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTT
Found at i:43612257 original size:97 final size:97
Alignment explanation
Indices: 43612091--43612322 Score: 337
Period size: 97 Copynumber: 2.4 Consensus size: 97
43612081 GACCTCAGCA
*
43612091 TGCTCTCTGAT-TATTAGCACG-CTAGTGCTCTCTAATTATTAGCACGCCAGTGCTCTCTAATTA
1 TGCTCTCTGATAT-TTAGCACGTC-AGTGCTCTCTGATTATTAGCACGCCAGTGCTCTCTAATTA
*
43612154 TTAGCACGCCAGTGCTTTCTGATTAGCACATTTG
64 TTAGCACGCCAGTGCTCTCTGATTAGCACATTTG
* * * *
43612188 TGCTCTCTGATATTTAGCACGTCAATGCTCTCTGA-TATTTAGCATGTCAGTGCTCTCTGA-TAT
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTA-TTAGCACGCCAGTGCTCTCTAATTA-
*
43612251 TTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
64 TTAGCACGCCAGTGCTCTCTGATTAGCACATTTG
43612285 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTA
1 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTA
43612323 GCACATTTGT
Statistics
Matches: 122, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
96 4 0.03
97 114 0.93
98 4 0.03
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (97 bp):
TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTATTAGCACGCCAGTGCTCTCTAATTATT
AGCACGCCAGTGCTCTCTGATTAGCACATTTG
Found at i:43612301 original size:25 final size:25
Alignment explanation
Indices: 43612091--43612320 Score: 237
Period size: 25 Copynumber: 9.4 Consensus size: 25
43612081 GACCTCAGCA
43612091 TGCTCTCTGAT-TATTAGCACG-CTAG
1 TGCTCTCTGATAT-TTAGCACGTC-AG
* *
43612116 TGCTCTCTAAT-TATTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGTCAG
* *
43612141 TGCTCTCTAAT-TATTAGCACGCCAG
1 TGCTCTCTGATAT-TTAGCACGTCAG
* * **
43612166 TGCTTTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
*
43612188 TGCTCTCTGATATTTAGCACGTCAA
1 TGCTCTCTGATATTTAGCACGTCAG
*
43612213 TGCTCTCTGATATTTAGCATGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
43612238 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
* **
43612263 TGCTCTCTG--A-TTAGCACATTTG
1 TGCTCTCTGATATTTAGCACGTCAG
43612285 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTGATATTTAGCACGTCAG
43612310 TGCTCTCTGAT
1 TGCTCTCTGAT
43612321 TAGCACATTT
Statistics
Matches: 176, Mismatches: 21, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
22 34 0.19
23 1 0.01
24 2 0.01
25 138 0.78
26 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
TGCTCTCTGATATTTAGCACGTCAG
Found at i:43613385 original size:46 final size:47
Alignment explanation
Indices: 43613333--43613435 Score: 111
Period size: 46 Copynumber: 2.2 Consensus size: 47
43613323 TATTCAATAT
* * *
43613333 AGACCATATCTGGGATATGGCATCA-GTGTGATATGTGA-TCTGTGTA
1 AGACCATAT-TGGGATATGGCATCAGGTGTGATATATGACTATGTGCA
* * *
43613379 AGACCATGGTTGGGCTATGGCTTCAGTGTGTGATATATGACTATGTGCA
1 AGACCAT-ATTGGGATATGGCATCAG-GTGTGATATATGACTATGTGCA
43613428 AGACCATA
1 AGACCATA
43613436 GTTTTACTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
46 20 0.43
47 1 0.02
48 12 0.26
49 13 0.28
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (47 bp):
AGACCATATTGGGATATGGCATCAGGTGTGATATATGACTATGTGCA
Found at i:43620836 original size:47 final size:47
Alignment explanation
Indices: 43620772--43620882 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
43620762 GACATTGAGT
* *
43620772 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTATTC
* * *
43620819 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
43620866 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
43620883 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 51 0.93
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTATTC
Found at i:43631163 original size:18 final size:20
Alignment explanation
Indices: 43631121--43631157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43631111 ATATTTTATG
*
43631121 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
43631140 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
43631158 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:43633274 original size:54 final size:54
Alignment explanation
Indices: 43633201--43634039 Score: 1678
Period size: 54 Copynumber: 15.5 Consensus size: 54
43633191 ATTGTCGTTG
43633201 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633255 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633309 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633363 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633417 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633471 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633525 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633579 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633633 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633687 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633741 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633795 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633849 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633903 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43633957 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
43634011 CAGGGGATTTAGCCTGGACTGGTAATCCC
1 CAGGGGATTTAGCCTGGACTGGTAATCCC
43634040 ACTGTAAGGA
Statistics
Matches: 785, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 785 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (54 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGTTTATATTA
Found at i:43634125 original size:46 final size:46
Alignment explanation
Indices: 43634073--43634345 Score: 352
Period size: 46 Copynumber: 6.0 Consensus size: 46
43634063 AGTGTGCTCT
* *
43634073 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
43634119 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
43634165 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACAATGGC-AC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
43634210 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** ****
43634256 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * *
43634302 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAACGTGTAAGACCATGGTTGAAAGATACCATGGCA
43634346 TCATGTCAAA
Statistics
Matches: 205, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
45 44 0.21
46 161 0.79
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (46 bp):
CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:43634241 original size:21 final size:21
Alignment explanation
Indices: 43634171--43634241 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
43634161 CAGCCTGATA
43634171 TGAAACGTGTAAGACCATGGT
1 TGAAACGTGTAAGACCATGGT
** *
43634192 TGAAA-GATACAATGGCACC-TGAT
1 TGAAACG-TGTAA--G-ACCATGGT
43634215 ATGAAACGTGTAAGACCATGGT
1 -TGAAACGTGTAAGACCATGGT
43634237 TGAAA
1 TGAAA
43634242 GATACCATGG
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 1 0.03
21 16 0.43
22 4 0.11
23 4 0.11
24 11 0.30
25 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (21 bp):
TGAAACGTGTAAGACCATGGT
Found at i:43634249 original size:91 final size:92
Alignment explanation
Indices: 43634073--43634345 Score: 361
Period size: 91 Copynumber: 3.0 Consensus size: 92
43634063 AGTGTGCTCT
*
43634073 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAACCTGATATGAAACGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATGAAACGTGTAAG
*
43634138 ACCATGGTTGAAAGATACCATGGCAGC
66 ACCATGGTTGAAAGATACCATGGCAAC
*
43634165 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACAATGGC-ACCTGATATGAAACGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATGAAACGTGTAAG
43634229 ACCATGGTTGAAAGATACCATGGCAAC
66 ACCATGGTTGAAAGATACCATGGCAAC
* *** *** * * * * *
43634256 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATG-AAACGTGTAA
* * *
43634320 GACCATAGTTGAAAGACACTATGGCA
65 GACCATGGTTGAAAGATACCATGGCA
43634346 TCATGTCAAA
Statistics
Matches: 160, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
91 82 0.51
92 78 0.49
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (92 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAACCTGATATGAAACGTGTAAG
ACCATGGTTGAAAGATACCATGGCAAC
Found at i:43634320 original size:137 final size:137
Alignment explanation
Indices: 43634073--43634345 Score: 368
Period size: 137 Copynumber: 2.0 Consensus size: 137
43634063 AGTGTGCTCT
* * * * * ***
43634073 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACGATGGCAACCTGATATGAAACGTGTAAG
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
* * * * * *
43634138 ACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAACGTGTAAGACCATGGTTGAAAGATACA
66 ACCATGGTTGAAAGATACCATGGCAACATGACATGAAACGAGTAAGACCATAGTTGAAAGACACA
43634203 ATGGCAC
131 ATGGCAC
* *
43634210 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATAAATAAG
1 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
*
43634275 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACAC
66 ACCATGGTTGAAAGATACCATGGCAACATGACATG-AAACGAGTAAGACCATAGTTGAAAGACAC
*
43634339 TATGGCA
130 AATGGCA
43634346 TCATGTCAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
136 1 0.01
137 116 0.99
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (137 bp):
CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAACAAATAAG
ACCATGGTTGAAAGATACCATGGCAACATGACATGAAACGAGTAAGACCATAGTTGAAAGACACA
ATGGCAC
Found at i:43636678 original size:131 final size:132
Alignment explanation
Indices: 43636515--43636752 Score: 307
Period size: 131 Copynumber: 1.8 Consensus size: 132
43636505 GTAATTCGTG
* * * * * * *
43636515 GAATCATGCCCTAACGTGTTAGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCTTTTA
1 GAATCATGCCCTAACGTGCTAGGTTGCAATTTCTCGTTCGCTCAAAATAATCAAAGATCCCTTCA
