Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 39 of 97
Found at i:16059838 original size:23 final size:22
Alignment explanation
Indices: 16059785--16059845 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
16059775 TGCGTGATTG
**
16059785 GTTTTTAGGCATTGCGTGACTA
1 GTTTTTAGGCATTGCGCAACTA
** *
16059807 GTTGATAGGGCATTGTGCAACTA
1 GTTTTTA-GGCATTGCGCAACTA
16059830 GTTTTTAGGCATTGCG
1 GTTTTTAGGCATTGCG
16059846 TGGCTGCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.38
Consensus pattern (22 bp):
GTTTTTAGGCATTGCGCAACTA
Found at i:16063491 original size:22 final size:22
Alignment explanation
Indices: 16063460--16063515 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
16063450 ATCCGACATT
*
16063460 GTATTACGTGACTAGTTTTTAG
1 GTATTGCGTGACTAGTTTTTAG
16063482 GTATTGCGTGACTAGTTTTTAG
1 GTATTGCGTGACTAGTTTTTAG
*
16063504 GCATTGCGTGAC
1 GTATTGCGTGAC
16063516 CCCACATCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (22 bp):
GTATTGCGTGACTAGTTTTTAG
Found at i:16065178 original size:63 final size:63
Alignment explanation
Indices: 16065090--16065373 Score: 241
Period size: 64 Copynumber: 4.5 Consensus size: 63
16065080 TAGAATCCCT
* * * *
16065090 TTTTTGAACGGTTCAAGCCTTGATCAAGTTAAGTAATTTTCAAGATTTTTAAAATCGAATCCA
1 TTTTTGAATGGATCAAGCCTTGATCAAGTCAAGTAATTTTCAATATTTTTAAAATCGAATCCA
* * * *
16065153 TTTTTGAATGGATCGAGCCTCGATCAAGTCAAATAGTTTTC-ATATTTTTCAAAAAAT-GAATCC
1 TTTTTGAATGGATCAAGCCTTGATCAAGTCAAGTAATTTTCAATATTTTT---AAAATCGAATCC
16065216 A
63 A
* * * * * * * *
16065217 ATTTTAAATGAATCAAGCCTTAATCAAGTCAAG-AAGTTTCCATATTTTCAAAATCAAATCCA
1 TTTTTGAATGGATCAAGCCTTGATCAAGTCAAGTAATTTTCAATATTTTTAAAATCGAATCCA
** * * ** * * ** *
16065279 TTTTTGAATGGATTGATCCTTGATCAAGTTAACCAGTTTTCAAAATTGTCAAAAATTGAATCCA
1 TTTTTGAATGGATCAAGCCTTGATCAAGTCAAGTAATTTTCAATATT-TTTAAAATCGAATCCA
* *
16065343 TTTTTTGAATGGATTAAGTCTTGATCAAGTC
1 -TTTTTGAATGGATCAAGCCTTGATCAAGTC
16065374 CACGTGGCTT
Statistics
Matches: 173, Mismatches: 40, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
61 5 0.03
62 37 0.21
63 48 0.28
64 52 0.30
65 31 0.18
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (63 bp):
TTTTTGAATGGATCAAGCCTTGATCAAGTCAAGTAATTTTCAATATTTTTAAAATCGAATCCA
Found at i:16065751 original size:30 final size:30
Alignment explanation
Indices: 16065716--16065789 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
16065706 TCAAGAAAAT
*
16065716 TCAAATAAGCCCTTGTACATTTATTTTGAG
1 TCAAATAAGCCCTTATACATTTATTTTGAG
* **
16065746 TCAAATAAACCCTTATATTTTTATTTTGAG
1 TCAAATAAGCCCTTATACATTTATTTTGAG
16065776 TCAAATAAGTCCCT
1 TCAAATAAG-CCCT
16065790 ATAACTAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (30 bp):
TCAAATAAGCCCTTATACATTTATTTTGAG
Found at i:16066705 original size:13 final size:13
Alignment explanation
Indices: 16066688--16066720 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
16066678 GTATTTTTTT
*
16066688 CTTTTTTT-TTAA
1 CTTTTTTTGGTAA
16066700 CTTTTTTTGGTAA
1 CTTTTTTTGGTAA
16066713 CTTTTTTT
1 CTTTTTTT
16066721 ATTTTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (13 bp):
CTTTTTTTGGTAA
Found at i:16066725 original size:19 final size:18
Alignment explanation