* * *
43636580 GAATTTCACCCATGTCTTTTAAAAATCCCTT-AAATGAAGGCGATGTGTGATATTTGGCAATTCA
66 AAATTTCACCCACGTCTTCTAAAAATCCCTTAAAATGAAGGCGATGTGTGATATTTGGCAATTCA
43636644 CA
131 CA
* * * * *
43636646 GAATCGTGCCTTAACGTGCTGGGTTGCAATTTCTCGTTCGCTTAAAATAATCAAATATCCCTTCA
1 GAATCATGCCCTAACGTGCTAGGTTGCAATTTCTCGTTCGCTCAAAATAATCAAAGATCCCTTCA
* * *
43636711 AAATTTCACTCGCGTCTTCTAAAAATCCTTTAAAATGAAGGC
66 AAATTTCACCCACGTCTTCTAAAAATCCCTTAAAATGAAGGC
43636753 AATACTCAGT
Statistics
Matches: 88, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
131 78 0.89
132 10 0.11
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (132 bp):
GAATCATGCCCTAACGTGCTAGGTTGCAATTTCTCGTTCGCTCAAAATAATCAAAGATCCCTTCA
AAATTTCACCCACGTCTTCTAAAAATCCCTTAAAATGAAGGCGATGTGTGATATTTGGCAATTCA
CA
Found at i:43637122 original size:132 final size:131
Alignment explanation
Indices: 43636632--43637126 Score: 383
Period size: 131 Copynumber: 3.8 Consensus size: 131
43636622 ATGTGTGATA
* * * * * * * *
43636632 TTTGGCAATTCACAGAATCGTGCCTTAACGTGCTGGGTTGCAATTTCTCGTTCGCTT-AAAATAA
1 TTTGGCAATTCAGAGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCTCATTTG-TTCGAAACAA
* * * * * **
43636696 TCAAATATCCCTTCAAAATTTCACTCGCGTCTTCTAAAAATCCTTTAAAATGAAGGCAATACTC-
65 TCAAATATCCCTTCAGAATTTCACTCACGTTTTCTAAAAA-CCTTTAAAACGAAGGAAATGTTCG
43636760 AGTG
129 A-TG
* * * ** * *
43636764 TTTGACAA-TCCGGGAATCA-TGCCCTATCGTGCTGGGTTGTGATTTCTCGTTTGCTCGAAACAA
1 TTTGGCAATTCAGAGAAT-AGTGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCGAAACAA
* * ** * *
43636827 TCAAATATTCCTTTAGGTTTTCACTCATGTTTAT-TAAAAACCTTTCAAAACGAAGGTAATGTTC
65 TCAAATATCCCTTCAGAATTTCACTCACGTTT-TCTAAAAACCTTT-AAAACGAAGGAAATGTTC
43636891 GATG
128 GATG
** * * * * ** * * * *
43636895 TTTGGTGATT-TGAGAATCGTGCCCTGTCGTTCTGGGTTGCGCTTTTTCATCTGTCCTAAACAAT
1 TTTGGCAATTCAGAGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCGAAACAAT
* * * *
43636959 CGAAGATCCCTTCGGAATTTCACTCACGTTTTCTAAAAACCCTTTAAAACGAAAGAAATGTTCGA
66 CAAATATCCCTTCAGAATTTCACTCACGTTTTCTAAAAA-CCTTTAAAACGAAGGAAATGTTCGA
*
43637024 CG
130 TG
* * * * *
43637026 TTTGGCAATTCGGGGAATAGTGCCCTATCGTGCTGGGCTGCAATTTCCCATTTGTTC-AAGATAA
1 TTTGGCAATTCAGAGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCGAA-ACAA
* * **
43637090 TCAAATATCTCTTCATAATTTCACTCGTGTTTTCTAA
65 TCAAATATCCCTTCAGAATTTCACTCACGTTTTCTAA
43637127 GGCGATGCAA
Statistics
Matches: 278, Mismatches: 74, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
130 7 0.03
131 189 0.68
132 82 0.29
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (131 bp):
TTTGGCAATTCAGAGAATAGTGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCGAAACAAT
CAAATATCCCTTCAGAATTTCACTCACGTTTTCTAAAAACCTTTAAAACGAAGGAAATGTTCGAT
G
Found at i:43644342 original size:18 final size:18
Alignment explanation
Indices: 43644319--43644355 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
43644309 TCATCTAAAT
43644319 TTTCATACGATATTTCTA
1 TTTCATACGATATTTCTA
43644337 TTTCATACGATATTTCTA
1 TTTCATACGATATTTCTA
43644355 T
1 T
43644356 CATACTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTCATACGATATTTCTA
Found at i:43649500 original size:15 final size:16
Alignment explanation
Indices: 43649480--43649509 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43649470 GAAAATTGCC
43649480 AAAATGGG-CTAAATA
1 AAAATGGGACTAAATA
43649495 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
43649510 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:43657101 original size:17 final size:19
Alignment explanation
Indices: 43657067--43657104 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
43657057 AAACCTTGAA
43657067 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTTCTTCTTTC
43657086 TTTTCTC-TTT-TTCTTTC
1 TTTTCTCTTTTCTTCTTTC
43657103 TT
1 TT
43657105 CCTTCCCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTCTTCTTTC
Found at i:43658526 original size:42 final size:43
Alignment explanation
Indices: 43658460--43658621 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 43
43658450 TCGTTTTCTT
** * *
43658460 GATGCCATAGTTCAACTATAGTCTTACACATCTTCACATAAT-
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAATC
* *
43658502 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATAT-ATC
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAATC
*
43658544 GATGCCATAGCCCAGCTATGGTCTTACACGTAATC-ACACATCACATATC
1 GATGCCATAGCCCAGCTATGGTCTTACAC---ATCTTCACAT---A-ATC
*
43658593 GATGCCATAGCCCAGTTATGGTCTTACAC
1 GATGCCATAGCCCAGCTATGGTCTTACAC
43658622 GAATCACATA
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.02
42 62 0.61
44 4 0.04
45 2 0.02
49 31 0.31
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (43 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAATC
Found at i:43658602 original size:49 final size:49
Alignment explanation
Indices: 43658528--43658711 Score: 193
Period size: 49 Copynumber: 3.8 Consensus size: 49
43658518 TATGGTCTTA
* *
43658528 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAGATATGGTCTTACACGTAAT
* *
43658578 CACACATCACATATCGATGCCATAGCCCAGTTATGGTCTTACACG-AAT
1 CACATATCACATATCGATGCCATAGCCCAGATATGGTCTTACACGTAAT
* * * *
43658626 CACATATCTCACTA---ATGCCATATCCCAGATATGGTCTTATACAGT-AG
1 CACATATCACA-TATCGATGCCATAGCCCAGATATGGTCTTACAC-GTAAT
* * *
43658673 CATATATCAC--ACCGATGCCATATCCCAGATATGGTCTTA
1 CACATATCACATATCGATGCCATAGCCCAGATATGGTCTTA
43658712 TACGGAAATC
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
44 1 0.01
46 25 0.21
47 35 0.30
48 12 0.10
49 39 0.33
50 5 0.04
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAGCCCAGATATGGTCTTACACGTAAT
Found at i:43658714 original size:47 final size:46
Alignment explanation
Indices: 43658543--43658711 Score: 185
Period size: 47 Copynumber: 3.6 Consensus size: 46
43658533 ATTCATATAT
* * *
43658543 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACACATCACATAT
1 CGATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCAC--AC
* * *
43658592 CGATGCCATAGCCCAGTTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
** * * * *
43658638 TAATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACAC
*
43658685 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATAGCCCAGATATGGTCTTA
43658712 TACGGAAATC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
46 26 0.25
47 37 0.36
48 10 0.10
49 30 0.29
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (46 bp):
CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
Found at i:43658768 original size:31 final size:31
Alignment explanation
Indices: 43658733--43658881 Score: 235
Period size: 31 Copynumber: 4.8 Consensus size: 31
43658723 CTTGTCACTT
* *
43658733 GTAGCCGGAGTTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
43658764 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
43658795 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
** * *
43658826 GTAGTAGAAGCTACCACTTTTCACTGCTCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
43658857 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
43658882 TGTTATTTGT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:43658961 original size:50 final size:50
Alignment explanation
Indices: 43658857--43659033 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
43658847 CACTGCTCAG
* * *
43658857 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* * *
43658908 GTAGTCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
43658958 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
43659008 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
43659034 GTTGCCATGG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
50 92 0.80
51 23 0.20
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:43662916 original size:29 final size:29
Alignment explanation
Indices: 43662874--43662933 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
43662864 AAACGGAAGT
43662874 TTTGGCACTAAGTGTG-CATTTAAACTAGC
1 TTTGGCACTAAGTGTGTCATTT-AACTAGC
*
43662903 TTTGGCACTAAGTGTGTGATTTAACTAGC
1 TTTGGCACTAAGTGTGTCATTTAACTAGC
43662932 TT
1 TT
43662934 CGACTACTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGTCATTTAACTAGC
Found at i:43671644 original size:19 final size:19
Alignment explanation
Indices: 43671617--43671656 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43671607 AAGTTTTTTA
43671617 TATTATTAA-ATTATATTAT
1 TATTATTAATA-TATATTAT
*
43671636 TATTTTTAATATATATTAT
1 TATTATTAATATATATTAT
43671655 TA
1 TA
43671657 ACTCTAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTAATATATATTAT
Found at i:43674362 original size:14 final size:15
Alignment explanation
Indices: 43674343--43674372 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43674333 TACGCATTTA
43674343 ATTTTTAAATATTGT
1 ATTTTTAAATATTGT
*
43674358 ATTTTTAATTATTGT
1 ATTTTTAAATATTGT
43674373 TACTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
ATTTTTAAATATTGT
Found at i:43675114 original size:15 final size:13
Alignment explanation
Indices: 43675084--43675119 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
43675074 TGTTTAACTA
43675084 ATAATTATAAATT
1 ATAATTATAAATT
43675097 ATAATTATAATTATT
1 ATAATTATAA--ATT
43675112 ATAATTAT
1 ATAATTAT
43675120 CACAATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:43675203 original size:117 final size:116
Alignment explanation
Indices: 43674996--43675227 Score: 303
Period size: 118 Copynumber: 2.0 Consensus size: 116
43674986 TAAAATTAAT
* *
43674996 TAATTATCACAATTTATTTCTATATTTATACTTAAAGTTCTATTTAAATAATAAATCTATTTTAA
1 TAATTATCACAATTTATTTCTATATTTATACTCAAAGTTCTATTCAAATAATAAATCTATTTTAA
* * *