Indices: 16066703--16066744 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16066693 TTTTTAACTT
*
16066703 TTTTTGGTAACTTTTTTTA
1 TTTTTGGTAA-ATTTTTTA
*
16066722 TTTTTTGTAAATTTTTTA
1 TTTTTGGTAAATTTTTTA
16066740 TTTTT
1 TTTTT
16066745 ATTTTGCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTGGTAAATTTTTTA
Found at i:16068032 original size:18 final size:18
Alignment explanation
Indices: 16068009--16068043 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16067999 TAAGAGTTAT
16068009 GTTTGTTCAAACAATTAA
1 GTTTGTTCAAACAATTAA
*
16068027 GTTTGTTCAAATAATTA
1 GTTTGTTCAAACAATTA
16068044 TGTTAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (18 bp):
GTTTGTTCAAACAATTAA
Found at i:16072409 original size:18 final size:18
Alignment explanation
Indices: 16072386--16072420 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16072376 TAAGAGTTAT
16072386 GTTTGTTCAAACAATTAA
1 GTTTGTTCAAACAATTAA
*
16072404 GTTTGTTCAAATAATTA
1 GTTTGTTCAAACAATTA
16072421 TGTTAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (18 bp):
GTTTGTTCAAACAATTAA
Found at i:16076296 original size:18 final size:18
Alignment explanation
Indices: 16076270--16076304 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16076260 CACTATACCA
*
16076270 TTTCTTTTACTTTATTTC
1 TTTCGTTTACTTTATTTC
16076288 TTTCGTTTACTTTATTT
1 TTTCGTTTACTTTATTT
16076305 TAGAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTCGTTTACTTTATTTC
Found at i:16078894 original size:15 final size:15
Alignment explanation
Indices: 16078876--16078924 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
16078866 AATATAATTA
16078876 CAAGTAATGTGATTG
1 CAAGTAATGTGATTG
*
16078891 CAAGTAATGTAATTG
1 CAAGTAATGTGATTG
*
16078906 CAAGCAATGTGATTG
1 CAAGTAATGTGATTG
16078921 CAAG
1 CAAG
16078925 GAAGATATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (15 bp):
CAAGTAATGTGATTG
Found at i:16078904 original size:30 final size:30
Alignment explanation
Indices: 16078864--16078924 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16078854 ACTTTACAAT
*
16078864 GTAATATAATTACAAGTAATGTGATTGCAA
1 GTAATATAATTACAAGCAATGTGATTGCAA
* *
16078894 GTAATGTAATTGCAAGCAATGTGATTGCAA
1 GTAATATAATTACAAGCAATGTGATTGCAA
16078924 G
1 G
16078925 GAAGATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (30 bp):
GTAATATAATTACAAGCAATGTGATTGCAA
Found at i:16079181 original size:33 final size:33
Alignment explanation
Indices: 16079144--16079225 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
16079134 AATGTCATAT
*
16079144 ATTTTATTTTTATTTCTTATTATAATCTTATAG
1 ATTTTATTTTTATTTCTTAATATAATCTTATAG
* * * *
16079177 ATTTTATTTTCATTTCTTAATATAATTTTCTAT
1 ATTTTATTTTTATTTCTTAATATAATCTTATAG
*
16079210 ATTATATATTTTATTT
1 ATTTTAT-TTTTATTT
16079226 TAGTTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 34 0.83
34 7 0.17
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (33 bp):
ATTTTATTTTTATTTCTTAATATAATCTTATAG
Found at i:16080996 original size:21 final size:21
Alignment explanation
Indices: 16080967--16081011 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16080957 CTCCACCAAG
* * *
16080967 CCTCTCCACTGTCGAACCCAC
1 CCTCCCCACCGTCAAACCCAC
16080988 CCTCCCCACCGTCAAACCCAC
1 CCTCCCCACCGTCAAACCCAC
16081009 CCT
1 CCT
16081012 TCTTAGTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.58, G:0.07, T:0.16
Consensus pattern (21 bp):
CCTCCCCACCGTCAAACCCAC
Found at i:16081222 original size:124 final size:124
Alignment explanation
Indices: 16080997--16081226 Score: 277
Period size: 124 Copynumber: 1.9 Consensus size: 124
16080987 CCCTCCCCAC
* * * * *
16080997 CGTCAAACCCACCCTTCTTAGTGTCGATTCCACTAGTTTTAACCTAGACCCATCGCAAATTTGTA
1 CGTCAAACCCACCCTTCTCACTATCGATTCCACCAGTTTTAACCTAGACCCATCGCAAATTTATA
*
16081062 AACTCACTACCGATTGAAAGTTGTTGAAATGTCACCTACTATTGATTGAGCCCTTTCGT
66 AACTCACTACCGATTGAAAGTTGTCGAAATGTCACCTACTATTGATTGAGCCCTTTCGT
* * *
16081121 CGTCGAACCCACCCTTCTCACTATTGATTCCACCCA-TTTTAACCTAGACCTA-CTGCAAATTTA
1 CGTCAAACCCACCCTTCTCACTATCGATTCCA-CCAGTTTTAACCTAGACCCATC-GCAAATTTA
* ** * * *
16081184 TAATCTCGTTGCTGATTGAAAGTTGGTCGAACT-TCACCTACTA
64 TAAACTCACTACCGATTGAAAGTT-GTCGAAATGTCACCTACTA
16081227 CCGACCCAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
123 1 0.01
124 79 0.90
125 8 0.09
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (124 bp):
CGTCAAACCCACCCTTCTCACTATCGATTCCACCAGTTTTAACCTAGACCCATCGCAAATTTATA
AACTCACTACCGATTGAAAGTTGTCGAAATGTCACCTACTATTGATTGAGCCCTTTCGT
Found at i:16085056 original size:2 final size:2
Alignment explanation
Indices: 16085035--16085087 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
16085025 GCTACATGCC
* * * *
16085035 AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16085077 AT AT AT -T AT AT
1 AT AT AT AT AT AT
16085088 TCATCCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16086584 original size:45 final size:45
Alignment explanation
Indices: 16086530--16086634 Score: 203
Period size: 45 Copynumber: 2.4 Consensus size: 45
16086520 TTTAAAGTGG
16086530 AAAA-AGTAATTTCTCTGTTTCAAAAAATACAATAAAATAAAGAA
1 AAAAGAGTAATTTCTCTGTTTCAAAAAATACAATAAAATAAAGAA
16086574 AAAAGAGTAATTTCTCTGTTTCAAAAAATACAATAAAATAAAGAA
1 AAAAGAGTAATTTCTCTGTTTCAAAAAATACAATAAAATAAAGAA
16086619 AAAAGAGTAATTTCTC
1 AAAAGAGTAATTTCTC
16086635 AAACTTCTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.07
45 56 0.93
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.28
Consensus pattern (45 bp):
AAAAGAGTAATTTCTCTGTTTCAAAAAATACAATAAAATAAAGAA
Found at i:16087021 original size:2 final size:2
Alignment explanation
Indices: 16087014--16087043 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16087004 TTGTAGCTTT
16087014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16087044 GTACGTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16087124 original size:2 final size:2
Alignment explanation
Indices: 16087117--16087146 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16087107 TAGTANTTAT
16087117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16087147 GGCTAGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16087308 original size:19 final size:20
Alignment explanation
Indices: 16087284--16087322 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16087274 TGGTTTTGTG
16087284 AATAG-TGG-AACAATGACAA
1 AATAGTTGGAAACAA-GACAA
16087303 AATAGTTGGAAACAAGACAA
1 AATAGTTGGAAACAAGACAA