43675061 ATTTTATCATATTTGTTTAACTAAT-AATTATAAATTATAATTATAATTATTA
66 ATATTAGCAAATTTGTTTAACTAATAAATT-TAAATTA-AATTATAATTATTA
* * *
43675113 TAATTATCACAATCTT-TTTCTATATTTTATGA-TCAATGTTCTATTCAAGTAATAAATTTATTT
1 TAATTATCACAAT-TTATTTCTATA-TTTAT-ACTCAAAGTTCTATTCAAATAATAAATCTATTT
43675176 TAAA-ATTAGCACAATTT-TTTAACTAATAAATTTAAATTAAATTATAATTATT
63 TAAATATTAGCA-AATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATT
43675228 TTTAAAGTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
116 13 0.13
117 43 0.42
118 45 0.44
119 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (116 bp):
TAATTATCACAATTTATTTCTATATTTATACTCAAAGTTCTATTCAAATAATAAATCTATTTTAA
ATATTAGCAAATTTGTTTAACTAATAAATTTAAATTAAATTATAATTATTA
Found at i:43680754 original size:45 final size:45
Alignment explanation
Indices: 43680704--43680794 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
43680694 TTCCTGCAGA
*
43680704 TTTCATGCCCTTGACGTCCAGCCCAAATAAATTTTGGGTCTAATT
1 TTTCATGCCCTTGACATCCAGCCCAAATAAATTTTGGGTCTAATT
*
43680749 TTTCATGCCCTTGCCATCCAGCCCAAATAAATTTTGGGTCTAATT
1 TTTCATGCCCTTGACATCCAGCCCAAATAAATTTTGGGTCTAATT
43680794 T
1 T
43680795 CCTTTTAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.36
Consensus pattern (45 bp):
TTTCATGCCCTTGACATCCAGCCCAAATAAATTTTGGGTCTAATT
Found at i:43681305 original size:19 final size:17
Alignment explanation
Indices: 43681281--43681324 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
43681271 CAAGTTAAAC
43681281 AAAGAAAGAAAGAAAATAA
1 AAAGAAAGAAAG-AAA-AA
43681300 AAAGAAAGAAAGAAAAA
1 AAAGAAAGAAAGAAAAA
43681317 AAAGAAAG
1 AAAGAAAG
43681325 GAATGCACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 10 0.40
18 3 0.12
19 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAGAAAGAAAGAAAAA
Found at i:43681320 original size:13 final size:14
Alignment explanation
Indices: 43681285--43681324 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
43681275 TTAAACAAAG
*
43681285 AAAGAAAGAAAATAA
1 AAAGAAAG-AAAGAA
43681300 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
43681314 AAA-AAAGAAAG
1 AAAGAAAGAAAG
43681325 GAATGCACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 8 0.33
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:43695963 original size:6 final size:6
Alignment explanation
Indices: 43695952--43695976 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43695942 AAGACTTTTC
43695952 AAATTA AAATTA AAATTA AAATTA A
1 AAATTA AAATTA AAATTA AAATTA A
43695977 GATTTCTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTA
Found at i:43710705 original size:22 final size:21
Alignment explanation
Indices: 43710676--43710719 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
43710666 TCAGGTCAAA
*
43710676 TTAGGAAAG-CTGTTAACTGAG
1 TTAGGAAAGTATGTTAAC-GAG
43710697 TTAGAGAAAGTATGTTAACGAG
1 TTAG-GAAAGTATGTTAACGAG
43710719 T
1 T
43710720 CATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 9 0.45
23 7 0.35
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (21 bp):
TTAGGAAAGTATGTTAACGAG
Found at i:43711410 original size:14 final size:14
Alignment explanation
Indices: 43711370--43711412 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
43711360 TTGTGATTAT
43711370 TTTAATTTTATTGTA
1 TTTAATTTTA-TGTA
* *
43711385 TATAATTATATGTA
1 TTTAATTTTATGTA
*
43711399 TTTACTTTTATGTA
1 TTTAATTTTATGTA
43711413 GGATAAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTAATTTTATGTA
Found at i:43720034 original size:21 final size:21
Alignment explanation
Indices: 43719997--43720050 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
43719987 TGCTATTCTG
*
43719997 TTGTTTTTCCATGTTTTG-CTA
1 TTGTTTTCCCATGTTTTGTC-A
43720018 TTGTTTTCCCACT-TTTTGTCA
1 TTGTTTTCCCA-TGTTTTGTCA
*
43720039 TTATTTTCCCAT
1 TTGTTTTCCCAT
43720051 CATTTCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 26 0.90
22 2 0.07
ACGTcount: A:0.11, C:0.20, G:0.09, T:0.59
Consensus pattern (21 bp):
TTGTTTTCCCATGTTTTGTCA
Found at i:43722268 original size:3 final size:3
Alignment explanation
Indices: 43722260--43722286 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43722250 CCATAGTGTT
43722260 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
43722287 CTACTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43726420 original size:45 final size:45
Alignment explanation
Indices: 43726370--43726524 Score: 197
Period size: 45 Copynumber: 3.4 Consensus size: 45
43726360 CTACTGTTAC
* *
43726370 TGTTACCGTTACTGTTACTGATTCGATACTTTGTGTGTCAAATAT
1 TGTTACCGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATAT
*
43726415 TGTTACTGTTACTGTTA-TCGATTCGACACTTTGTGTGTCGAATAT
1 TGTTACCGTTACTGTTACT-GATTCGACACTTTGTGTGTCGAATAT
* * * *
43726460 TGTTATCGTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATAC
1 TGTTACCGTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATAT
* *
43726505 TGTTACTGTTACTGCTACTG
1 TGTTACCGTTACTGTTACTG
43726525 CTACCGTTAC
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.02
45 93 0.98
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (45 bp):
TGTTACCGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATAT
Found at i:43726533 original size:18 final size:18
Alignment explanation
Indices: 43726502--43726536 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43726492 GTGTGTTGAA
* *
43726502 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
43726520 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
43726537 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:43733431 original size:12 final size:12
Alignment explanation
Indices: 43733414--43733438 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43733404 GCCGACTACT
43733414 GTTACTGTTACC
1 GTTACTGTTACC
43733426 GTTACTGTTACC
1 GTTACTGTTACC
43733438 G
1 G
43733439 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:43733469 original size:45 final size:45
Alignment explanation
Indices: 43733419--43733559 Score: 221
Period size: 45 Copynumber: 3.1 Consensus size: 45
43733409 CTACTGTTAC
43733419 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
1 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
*
43733464 TGTTACCGTTACTGTTACCGATTTGACACTTTGTGTGTCGAATAT
1 TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
* * * *
43733509 TGTTACTGTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATAC
1 TGTTACCGTTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATAT
43733554 TGTTAC
1 TGTTAC
43733560 TATTACTGCT
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 1 0.01
45 88 0.99
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (45 bp):
TGTTACCGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAT
Found at i:43741311 original size:35 final size:32
Alignment explanation
Indices: 43741271--43741337 Score: 80
Period size: 35 Copynumber: 2.0 Consensus size: 32
43741261 CAATCAGTAA
* *
43741271 TATTCATTAACATTCAGCTAATCAGAACAATTATT
1 TATTCAATAACAGTCAG-TAA-CA-AACAATTATT
*
43741306 TATTCAATAACAGTCAGTAACAATCAATTATT
1 TATTCAATAACAGTCAGTAACAAACAATTATT
43741338 CAATAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 9 0.31
33 2 0.07
34 3 0.10
35 15 0.52
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (32 bp):
TATTCAATAACAGTCAGTAACAAACAATTATT
Found at i:43744067 original size:26 final size:26
Alignment explanation
Indices: 43744036--43744195 Score: 266
Period size: 26 Copynumber: 6.2 Consensus size: 26
43744026 TGAAATGCCC
* *
43744036 ATCATGGAATATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
43744062 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43744088 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43744114 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
43744140 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
43744166 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
43744192 ATCA
1 ATCA
43744196 ATTTGTACCA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 124 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:43744093 original size:52 final size:52
Alignment explanation
Indices: 43744036--43744195 Score: 311
Period size: 52 Copynumber: 3.1 Consensus size: 52
43744026 TGAAATGCCC
*
43744036 ATCATGGAATATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
43744088 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
43744140 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
43744192 ATCA
1 ATCA
43744196 ATTTGTACCA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 107 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (52 bp):
ATCATGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATT
Found at i:43746703 original size:6 final size:6
Alignment explanation
Indices: 43746694--43746730 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
43746684 CCGAAGCCGA
*
43746694 AACAGT AACAGT AACAGT AACAGT AACAGT AATAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
43746731 CGGTACACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (6 bp):
AACAGT
Found at i:43746776 original size:6 final size:6
Alignment explanation
Indices: 43746765--43746804 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
43746755 ACAAATCCGG
**
43746765 AACAGT AACAGT AACAGT AATGGT AACAGT AACAGT AACA
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACA
43746805 ATATCCAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.17
Consensus pattern (6 bp):
AACAGT
Found at i:43749241 original size:6 final size:6
Alignment explanation
Indices: 43749227--43749260 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
43749217 AGGAAACAAG
*
43749227 AAAACT AAAATT AAAACT AAAACT AAAACT AAAA