16087323 GCAGGGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (20 bp):
AATAGTTGGAAACAAGACAA
Found at i:16091763 original size:32 final size:33
Alignment explanation
Indices: 16091718--16091779 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
16091708 GCAATTGTCT
16091718 ATTTTTTATTTATTATTATTTTC-ATTTTATCAC
1 ATTTTTTATTTATTA-TATTTTCTATTTTATCAC
16091751 ATTTTTTA-TTATTATATTTTCTATTTTAT
1 ATTTTTTATTTATTATATTTTCTATTTTAT
16091780 TCCTTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 7 0.25
32 13 0.46
33 8 0.29
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (33 bp):
ATTTTTTATTTATTATATTTTCTATTTTATCAC
Found at i:16091930 original size:22 final size:20
Alignment explanation
Indices: 16091897--16091941 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
16091887 TTTTAAATTA
16091897 ATTATTGTCTTATATTTTTATT
1 ATTATTGTCTTAT-TTTTT-TT
16091919 ATTATT-TACTTATTTTTTTT
1 ATTATTGT-CTTATTTTTTTT
16091939 ATT
1 ATT
16091942 TTCCTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 6 0.27
22 11 0.50
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTATTGTCTTATTTTTTTT
Found at i:16093751 original size:72 final size:72
Alignment explanation
Indices: 16093613--16093752 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
16093603 TTTGTAGGGT
* * * **
16093613 GTCCTCCCACTACTTTGCCAGACGCGATTTTCGCGTCTAGCACTGTAGTGGTTGTTTGGTGTTGG
1 GTCCTCCCACTACGTTGCCAGACGCGATTTTCACGTCTAGCACTGTAGTGGTTGCTTGGTACTGG
16093678 CAGAGGC
66 CAGAGGC
* *
16093685 GTCCTCCCACTACGTTGCCAGACGCGATTTTCACGTCTGGCACTGTAGTGTTTGCTTGGTACTGG
1 GTCCTCCCACTACGTTGCCAGACGCGATTTTCACGTCTAGCACTGTAGTGGTTGCTTGGTACTGG
16093750 CAG
66 CAG
16093753 GGGCATCCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.31
Consensus pattern (72 bp):
GTCCTCCCACTACGTTGCCAGACGCGATTTTCACGTCTAGCACTGTAGTGGTTGCTTGGTACTGG
CAGAGGC
Found at i:16093955 original size:1 final size:1
Alignment explanation
Indices: 16093949--16093996 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
16093939 ATCAAAGCTC
* * * * *
16093949 TTTTTTTTTTGTTGTTTTTTGTTTTTTTTTATTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16093997 AATGAACTCC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:16093996 original size:10 final size:10
Alignment explanation
Indices: 16093950--16093996 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
16093940 TCAAAGCTCT
*
16093950 TTTTTTTTTG
1 TTTTTTTTTA
* *
16093960 TTGTTTTTTG
1 TTTTTTTTTA
16093970 TTTTTTTTTA
1 TTTTTTTTTA
16093980 TTTTTTTTTA
1 TTTTTTTTTA
16093990 TTTTTTT
1 TTTTTTT
16093997 AATGAACTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.04, C:0.00, G:0.06, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:16094123 original size:75 final size:75
Alignment explanation
Indices: 16093997--16094322 Score: 383
Period size: 75 Copynumber: 4.4 Consensus size: 75
16093987 TTATTTTTTT
** * * * * * *
16093997 AATGAACTCCTCAAAGTTGAAGCAATGAGACTTTTAAAAATGAATTTCTCAAAATTGAGGCGACG
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
16094062 AGACTTTTAAA
66 AGAC-TTTAAA
* *
16094073 AATGAACTCCTCAAAACTGAGGCAACGAGA-TTTTAAAAATGAACTCCTCAAATCTGAGG-TACT
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAAC-
16094136 GAGACTTTAAA
65 GAGACTTTAAA
* * **
16094147 AATGAACTCCTCAAAACTGAGGCACCGAAAC-TTT-AAAATGAACTCCTCAAAACTGAGGCAATA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
*
16094210 AGACTTCAAA
66 AGACTTTAAA
* ** *
16094220 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAAAATGAGTTCCTCAAAGCTGAGGCAACG
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
*
16094285 TA-CCTTTAAA
66 -AGACTTTAAA
* * *
16094295 AATGAATTCCTAAAAATTGAGGCAACGA
1 AATGAACTCCTCAAAACTGAGGCAACGA
16094323 AACCTTTTTT
Statistics
Matches: 215, Mismatches: 29, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
73 61 0.28
74 42 0.20
75 85 0.40
76 27 0.13
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (75 bp):
AATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAAATGAACTCCTCAAAACTGAGGCAACG
AGACTTTAAA
Found at i:16094329 original size:38 final size:37
Alignment explanation
Indices: 16093997--16094322 Score: 379
Period size: 37 Copynumber: 8.8 Consensus size: 37
16093987 TTATTTTTTT
** * *
16093997 AATGAACTCCTCAAAGTTGAAGCAATGAGACTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGAC-TTTAAA
* * * *
16094035 AATGAATTTCTCAAAATTGAGGCGACGAGACTTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGAC-TTTAAA
*
16094073 AATGAACTCCTCAAAACTGAGGCAACGAGATTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
* *
16094110 AATGAACTCCTCAAATCTGAGG-TACTGAGACTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAAC-GAGACTTTAAA
* *
16094147 AATGAACTCCTCAAAACTGAGGCACCGAAACTTT-AA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
** *
16094183 AATGAACTCCTCAAAACTGAGGCAATAAGACTTCAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
16094220 AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAAA
1 AATGAACTCCTCAAAACTGAGGCAACGAGACTTT-AAA
** * *
16094258 AATGAGTTCCTCAAAGCTGAGGCAACGTA-CCTTTAAA
1 AATGAACTCCTCAAAACTGAGGCAACG-AGACTTTAAA
* * *
16094295 AATGAATTCCTAAAAATTGAGGCAACGA
1 AATGAACTCCTCAAAACTGAGGCAACGA
16094323 AACCTTTTTT
Statistics
Matches: 249, Mismatches: 34, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
36 34 0.14
37 124 0.50
38 90 0.36
39 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (37 bp):
AATGAACTCCTCAAAACTGAGGCAACGAGACTTTAAA
Found at i:16095217 original size:16 final size:16
Alignment explanation
Indices: 16095177--16095217 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16095167 AACTTGAAAA
16095177 TTTTCTTTTTTTCTTC
1 TTTTCTTTTTTTCTTC
* *
16095193 TTCTCTTTTTTTTTTC
1 TTTTCTTTTTTTCTTC
16095209 TTTT-TTTTT
1 TTTTCTTTTT
16095218 ATGCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTTTCTTC
Found at i:16106696 original size:32 final size:31
Alignment explanation
Indices: 16106611--16106703 Score: 77
Period size: 32 Copynumber: 2.9 Consensus size: 31
16106601 ATTGTCTATT
**
16106611 TTTTATTTATTATTA-TTTAGTTATTATTTTCA
1 TTTTATTCCTTATTATTTTA-TTA-TATTTTCA
16106643 TTTTA-TCACATT-TT-TTATTATTATATTTTCTA
1 TTTTATTC-C-TTATTATT-TTATTATATTTTC-A
*
16106675 TTTTATTCCTTATTATTTTATTATTTTTT
1 TTTTATTCCTTATTATTTTATTATATTTT
16106704 TATATCTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
31 10 0.20
32 31 0.62
33 9 0.18
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (31 bp):