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAA
43749261 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAACT
Found at i:43749266 original size:18 final size:18
Alignment explanation
Indices: 43749227--43749266 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43749217 AGGAAACAAG
* **
43749227 AAAACTAAAATTAAAACT
1 AAAACTAAAACTAAAAAA
43749245 AAAACTAAAACTAAAAAA
1 AAAACTAAAACTAAAAAA
43749263 AAAA
1 AAAA
43749267 AGAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAACTAAAACTAAAAAA
Found at i:43751569 original size:20 final size:18
Alignment explanation
Indices: 43751538--43751594 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 18
43751528 TCATTTTTCA
43751538 ATAAATTCAATTTCAATAATT
1 ATAAA-TCAATTT-AAT-ATT
43751559 -TAATATCAATTTAATATT
1 ATAA-ATCAATTTAATATT
43751577 ATAAATCAATTATAATAT
1 ATAAATCAATT-TAATAT
43751595 AGTGTGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.30
19 12 0.36
20 10 0.30
21 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATCAATTTAATATT
Found at i:43762574 original size:39 final size:39
Alignment explanation
Indices: 43762518--43762614 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
43762508 TGATTTGAAA
* * * *
43762518 CCCGAAGTCTAGCTAAAGCACATAAGTGCTAAATGGAAG
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
* *
43762557 CTCGAAGGCTAACTAAAGCACACAAGTGTTAAACGGAAG
1 CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
*
43762596 CCCGAAGGCTAACTGAAGC
1 CCCGAAGGCTAACTAAAGC
43762615 TCATCAGAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (39 bp):
CCCGAAGGCTAACTAAAGCACACAAGTGCTAAACGGAAG
Found at i:43773841 original size:26 final size:26
Alignment explanation
Indices: 43773812--43773871 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
43773802 TCCCTTTGAA
* *
43773812 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTTGCACACTAAGTG
43773838 TCATTCTCAATATCTTGCACACTAAGTG
1 TCA-T-TCAATATCTTGCACACTAAGTG
*
43773866 CCATTC
1 TCATTC
43773872 TCAATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTTGCACACTAAGTG
Found at i:43773855 original size:28 final size:28
Alignment explanation
Indices: 43773819--43773878 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
43773809 GAATCATTCG
* *
43773819 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATCTTGCACACTAAGTGCCATTCTCA
43773847 ATATCTTGCACACTAAGTGCCATTCTCA
1 ATATCTTGCACACTAAGTGCCATTCTCA
43773875 ATAT
1 ATAT
43773879 TTCGTACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (28 bp):
ATATCTTGCACACTAAGTGCCATTCTCA
Found at i:43778690 original size:57 final size:57
Alignment explanation
Indices: 43778599--43778896 Score: 452
Period size: 57 Copynumber: 5.2 Consensus size: 57
43778589 GATCTCATTT
* * * *
43778599 CACACACTTAGTGCCCCAAAAACCGATCTTGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* *
43778658 CACACACAGTGCCTCACCAACCGATCTCGCACACACAGTGCTCAGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
43778715 CGCACACAGTGCCTCAACAACCGATCTCGCACATACAGTGCTCGGTTATGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* *
43778772 CGCACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
43778829 CACACATAGTGCCTCAACAATCGATCTCGCACACACAATGCTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
43778886 CACACACAGTG
1 CACACACAGTG
43778897 TCTATGTTCA
Statistics
Matches: 219, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
57 212 0.97
59 7 0.03
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.18
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:43778695 original size:29 final size:29
Alignment explanation
Indices: 43778654--43778865 Score: 178
Period size: 29 Copynumber: 7.4 Consensus size: 29
43778644 GGTTACGGAA
*
43778654 CTCGCACACACAGTGCCTCACCAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
*** * *
43778683 CTCGCACACACAGTG-CTCAGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
*
43778711 CTCGCGCACACAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
* **** ** *
43778740 CTCGCACATACAGTG-CTCGGTTATGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
*
43778768 CTCGCGCACACAGTGCCTCAACAACCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
**** * *
43778797 CTCGCACACACAGTG-CTCGGTTACGGAA
1 CTCGCACACACAGTGCCTCAACAACCGAT
* * *
43778825 CTCACACACATAGTGCCTCAACAATCGAT
1 CTCGCACACACAGTGCCTCAACAACCGAT
43778854 CTCGCACACACA
1 CTCGCACACACA
43778866 ATGCTCGGTT
Statistics
Matches: 133, Mismatches: 47, Indels: 6
0.72 0.25 0.03
Matches are distributed among these distances:
28 61 0.46
29 72 0.54
ACGTcount: A:0.28, C:0.37, G:0.18, T:0.17
Consensus pattern (29 bp):
CTCGCACACACAGTGCCTCAACAACCGAT
Found at i:43779710 original size:46 final size:46
Alignment explanation
Indices: 43779651--43780532 Score: 1550
Period size: 46 Copynumber: 19.2 Consensus size: 46
43779641 CATTTTTTTG
** * *
43779651 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATG
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
* * **** * *
43779697 TCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCTG
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
* *
43779743 TCATGTTGCCATTGTATCTTTCAACCATGGTC-TACACATTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
* * * *
43779788 TCAGGCTGCCATGGTATCTTTCAACCATGGTCTAACATGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
* *
43779834 TCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43779880 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43779926 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43779972 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780018 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780064 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780110 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780156 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780202 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780248 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780294 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780340 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780386 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
43780432 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
* *
43780478 TCATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
*
43780524 TCAGGTTGC
1 TCATGTTGC
43780533 TCACACATTT
Statistics
Matches: 809, Mismatches: 26, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
45 37 0.05
46 772 0.95
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATA
Found at i:43780542 original size:23 final size:23
Alignment explanation
Indices: 43780512--43780555 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
43780502 CCATGGTCTT
43780512 ACACATTTCATATCAGGTTGCTC
1 ACACATTTCATATCAGGTTGCTC
43780535 ACACATTTCATATCAGGTTGC
1 ACACATTTCATATCAGGTTGC
43780556 CATGGTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (23 bp):
ACACATTTCATATCAGGTTGCTC
Found at i:43780557 original size:69 final size:69
Alignment explanation
Indices: 43780466--43780601 Score: 227
Period size: 69 Copynumber: 2.0 Consensus size: 69
43780456 CCATGGTCTT
* *
43780466 ACACGTTTCATATCATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
1 ACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
43780531 GCTC
66 GCTC
* * *
43780535 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGTT
1 ACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
43780600 GC
66 GC
43780602 CATGGTATCT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (69 bp):
ACACATTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTT
GCTC
Found at i:43780562 original size:115 final size:114
Alignment explanation
Indices: 43780420--43780641 Score: 392
Period size: 115 Copynumber: 1.9 Consensus size: 114
43780410 CCATGGTCTT
* *
43780420 ACACGTTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGCT
1 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGCT
43780485 GCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCTC
66 GCCATGGTATCTTTCAACCATGGTCTTAC-CATTTTC-TATCAGGTTGCTC
*
43780535 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGTT
1 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGCT
43780600 GCCATGGTATCTTTCAACCATGGTCTTACCATTTTCTATCAG
66 GCCATGGTATCTTTCAACCATGGTCTTACCATTTTCTATCAG
43780642 AGAGCACACT
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
114 8 0.08
115 95 0.92
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (114 bp):
ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCATGCT
GCCATGGTATCTTTCAACCATGGTCTTACCATTTTCTATCAGGTTGCTC
Found at i:43780593 original size:46 final size:46
Alignment explanation
Indices: 43780535--43780641 Score: 173
Period size: 46 Copynumber: 2.3 Consensus size: 46
43780525 CAGGTTGCTC
43780535 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
* *
43780581 ACACGTTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
43780627 AC-CATTTTC-TATCAG
1 ACACA-TTTCATATCAG
43780642 AGAGCACACT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 6 0.11
46 50 0.89
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
ACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
Found at i:43782814 original size:18 final size:20
Alignment explanation
Indices: 43782799--43782835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43782789 TAATAATAAA
*
43782799 ATATCTCATTAAAATAATAT
1 ATATCTAATTAAAATAATAT
43782819 ATATCTAATT-AAATAAT
1 ATATCTAATTAAAATAAT
43782836 CATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATCTAATTAAAATAATAT
Found at i:43784889 original size:26 final size:26
Alignment explanation