TTTTATTCCTTATTATTTTATTATATTTTCA
Found at i:16107407 original size:24 final size:26
Alignment explanation
Indices: 16107380--16107440 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
16107370 ATTACTTATC
16107380 ATATATTTAAATATA-TTT-ATTCCT
1 ATATATTTAAATATACTTTCATTCCT
* *
16107404 ATAT-TTT-CATATACTTTCATTTCT
1 ATATATTTAAATATACTTTCATTCCT
16107428 ATATATTATAAAT
1 ATATATT-TAAAT
16107441 CACTCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 5 0.17
23 6 0.21
24 13 0.45
25 2 0.07
26 1 0.03
27 2 0.07
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATATTTAAATATACTTTCATTCCT
Found at i:16107415 original size:22 final size:24
Alignment explanation
Indices: 16107381--16107431 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
16107371 TTACTTATCA
16107381 TATATTTAAATATA-TTT-ATTCC
1 TATATTTAAATATACTTTCATTCC
** *
16107403 TATATTTTCATATACTTTCATTTC
1 TATATTTAAATATACTTTCATTCC
16107427 TATAT
1 TATAT
16107432 ATTATAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.50
23 3 0.12
24 9 0.38
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTTAAATATACTTTCATTCC
Found at i:16112992 original size:2 final size:2
Alignment explanation
Indices: 16112980--16113023 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
16112970 TTAAGTTTTA
16112980 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16113021 AT A
1 AT A
16113024 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16122022 original size:14 final size:14
Alignment explanation
Indices: 16122003--16122037 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16121993 AAGTATATAT
16122003 ATAAATAAAAAATA
1 ATAAATAAAAAATA
*
16122017 ATAAATAACAAATA
1 ATAAATAAAAAATA
16122031 ATCAAAT
1 AT-AAAT
16122038 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAATAAAAAATA
Found at i:16127068 original size:66 final size:65
Alignment explanation
Indices: 16126962--16127095 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 65
16126952 GAAGAGTTTG
* * * * *
16126962 AGAAACATAATCAATTTAGTCAACCAAGTCAATCGACTAAGTGCTCTATG-CTAGAATTTGCAAA
1 AGAAACAGAACCAACTTAGTCAACCAAGTCAATCGACTAAGAGCTCTATGTCTACAATTTG--AA
16127026 CC
64 CC
* * * *
16127028 AGAAACAGAACCAACTTATTCAACCAAGTTAGTCGACTAAGAGCTCTCTGTCTACAATTTGAACC
1 AGAAACAGAACCAACTTAGTCAACCAAGTCAATCGACTAAGAGCTCTATGTCTACAATTTGAACC
16127093 AGA
1 AGA
16127096 GCACTACAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
65 7 0.12
66 42 0.72
67 9 0.16
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (65 bp):
AGAAACAGAACCAACTTAGTCAACCAAGTCAATCGACTAAGAGCTCTATGTCTACAATTTGAACC
Found at i:16128067 original size:2 final size:2
Alignment explanation
Indices: 16128060--16128091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16128050 AATTCAAATC
16128060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16128092 CATTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16137715 original size:12 final size:12
Alignment explanation
Indices: 16137698--16137727 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16137688 TTCTTAGACA
16137698 GTGCAGCCACTT
1 GTGCAGCCACTT
16137710 GTGCAGCCACTT
1 GTGCAGCCACTT
*
16137722 GAGCAG
1 GTGCAG
16137728 TTAAAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (12 bp):
GTGCAGCCACTT
Found at i:16149438 original size:50 final size:49
Alignment explanation
Indices: 16149324--16149441 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 49
16149314 CAGTTAATCT
* * * *
16149324 CATTAAAAAGTAGGAATCCCTTGTTGATTGTGCAAGGATTATCGCTTCC
1 CATTAAAAAGTAAGAATCCCTTGTGGATTATGCAAGGATTATCACTTCC
** * *
16149373 CATTAAAAAGTAAGAATCCCTTTGTGGATTATGTGAGGGTTATCACTTCT
1 CATTAAAAAGTAAGAATCCC-TTGTGGATTATGCAAGGATTATCACTTCC
* *
16149423 TATTAAAAAGCAAGAATCC
1 CATTAAAAAGTAAGAATCC
16149442 TTGATTATGG
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 19 0.33
50 39 0.67
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (49 bp):
CATTAAAAAGTAAGAATCCCTTGTGGATTATGCAAGGATTATCACTTCC
Found at i:16158254 original size:12 final size:12
Alignment explanation
Indices: 16158237--16158261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16158227 ATTATGGTGT
16158237 GGAAAAGTAGTA
1 GGAAAAGTAGTA
16158249 GGAAAAGTAGTA
1 GGAAAAGTAGTA
16158261 G
1 G
16158262 AATTGACAGA
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:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (12 bp):
GGAAAAGTAGTA
Found at i:16160865 original size:14 final size:14
Alignment explanation
Indices: 16160843--16160874 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16160833 TAACACACAC
*
16160843 ATATGTATATGTAT
1 ATATATATATGTAT
16160857 ATATATATATGTAT
1 ATATATATATGTAT
16160871 ATAT
1 ATAT
16160875 TCACATGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
ATATATATATGTAT
Found at i:16160957 original size:83 final size:83
Alignment explanation
Indices: 16160790--16160957 Score: 273
Period size: 83 Copynumber: 2.0 Consensus size: 83
16160780 AACATGCAAG
* * *
16160790 ATTCACATGTGCAACACCATATACCATACTCATGAACTTTCTATAACACACACATATGTATATGT
1 ATTCACATGTGCAACACCATATACCATACTCATGAACTTTCTATAACACACACACATATATATAT
* *
16160855 ATATATATATATGTATAT
66 ATATACATACATGTATAT
16160873 ATTCACATGTGCAACACCATATACCATACTCATGAACTTTCTATAACACACACACATATATATAT
1 ATTCACATGTGCAACACCATATACCATACTCATGAACTTTCTATAACACACACACATATATATAT
* *
16160938 GTATACATACATGTCTAT
66 ATATACATACATGTATAT
16160956 AT
1 AT
16160958 ACATATATAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (83 bp):
ATTCACATGTGCAACACCATATACCATACTCATGAACTTTCTATAACACACACACATATATATAT
ATATACATACATGTATAT
Found at i:16160959 original size:12 final size:12
Alignment explanation
Indices: 16160928--16160970 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16160918 ACACACACAC
*
16160928 ATATATATATGT
1 ATATATACATGT
*
16160940 ATACATACATGT
1 ATATATACATGT
* *
16160952 CTATATACATAT
1 ATATATACATGT
16160964 ATATATA
1 ATATATA
16160971 TCTATCACCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (12 bp):
ATATATACATGT
Found at i:16161070 original size:42 final size:42
Alignment explanation
Indices: 16161012--16161165 Score: 200
Period size: 42 Copynumber: 3.7 Consensus size: 42
16161002 CAGCTCATAT
* * * *
16161012 GCACTCCCACTAGCACATGGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCGCACATAGCCGGGTCAGCATCGGCTTATGC
* * **
16161054 GCACTCTTACTCGCACATAGCCGGGTCAGCATCGACTTATTT
1 GCACTCCTACTCGCACATAGCCGGGTCAGCATCGGCTTATGC