Indices: 43784860--43784919 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
43784850 TCCCTTTGAA
* * *
43784860 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
43784886 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
43784914 TCATTC
1 TCATTC
43784920 TCAATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:43784935 original size:28 final size:28
Alignment explanation
Indices: 43784867--43784945 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
43784857 GAATCATTCG
43784867 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGTCATTCTCA
* *
43784895 ATATCTCGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGTCATTCTCA
* * *
43784923 ATATTTTGTACACTGAGTATCAT
1 ATATTTTGCACACTAAGTGTCAT
43784946 ATTTGATTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGTCATTCTCA
Found at i:43788414 original size:7 final size:7
Alignment explanation
Indices: 43788402--43788430 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
43788392 TTACATATTA
43788402 TAAATTT
1 TAAATTT
43788409 TAAATTT
1 TAAATTT
43788416 TAAATTT
1 TAAATTT
43788423 TAAATTT
1 TAAATTT
43788430 T
1 T
43788431 CGTATATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:43792363 original size:64 final size:64
Alignment explanation
Indices: 43792290--43792414 Score: 196
Period size: 64 Copynumber: 2.0 Consensus size: 64
43792280 TCATTCATAA
* * * *
43792290 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATACCATCCTAATTATTTGACATAAGTAT
1 CACATCTAGTTAAGAACATTTGATTCATGTCGATCATACAATCCTAATTATTTGACATAAGTAT
* *
43792354 CACATCTAGTTAAGAACATTTTATTCATGTCGATCATAGAATCCTAATTATTTGACATAAG
1 CACATCTAGTTAAGAACATTTGATTCATGTCGATCATACAATCCTAATTATTTGACATAAG
43792415 CATAGGCCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (64 bp):
CACATCTAGTTAAGAACATTTGATTCATGTCGATCATACAATCCTAATTATTTGACATAAGTAT
Found at i:43792669 original size:133 final size:133
Alignment explanation
Indices: 43792431--43792860 Score: 682
Period size: 133 Copynumber: 3.2 Consensus size: 133
43792421 CCTATGAAAC
* * * *
43792431 AGATTGTAAATCTTGTCTCCCTGAAGTTGCAATGGACCAAAGCAAAGATGACGAATCTTGGCTTC
1 AGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTTC
*
43792496 CTGAAGTTGCAGTGAAATAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
66 CTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
43792561 TAA
131 TAA
* * * * *
43792564 AGATTGTAGATCTTGTCTCCCTAAAATTGCAGTGGGGCAAATCAAAGATAACGAATCTTTGCTTC
1 AGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTTC
* * *
43792629 CTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCTCTAGACTTGTAGTGGAGTAGGC
66 CTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
43792694 TAA
131 TAA
*
43792697 AGATTGTAGATCTTGTCTCCCTGAAGTTGTAGTGGAGCAAAT-AGAAGATGACGAATCTTGGCTT
1 AGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCA-AAGATGACGAATCTTGGCTT
* *
43792761 CCTGAAGTTGCAGTGAAGCAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGAAGG
65 CCTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGG
*
43792826 CTGA
130 CTAA
*
43792830 AGATTATAGATCTTGTCTCCCTGAAGTTGCA
1 AGATTGTAGATCTTGTCTCCCTGAAGTTGCA
43792861 ACAGAGCAAA
Statistics
Matches: 269, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
132 1 0.00
133 268 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (133 bp):
AGATTGTAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCAAATCAAAGATGACGAATCTTGGCTTC
CTGAAGTTGCAGTGAAACAGATTTAAGCCACCATCCTAGCTCCCTAAAGTTGTAGTGGAGTAGGC
TAA
Found at i:43792930 original size:89 final size:88
Alignment explanation
Indices: 43792801--43793035 Score: 274
Period size: 88 Copynumber: 2.6 Consensus size: 88
43792791 ACCATCCTAG
* * *
43792801 CTCCCTAAAGTTGTAGTGGAGA-AGGCTGAAGATTATAGATCTTGTCTCCCTGAAGTTGCAACAG
1 CTCCCT-AAGTCGTAG-GGTGACAGGCTGAAGATTATAGATCTTGTCTCTCTGAAGTTGCAACAG
* * **
43792865 AGCAAATCGAAGACGGCAAGCCTTAA
64 AGCAAAT-AAAAAAAGCAAGCCTTAA
* * * * * *
43792891 CTCCCTAAGTCGTAGGGTGACAGGCTGAAGATTGTAGATCTTGTCTTTCTGAACTCGCAGCGGAG
1 CTCCCTAAGTCGTAGGGTGACAGGCTGAAGATTATAGATCTTGTCTCTCTGAAGTTGCAACAGAG
43792956 CAAATAAAAAAAGCAAGCCTTAA
66 CAAATAAAAAAAGCAAGCCTTAA
* * * * *
43792979 CACCCTAAGTCGTAGGGTAACAGGCTGAAGTTTACAGATCTCGTCTCTCTGAAGTTG
1 CTCCCTAAGTCGTAGGGTGACAGGCTGAAGATTATAGATCTTGTCTCTCTGAAGTTG
43793036 TAGTGGAACA
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
88 66 0.54
89 50 0.41
90 6 0.05
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (88 bp):
CTCCCTAAGTCGTAGGGTGACAGGCTGAAGATTATAGATCTTGTCTCTCTGAAGTTGCAACAGAG
CAAATAAAAAAAGCAAGCCTTAA
Found at i:43793048 original size:88 final size:87
Alignment explanation
Indices: 43792880--43793106 Score: 228
Period size: 88 Copynumber: 2.6 Consensus size: 87
43792870 ATCGAAGACG
* ** * *
43792880 GCAAGCCTTAACTCCCTAAGTCGTAGGGTGACAGGCTGAAGATTGTAGATCTTGTCTTTCTGAAC
1 GCAAGCCTTAAC-CCCTAAGTCGTAGGGTAACAGGCTGAAG-TTACAGATCTCGTCTCTCTGAAC
*
43792945 TCGCAGCGGAGCAAAT-AAAAAAA
64 TCGCAGCGGAACAAATCAAAAAAA
*
43792968 GCAAGCCTTAACACCCTAAGTCGTAGGGTAACAGGCTGAAGTTTACAGATCTCGTCTCTCTGAAG
1 GCAAGCCTTAAC-CCCTAAGTCGTAGGGTAACAGGCTGAAG-TTACAGATCTCGTCTCTCTGAAC
* * * * *
43793033 TTGTAGTGGAACAAATCAAAGAAG
64 TCGCAGCGGAACAAATCAAAAAAA
* * *
43793057 GTGAA-CCTTAACCCACTAAG-CAATAGGGTAACAGACTGAA-TTACAGATCT
1 G-CAAGCCTTAACCC-CTAAGTC-GTAGGGTAACAGGCTGAAGTTACAGATCT
43793107 TATCTCCTTG
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
87 10 0.08
88 72 0.61
89 34 0.29
90 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (87 bp):
GCAAGCCTTAACCCCTAAGTCGTAGGGTAACAGGCTGAAGTTACAGATCTCGTCTCTCTGAACTC
GCAGCGGAACAAATCAAAAAAA
Found at i:43794503 original size:46 final size:46
Alignment explanation
Indices: 43794392--43794666 Score: 336
Period size: 46 Copynumber: 6.0 Consensus size: 46
43794382 TTATCTTTGA
* * * * * **
43794392 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGT
**
43794439 CATG-TCGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGCT-GCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
*** **
43794485 CATGCTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* * *
43794531 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* *
43794577 CAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
* *
43794623 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
43794667 ATCAGAGAGC
Statistics
Matches: 205, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
46 172 0.84
47 33 0.16
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGT
Found at i:43794671 original size:92 final size:92
Alignment explanation
Indices: 43794397--43794671 Score: 379
Period size: 92 Copynumber: 3.0 Consensus size: 92
43794387 TTTGACATGA
* * * ** *
43794397 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTTGTCATGTCGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATGGTATCTTTCAA
** * *
43794462 CCATGGTCTTATTCATTTCATGTCATGC
65 CCATGGTCTTACACATTTCATATCAGGC
* * ** *
43794490 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTCATGTTGTCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
43794555 CATGGTCTTACACATTTCATATCAGGC
66 CATGGTCTTACACATTTCATATCAGGC
* * *
43794582 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
43794647 CATGGTCTTACACATTTCATATCAG
66 CATGGTCTTACACATTTCATATCAG
43794672 AGAGCACACT
Statistics
Matches: 160, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
92 132 0.82
93 28 0.17
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGC
Found at i:43799266 original size:3 final size:3
Alignment explanation
Indices: 43799252--43799298 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
43799242 AATTTGTTTT
* *
43799252 TTA TTA TT- TTA TTA TTA TTA TTA TTT TTA -TA TTA TTT TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
43799296 TTA
1 TTA
43799299 ATAGAGTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:43799274 original size:17 final size:17
Alignment explanation
Indices: 43799252--43799293 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
43799242 AATTTGTTTT
43799252 TTATTA-TTTTATTATTA
1 TTATTATTTTTA-TATTA
43799269 TTATTATTTTTATATTA
1 TTATTATTTTTATATTA
*
43799286 TTTTTATT
1 TTATTATT
43799294 CATTAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTATTTTTATATTA
Found at i:43799806 original size:131 final size:131
Alignment explanation
Indices: 43799460--43799816 Score: 464
Period size: 130 Copynumber: 2.7 Consensus size: 131
43799450 AACAAAAGCG
* * * * * *
43799460 ATGTTTGACGTTTAGAAATTCGAGGAATTGTGCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGT
1 ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGT
* * *
43799525 TCAAAACGATCGAATATTTCTTTAGAATTTCGCACATGTCTTTAAAAATTCTTCTAAACGAAGGC
66 TCAAAACAATCGAATATTCCTTTAGAATTTCGCACATGTCTTTAAAAATTCTTCAAAACGAAGGC
43799590 A
131 A
** * * * *
43799591 ATACTCGATGCTTGTCAATTC-GGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCCCGTTTGT
1 ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGT
* ** * *
43799655 TCAAAACAATCGAATATTCCTTTGGAATTTCGTTCATGTCTTTAAAAATTCTTCAAAACGAATGT
66 TCAAAACAATCGAATATTCCTTTAGAATTTCGCACATGTCTTTAAAAATTCTTCAAAACGAAGGC
43799720 A
131 A
* * * * *
43799721 ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCATGCTAGGTTGTGATCTCTTGTTTGT
1 ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGT
* *
43799786 TCCAAATAATCGAATATTCCTTTAGAATTTC
66 TCAAAACAATCGAATATTCCTTTAGAATTTC
43799817 ACTCATTCTA
Statistics
Matches: 191, Mismatches: 34, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
130 113 0.59
131 78 0.41
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (131 bp):
ATGTTCGACGTTTGGCAATTCGGGGAATCGTGCCCTATCGTGCTGGGTTGCGATTTCTCGTTTGT
TCAAAACAATCGAATATTCCTTTAGAATTTCGCACATGTCTTTAAAAATTCTTCAAAACGAAGGC
A
Found at i:43800768 original size:24 final size:24
Alignment explanation
Indices: 43800740--43800786 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
43800730 CATAAAAAAA
43800740 ATTAATGATTAATAACCAATCACC
1 ATTAATGATTAATAACCAATCACC
* * *
43800764 ATTAATTATTAATTATCAATCAC
1 ATTAATGATTAATAACCAATCAC
43800787 GTTTTAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (24 bp):
ATTAATGATTAATAACCAATCACC
Found at i:43826002 original size:21 final size:23
Alignment explanation
Indices: 43825978--43826020 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
43825968 TTGATAGTAT
43825978 AATTATATTATT-TAA-TATTTG
1 AATTATATTATTATAATTATTTG
*
43825999 AATTATTTTATTATAATTATTT
1 AATTATATTATTATAATTATTT
43826021 TTAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTATATTATTATAATTATTTG
Found at i:43848557 original size:15 final size:15
Alignment explanation
Indices: 43848534--43848583 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
43848524 TTTATTTAAT
43848534 TTATATTGATTGAAA
1 TTATATTGATTGAAA
*
43848549 TTATTTTGATTGAAA
1 TTATATTGATTGAAA
43848564 TTATATTGATTG-AA
1 TTATATTGATTGAAA
43848578 TTATAT
1 TTATAT
43848584 AATATATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
14 8 0.24
15 25 0.76
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:43849222 original size:19 final size:20
Alignment explanation
Indices: 43849198--43849239 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
43849188 ATGAAACGAG
43849198 AAATTGA-AT-TGAGAATTGA
1 AAATTGAGATATGAG-ATTGA
43849217 AAATTGAGATATGAGATTGA
1 AAATTGAGATATGAGATTGA
43849237 AAA
1 AAA
43849240 CATGAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (20 bp):
AAATTGAGATATGAGATTGA
Found at i:43867915 original size:17 final size:16
Alignment explanation
Indices: 43867889--43867924 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
43867879 TAAAAATTGA
43867889 TAATTTTAATTATAAT
1 TAATTTTAATTATAAT
*
43867905 TAATATTTAATTATATT
1 TAAT-TTTAATTATAAT
43867922 TAA
1 TAA
43867925 CAAAGGGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTTAATTATAAT
Found at i:43883500 original size:21 final size:20
Alignment explanation
Indices: 43883478--43883531 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
43883468 AGTTATTTAT
43883478 TTTATATATTGTTAAATTAA
1 TTTATATATTGTTAAATTAA
* * *
43883498 TTTATCCTAATGTCAAATTAA
1 TTTAT-ATATTGTTAAATTAA
*
43883519 TTTATACATTGTT
1 TTTATATATTGTT
43883532 GTTGGAGTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTATATATTGTTAAATTAA
Found at i:43884848 original size:27 final size:28
Alignment explanation
Indices: 43884788--43884849 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
43884778 ACCTCGAACC
43884788 TCGAGG-TTTAGGGTTTGGATTTAGGAT
1 TCGAGGTTTTAGGGTTTGGATTTAGGAT
** *
43884815 TTAAGGTTTTA-GGTTTGGGTTT-GAGAT
1 TCGAGGTTTTAGGGTTTGGATTTAG-GAT
43884842 TCGAGGTT
1 TCGAGGTT
43884850 CGAGGTTCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 1 0.04
27 23 0.82
28 4 0.14
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.44
Consensus pattern (28 bp):
TCGAGGTTTTAGGGTTTGGATTTAGGAT
Found at i:43884853 original size:7 final size:7
Alignment explanation
Indices: 43884841--43884871 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
43884831 GGGTTTGAGA
43884841 TTCGAGG
1 TTCGAGG
43884848 TTCGAGG
1 TTCGAGG
43884855 TTCGAGG
1 TTCGAGG
43884862 TTCGAGG
1 TTCGAGG
43884869 TTC
1 TTC
43884872 AAGATTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.39, T:0.32
Consensus pattern (7 bp):
TTCGAGG
Found at i:43884865 original size:21 final size:21
Alignment explanation
Indices: 43884832--43884871 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43884822 TTTAGGTTTG
*
43884832 GGTTTGAGATTCGAGGTTCGA
1 GGTTCGAGATTCGAGGTTCGA
*
43884853 GGTTCGAGGTTCGAGGTTC
1 GGTTCGAGATTCGAGGTTC
43884872 AAGATTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.40, T:0.33
Consensus pattern (21 bp):
GGTTCGAGATTCGAGGTTCGA
Found at i:43886971 original size:57 final size:57
Alignment explanation
Indices: 43886883--43886995 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
43886873 AATTTTCCTA
*
43886883 CTGATTTCATACCCTTGCCGTCCAGCCCAAATAACTTTTGGGTCTAATTGCCTTTTG
1 CTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTG
*
43886940 CTGATTTCATGCCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTT
1 CTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTT
43886996 AAATCCTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.37
Consensus pattern (57 bp):
CTGATTTCATACCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTG
Found at i:43888055 original size:46 final size:44
Alignment explanation
Indices: 43887996--43888110 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
43887986 ACAGGACAGA
* *
43887996 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* * *
43888042 ACGGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
43888086 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
43888111 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:43888102 original size:44 final size:45
Alignment explanation
Indices: 43887996--43888129 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 45
43887986 ACAGGACAGA
* * *
43887996 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
43888042 ACGGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * *
43888086 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
43888130 CAGGGTATTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
44 35 0.49
45 1 0.01
46 36 0.50
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:43889514 original size:7 final size:7
Alignment explanation
Indices: 43889502--43889529 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
43889492 AAGCCATTAC
43889502 ATGTTCA
1 ATGTTCA
43889509 ATGTTCA
1 ATGTTCA
43889516 ATGTTCA
1 ATGTTCA
43889523 ATGTTCA
1 ATGTTCA
43889530 CTATTCACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
ATGTTCA
Found at i:43892845 original size:21 final size:21
Alignment explanation
Indices: 43892819--43892868 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
43892809 ACCTATTGTA
*
43892819 TTCACACACACCATA-AGCATG
1 TTCACACACAACATATAG-ATG
**
43892840 TTCACACTTAACATATAGATG
1 TTCACACACAACATATAGATG
43892861 TTCACACA
1 TTCACACA
43892869 TAGGTCATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (21 bp):
TTCACACACAACATATAGATG
Found at i:43897537 original size:56 final size:56
Alignment explanation
Indices: 43897453--43897562 Score: 184
Period size: 56 Copynumber: 2.0 Consensus size: 56
43897443 AAATAATTTA
* * *
43897453 TTGTGTTTATCTTTGTTTTATCGTAATGATACAACCAATACTGCTCATAGCAATTG
1 TTGTGTTTATCTTAGTTTTATCGCAATGATACAACCAATACTACTCATAGCAATTG
*
43897509 TTGTGTTTATCTTAGTTTTATCGCAATGATGCAACCAATACTACTCATAGCAAT
1 TTGTGTTTATCTTAGTTTTATCGCAATGATACAACCAATACTACTCATAGCAAT
43897563 GTTTCAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (56 bp):
TTGTGTTTATCTTAGTTTTATCGCAATGATACAACCAATACTACTCATAGCAATTG
Found at i:43897703 original size:27 final size:27
Alignment explanation
Indices: 43897651--43897703 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43897641 TTTTAATTAC
*
43897651 AAAATAATGAAAAATTAATTACATTTT
1 AAAATAATGAAAAATTAAATACATTTT
*
43897678 AAAATAA-GATAAAATTAAATATATTT
1 AAAATAATGA-AAAATTAAATACATTT
43897704 AATTTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (27 bp):
AAAATAATGAAAAATTAAATACATTTT
Found at i:43900267 original size:14 final size:15
Alignment explanation
Indices: 43900248--43900303 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
43900238 AATCTTCAAT
43900248 GATATG-CAATCTTA
1 GATATGACAATCTTA
43900262 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
43900279 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
43900297 GATATGA
1 GATATGA
43900304 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:43900292 original size:35 final size:37
Alignment explanation
Indices: 43900246--43900324 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
43900236 ATAATCTTCA
43900246 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
43900282 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
43900318 A-GATATG
1 ATGATATG
43900325 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:43900324 original size:17 final size:19
Alignment explanation
Indices: 43900246--43900317 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
43900236 ATAATCTTCA
43900246 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43900265 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43900282 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43900300 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
43900318 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:43900343 original size:22 final size:22
Alignment explanation
Indices: 43900246--43900340 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
43900236 ATAATCTTCA
43900246 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43900265 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43900282 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43900300 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
43900322 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
43900341 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:43901836 original size:47 final size:47
Alignment explanation
Indices: 43901785--43901879 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
43901775 GAGGTTTGCA
43901785 TCTTAAAACTTTCAAATTTCCGACATTAAAGACACTTGATAATCAAT
1 TCTTAAAACTTTCAAATTTCCGACATTAAAGACACTTGATAATCAAT
*
43901832 TCTTAAAACTTTCAAATTTTCGACATTAAAGACACTTGATAATCAAT
1 TCTTAAAACTTTCAAATTTCCGACATTAAAGACACTTGATAATCAAT
43901879 T
1 T
43901880 AGGTACCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (47 bp):
TCTTAAAACTTTCAAATTTCCGACATTAAAGACACTTGATAATCAAT
Found at i:43903768 original size:14 final size:12
Alignment explanation
Indices: 43903741--43903774 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43903731 TAAAGTTATT
43903741 AAAAAGAGAAAG
1 AAAAAGAGAAAG
*
43903753 AAAAAGAGAGAG
1 AAAAAGAGAAAG
*
43903765 AGAAAGAGAA
1 AAAAAGAGAA
43903775 GAGGGTCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:43906305 original size:11 final size:11
Alignment explanation
Indices: 43906289--43906326 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
43906279 ACTTCTATTT
43906289 AAAAAAAAAGA
1 AAAAAAAAAGA
43906300 AAAAAAAAAGA
1 AAAAAAAAAGA
43906311 AAAAGAAAAAGA
1 AAAA-AAAAAGA
43906323 AAAA
1 AAAA
43906327 TGAAGAGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:43906306 original size:12 final size:12
Alignment explanation
Indices: 43906289--43906326 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
43906279 ACTTCTATTT
43906289 AAAAAAAAAG-A
1 AAAAAAAAAGAA
43906300 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
43906312 AAAGAAAAAGAA
1 AAAAAAAAAGAA
43906324 AAA
1 AAA
43906327 TGAAGAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:43907278 original size:44 final size:44
Alignment explanation
Indices: 43907226--43907485 Score: 217
Period size: 44 Copynumber: 5.9 Consensus size: 44
43907216 CAAGGTTTGG
43907226 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** * *
43907270 CATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG-TATGT
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * * *
43907314 CATCCCTGTGTTTATAGGGAACA-AGTTGAATATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
43907358 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * * * ** *
43907402 CA-CTCCAGTGCTAACAGCGAAGCAGATCGAGGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
*
43907446 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGAT
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGAT
43907486 TTGGCATCTC
Statistics
Matches: 164, Mismatches: 41, Indels: 21
0.73 0.18 0.09
Matches are distributed among these distances:
42 2 0.01
43 24 0.15
44 107 0.65
45 31 0.19
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:43907458 original size:132 final size:132
Alignment explanation
Indices: 43907221--43907498 Score: 475
Period size: 132 Copynumber: 2.1 Consensus size: 132
43907211 AGAAACAAGG
* * * *
43907221 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACA
1 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
* * *
43907286 GCGAAGCAGATCGAAGATTTCAGTATGTCATCCCTGTGTTTATAGGGAACAAGTTGAATATAGCA
66 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
43907351 GA
131 GA
43907353 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
1 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
*
43907418 GCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
66 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
43907483 GA
131 GA
*
43907485 TTTGGCATCTCTGT
1 TTTGGCATCCCTGT
43907499 ATTGTCAGAG
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 137 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
GA
Found at i:43907515 original size:132 final size:132
Alignment explanation
Indices: 43907221--43907535 Score: 443
Period size: 132 Copynumber: 2.4 Consensus size: 132
43907211 AGAAACAAGG
* * * * * * *
43907221 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACA
1 TTTGGCATCCCTGTATTTACAGAGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
* * *
43907286 GCGAAGCAGATCGAAGATTTCAGTATGTCATCCCTGTGTTTATAGGGAACAAGTTGAATATAGCA
66 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
43907351 GA
131 GA
* * *
43907353 TTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
1 TTTGGCATCCCTGTATTTACAGAGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
*
43907418 GCGAAGCAGATCGAGGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
66 GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
43907483 GA
131 GA
* * * * *
43907485 TTTGGCATCTCTGTATTGT-CAGAGAGCAGATCGAATATACCAGATTTGACA
1 TTTGGCATCCCTGTATT-TACAGAGAACAGATCGAAGATAACAGATCTGACA
43907536 TATCTGTATT
Statistics
Matches: 166, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
132 165 0.99
133 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
TTTGGCATCCCTGTATTTACAGAGAACAGATCGAAGATAACAGATCTGACACTCCAGTGCTAACA
GCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCA
GA
Found at i:43907909 original size:205 final size:205
Alignment explanation
Indices: 43907558--43908260 Score: 1184
Period size: 205 Copynumber: 3.5 Consensus size: 205
43907548 CGGAGAGCAG
* * *
43907558 ATCGAAGACATAGCTGATTTGGCTTTCA-GTGTTTACGTTGAAGTAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
* * * *
43907622 TCTCTTTATTGTCAGAGAACAAATCAAAGTTTGGCATCTCCATTTCTACGGAGAGCAGATACATA
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATA
43907687 GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
131 GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
43907752 CAAGGAACAA
196 CAAGGAACAA
43907762 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
* *
43907827 TCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGCATCTCCATTTCGACGAAGAGCAGATACATA
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATA
*
43907892 GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCATTGTGCTTA
131 GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
43907957 CAAGGAACAA
196 CAAGGAACAA
* * *
43907967 GTCGAAGACATAGCTGATTTGGCTTTAACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
*
43908032 TCTTTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATA
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATA
43908097 GCAGATCTAACCTTCAGATG-----ACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
131 GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
*
43908157 CAATGAACAA
196 CAAGGAACAA
* * * *
43908167 ATCAAAGACATAGCTGATTTGGTTTTCGCGTACTTACGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
*
43908232 TCTCTGTATTGTTAGAGAACAAATCGAAG
66 TCTCTGTATTGTCAGAGAACAAATCGAAG
43908261 AAAAGATTTG
Statistics
Matches: 471, Mismatches: 27, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
200 133 0.28
204 28 0.06
205 310 0.66
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (205 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATTTCGACGGAGAGCAGATACATA
GCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTGCTTA
CAAGGAACAA
Found at i:43908905 original size:14 final size:15
Alignment explanation
Indices: 43908886--43908941 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
43908876 AATCTTCAAT
43908886 GATATG-CAATCTTA
1 GATATGACAATCTTA
43908900 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
43908917 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
43908935 GATATGA
1 GATATGA
43908942 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:43908930 original size:35 final size:37
Alignment explanation
Indices: 43908884--43908962 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
43908874 ATAATCTTCA
43908884 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
43908920 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
43908956 A-GATATG
1 ATGATATG
43908963 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:43908962 original size:17 final size:19
Alignment explanation
Indices: 43908884--43908955 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
43908874 ATAATCTTCA
43908884 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43908903 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43908920 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
43908938 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
43908956 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:43908981 original size:22 final size:22
Alignment explanation
Indices: 43908884--43908978 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
43908874 ATAATCTTCA
43908884 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43908903 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43908920 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
43908938 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
43908960 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
43908979 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:43915995 original size:54 final size:54
Alignment explanation
Indices: 43915913--43916024 Score: 197
Period size: 54 Copynumber: 2.1 Consensus size: 54
43915903 ATGCACATAA
*
43915913 AGACTAAAACATGAAGTTAAGGCAGCGGCTAGTTATTGGTGTTGGTTCCTAAAT
1 AGACTAAAACATGAAGTTAAGGCAGCGGCTAGATATTGGTGTTGGTTCCTAAAT
* *
43915967 AGACTAAAATATGAAGTTAAGGCAGCGGCTAGATATTGGTGTTGGTTCCTAAGT
1 AGACTAAAACATGAAGTTAAGGCAGCGGCTAGATATTGGTGTTGGTTCCTAAAT
43916021 AGAC
1 AGAC
43916025 CTATTTATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (54 bp):
AGACTAAAACATGAAGTTAAGGCAGCGGCTAGATATTGGTGTTGGTTCCTAAAT
Found at i:43916347 original size:30 final size:31
Alignment explanation
Indices: 43916313--43916378 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 31
43916303 TGTTTTATTA
*
43916313 TTAATTTTGTTATTATTTTAGAGGCATTTG-
1 TTAATTCTGTTATTATTTTAGAGGCATTTGC
43916343 TTAATTCTGTTATTATTTTAGAGGCATTTGC
1 TTAATTCTGTTATTATTTTAGAGGCATTTGC
43916374 TTAAT
1 TTAAT
43916379 AAGTTACATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.55
Consensus pattern (31 bp):
TTAATTCTGTTATTATTTTAGAGGCATTTGC
Found at i:43920000 original size:244 final size:244
Alignment explanation
Indices: 43919567--43920055 Score: 924
Period size: 244 Copynumber: 2.0 Consensus size: 244
43919557 TGTACTAGTT
43919567 TTAAAGAATATCCAGGTTTCCATGCATCAAATGTTAAAAGAAACAAACTTTTTTCTTGTTTTTGT
1 TTAAAGAATATCCAGGTTTCCATGCATCAAATGTTAAAAGAAACAAACTTTTTTCTTGTTTTTGT
*
43919632 GCATTAACTCTTGAGATAACGAGTTCAGATGCGAACTGAACGTGCATGGATAAAATATTTTCTCA
66 GCATTAACTCTTAAGATAACGAGTTCAGATGCGAACTGAACGTGCATGGATAAAATATTTTCTCA
43919697 TGAACTTTGTTTTAACAGGAAGGGTTGAGATATCATTTATTTTTAAAGCAACAAAACATAGAATG
131 TGAACTTTGTTTTAACAGGAAGGGTTGAGATATCATTTATTTTTAAAGCAACAAAACATAGAATG
43919762 ATGTAATTTATTTATTTATTTATTTTTGTGGATGCTTCTAGGTTCTGAA
196 ATGTAATTTATTTATTTATTTATTTTTGTGGATGCTTCTAGGTTCTGAA
*
43919811 TTAAAGAATATCCAGGTTTCCATGCATCAAATGTTAAAAGCAACAAACTTTTTTCTTGTTTTTGT
1 TTAAAGAATATCCAGGTTTCCATGCATCAAATGTTAAAAGAAACAAACTTTTTTCTTGTTTTTGT
* * *
43919876 GCATTAACTCTTAAGATAATGGGTTCAGATGCGAACTGAATGTGCATGGATAAAATATTTTCTCA
66 GCATTAACTCTTAAGATAACGAGTTCAGATGCGAACTGAACGTGCATGGATAAAATATTTTCTCA
*
43919941 TGAACTTTGTTTTAACAGGAAGGGTTGAGATATCATTTATTTTTAAAGCAACTAAACATAGAATG
131 TGAACTTTGTTTTAACAGGAAGGGTTGAGATATCATTTATTTTTAAAGCAACAAAACATAGAATG
43920006 ATGTAATTTATTTATTTATTTATTTTTGTGGATGCTTCTAGGTTCTGAA
196 ATGTAATTTATTTATTTATTTATTTTTGTGGATGCTTCTAGGTTCTGAA
43920055 T
1 T
43920056 GAGGTCCAAC
Statistics
Matches: 239, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
244 239 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (244 bp):
TTAAAGAATATCCAGGTTTCCATGCATCAAATGTTAAAAGAAACAAACTTTTTTCTTGTTTTTGT
GCATTAACTCTTAAGATAACGAGTTCAGATGCGAACTGAACGTGCATGGATAAAATATTTTCTCA
TGAACTTTGTTTTAACAGGAAGGGTTGAGATATCATTTATTTTTAAAGCAACAAAACATAGAATG
ATGTAATTTATTTATTTATTTATTTTTGTGGATGCTTCTAGGTTCTGAA
Found at i:43923964 original size:24 final size:24
Alignment explanation
Indices: 43923936--43924013 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
43923926 GCTTAACGTT
43923936 TATGGGTTTTCATATGTATAGAGG
1 TATGGGTTTTCATATGTATAGAGG
** *
43923960 TATGGG--TGAAAATGCT-TA-AGG
1 TATGGGTTTTCATATG-TATAGAGG
43923981 TTTATGGGTTTTCATATGTATAGAGG
1 --TATGGGTTTTCATATGTATAGAGG
43924007 TATGGGT
1 TATGGGT
43924014 GTTAAATCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 3 0.07
22 7 0.17
23 7 0.17
24 14 0.34
25 7 0.17
26 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.40
Consensus pattern (24 bp):
TATGGGTTTTCATATGTATAGAGG
Found at i:43923973 original size:47 final size:47
Alignment explanation
Indices: 43923921--43924014 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
43923911 GGTGGGTGGC
43923921 AAAATGCTTAACGTTTATGGGTTTTCATATGTATAGAGGTATGGGTG
1 AAAATGCTTAACGTTTATGGGTTTTCATATGTATAGAGGTATGGGTG
*
43923968 AAAATGCTTAAGGTTTATGGGTTTTCATATGTATAGAGGTATGGGTG
1 AAAATGCTTAACGTTTATGGGTTTTCATATGTATAGAGGTATGGGTG
43924015 TTAAATCAAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.38
Consensus pattern (47 bp):
AAAATGCTTAACGTTTATGGGTTTTCATATGTATAGAGGTATGGGTG
Found at i:43924657 original size:13 final size:13
Alignment explanation
Indices: 43924639--43924664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43924629 GCAGAGCCTG
43924639 CAAAATCTATGGC
1 CAAAATCTATGGC
43924652 CAAAATCTATGGC
1 CAAAATCTATGGC
43924665 AACATTTTAT
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
CAAAATCTATGGC
Found at i:43926569 original size:22 final size:21
Alignment explanation
Indices: 43926502--43926571 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
43926492 TATATATTAT
43926502 TTATTTTAAATTGTTTTATATA
1 TTATTTTAAA-TGTTTTATATA
** *
43926524 TTATTTGTTGAT-TTTT-TAAA
1 TTATTT-TAAATGTTTTATATA
*
43926544 TTATTTTAAACTGTTTTATATT
1 TTATTTTAAA-TGTTTTATATA
43926566 TTATTT
1 TTATTT
43926572 ACCTTAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 10 0.27
21 8 0.22
22 15 0.41
23 2 0.05
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (21 bp):
TTATTTTAAATGTTTTATATA
Found at i:43926596 original size:47 final size:42
Alignment explanation
Indices: 43926502--43926599 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 42
43926492 TATATATTAT
* * *
43926502 TTATTTTAAATTGTTTTATATATTATTTGTTGATTTTTTAAA
1 TTATTTTAAACTGTTTTATATATTATTTCTTAATTTTTTAAA
* *
43926544 TTATTTTAAACTGTTTTATATTTTATTTACCTTAAATTGTTTGTATA
1 TTATTTTAAACTGTTTTATATATTATTT--CTT-AATT-TTT-TAAA
43926591 TTATTTTAA
1 TTATTTTAA
43926600 TTCATTTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
42 26 0.57
44 2 0.04
45 3 0.07
46 3 0.07
47 12 0.26
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (42 bp):
TTATTTTAAACTGTTTTATATATTATTTCTTAATTTTTTAAA
Found at i:43926598 original size:26 final size:26
Alignment explanation
Indices: 43926549--43926598 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
43926539 TTAAATTATT
*
43926549 TTAAACTGTTTTATATTTTATTTACC
1 TTAAACTGTTTTATATTATATTTACC
*
43926575 TTAAATTGTTTGTATATTAT-TTTA
1 TTAAACTGTTT-TATATTATATTTA
43926599 ATTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (26 bp):
TTAAACTGTTTTATATTATATTTACC
Found at i:43933557 original size:29 final size:29
Alignment explanation
Indices: 43933490--43933557 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
43933480 TGAATATGAC
* * *
43933490 TGGGTCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
*
43933519 TGGGCCTAATGGGCCATATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAAGGTGATT
43933548 TGGGCCTAAT
1 TGGGCCTAAT
43933558 AGGCTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAAGGTGATT
Found at i:43933575 original size:29 final size:29
Alignment explanation
Indices: 43933501--43933576 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
43933491 GGGTCTAACG
* *
43933501 GGCCATATAAATGTGATTTGGGCCTAATG
1 GGCCATACAAATGTGATTTGGGCCTAATA
* * *
43933530 GGCCATATACAGGTGATTTGGGCCTAATA
1 GGCCATACAAATGTGATTTGGGCCTAATA
* *
43933559 GGCTATACAAATATGATT
1 GGCCATACAAATGTGATT
43933577 AGGCTTAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (29 bp):
GGCCATACAAATGTGATTTGGGCCTAATA
Found at i:43937583 original size:24 final size:24
Alignment explanation
Indices: 43937539--43937585 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
43937529 GAGGCAGCAA
*
43937539 AAAAAAACAAAAAAATAAAAAAAT
1 AAAAAAACAAAAAAAGAAAAAAAT
*
43937563 AAAAAAACAAAAAAAGCAAAAAA
1 AAAAAAACAAAAAAAGAAAAAAA
43937586 GATCATGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.87, C:0.06, G:0.02, T:0.04
Consensus pattern (24 bp):
AAAAAAACAAAAAAAGAAAAAAAT
Found at i:43937586 original size:8 final size:8
Alignment explanation
Indices: 43937539--43937585 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
43937529 GAGGCAGCAA
43937539 AAAAAAAC
1 AAAAAAAC
*
43937547 AAAAAAAT
1 AAAAAAAC
*
43937555 AAAAAAAT
1 AAAAAAAC
43937563 AAAAAAAC
1 AAAAAAAC
43937571 AAAAAAAGC
1 AAAAAAA-C
43937580 AAAAAA
1 AAAAAA
43937586 GATCATGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 29 0.81
9 7 0.19
ACGTcount: A:0.87, C:0.06, G:0.02, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:43938030 original size:19 final size:20
Alignment explanation
Indices: 43937989--43938030 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
43937979 ATACCGAATT
* *
43937989 AAGAAGGACCTTATGTGGTA
1 AAGAAGGACCTTATCTGGAA
*
43938009 AAGAAGG-CCTTCTCTGGAA
1 AAGAAGGACCTTATCTGGAA
43938028 AAG
1 AAG
43938031 CGTTGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (20 bp):
AAGAAGGACCTTATCTGGAA
Found at i:43938563 original size:53 final size:53
Alignment explanation
Indices: 43938479--43938585 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
43938469 GCTCCCAATC
* *
43938479 AATTTTCTTCTTATTACATTTGCTATTTTTGATTAACTTATTCATTTCAAGTT
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCAAGTT
* * *
43938532 AATTTCCTTCTTATTGCATTTGCTATCTTTGATTAATTTATTCATTTCGAGTT
1 AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCAAGTT
43938585 A
1 A
43938586 TGCTCCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.55
Consensus pattern (53 bp):
AATTTCCTTCTTATTACATTTGCTATCTTTGATTAACTTATTCATTTCAAGTT
Found at i:43939067 original size:46 final size:46
Alignment explanation
Indices: 43939016--43939153 Score: 170
Period size: 46 Copynumber: 3.0 Consensus size: 46
43939006 GCAAATTGAC
* *
43939016 TGAAGAAGATACAAATTCTATACCCCTGAATTGTAGTGGGATGGTT
1 TGAAGAAGATACAAATTCTATACCCCTGAATTGCAGTGGGATGGAT
* *
43939062 TGAAGAAGATACAAA-TCTTATACCCCTGAGTTGCAGTGGGATTGAT
1 TGAAGAAGATACAAATTC-TATACCCCTGAATTGCAGTGGGATGGAT
* * * * * *
43939108 TGAAGATGGTACAAATCCTATACCCCTGAGTTACAGTGAGATGGAT
1 TGAAGAAGATACAAATTCTATACCCCTGAATTGCAGTGGGATGGAT
43939154 AAAAAAAACC
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.03
46 77 0.96
47 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (46 bp):
TGAAGAAGATACAAATTCTATACCCCTGAATTGCAGTGGGATGGAT
Found at i:43939966 original size:46 final size:46
Alignment explanation
Indices: 43939910--43940029 Score: 120
Period size: 46 Copynumber: 2.6 Consensus size: 46
43939900 AGATCGAAGC
43939910 CACAATCCTTATCTCTCTGAAGTTGCAGTCGAACAGGATAAAAATA
1 CACAATCCTTATCTCTCTGAAGTTGCAGTCGAACAGGATAAAAATA
* * * * * * * *
43939956 CACAAACCTTATCT-TCCTGAAATTGTAGTGGAATAGGTTGAAATTA
1 CACAATCCTTATCTCT-CTGAAGTTGCAGTCGAACAGGATAAAAATA
*
43940002 C-CAATCCTTATCTC-CTTGAAGTTTCAGT
1 CACAATCCTTATCTCTC-TGAAGTTGCAGT
43940030 AGAGTAGATC
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
44 1 0.02
45 21 0.36
46 37 0.63
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (46 bp):
CACAATCCTTATCTCTCTGAAGTTGCAGTCGAACAGGATAAAAATA
Done.