** *
16161096 GCACTCCCCCTCGCACATAGCTGGGTCAGCATCGGCTTATGC
1 GCACTCCTACTCGCACATAGCCGGGTCAGCATCGGCTTATGC
*
16161138 ACACTCCTACTCGCACATAGCCGGGTCA
1 GCACTCCTACTCGCACATAGCCGGGTCA
16161166 ATATCATTGC
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.23
Consensus pattern (42 bp):
GCACTCCTACTCGCACATAGCCGGGTCAGCATCGGCTTATGC
Found at i:16161152 original size:84 final size:84
Alignment explanation
Indices: 16161011--16161165 Score: 265
Period size: 84 Copynumber: 1.8 Consensus size: 84
16161001 TCAGCTCATA
* * *
16161011 TGCACTCCCACTAGCACATGGCTGGGTCAGCATCGGCTTATGCGCACTCTTACTCGCACATAGCC
1 TGCACTCCCACTAGCACATAGCTGGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCC
16161076 GGGTCAGCATCGACTTATT
66 GGGTCAGCATCGACTTATT
* *
16161095 TGCACTCCCCCTCGCACATAGCTGGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCC
1 TGCACTCCCACTAGCACATAGCTGGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCC
16161160 GGGTCA
66 GGGTCA
16161166 ATATCATTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.23
Consensus pattern (84 bp):
TGCACTCCCACTAGCACATAGCTGGGTCAGCATCGGCTTATGCACACTCCTACTCGCACATAGCC
GGGTCAGCATCGACTTATT
Found at i:16161199 original size:2 final size:2
Alignment explanation
Indices: 16161192--16161242 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
16161182 TTATTCGTAT
16161192 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
16161234 AC AC AC AC A
1 AC AC AC AC A
16161243 TATATATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16180243 original size:59 final size:56
Alignment explanation
Indices: 16180152--16180315 Score: 193
Period size: 59 Copynumber: 2.8 Consensus size: 56
16180142 TTTTGTCTTT
* * *
16180152 AATTAAGACATAAATATTTTATGTTGTCTAAATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAAAATATTTT-T-TTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
* * *
16180210 GATTAAGACAAATAATATTTTTCTTGTCTTAAATTAAGCCAAACATATTTTCTTGTCTA
1 AATTAAGACAAA-AATATTTTT-TTGTC-TAAATTAAGACAAACATGTTTTCTTGTCTA
* * *
16180269 AATTAAGACCAAACATGTTTTTTTGTCTGAATTAAGACAAACATGTT
1 AATTAAGA-CAAAAATATTTTTTTGTCTAAATTAAGACAAACATGTT
16180316 AAAGTTGTCA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
57 17 0.19
58 21 0.23
59 48 0.53
60 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (56 bp):
AATTAAGACAAAAATATTTTTTTGTCTAAATTAAGACAAACATGTTTTCTTGTCTA
Found at i:16180280 original size:29 final size:28
Alignment explanation
Indices: 16180152--16180312 Score: 162
Period size: 29 Copynumber: 5.5 Consensus size: 28
16180142 TTTTGTCTTT
*
16180152 AATTAAGACATAA-ATATTTTATGTTGTCTA
1 AATTAAGACA-AACATA-TTT-TCTTGTCTA
* * *
16180182 AATTGAGACAAATATGTTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* *
16180210 GATTAAGACAAATAATATTTTTCTTGTCTTA
1 AATTAAGACAAA-CATA-TTTTCTTGTC-TA
*
16180241 AATTAAGCCAAACATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* * *
16180269 AATTAAGACCAAACATGTTTTTTTGTCTG
1 AATTAAGA-CAAACATATTTTCTTGTCTA
16180298 AATTAAGACAAACAT
1 AATTAAGACAAACAT
16180313 GTTAAAGTTG
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
28 34 0.30
29 42 0.38
30 24 0.21
31 12 0.11
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:16180323 original size:29 final size:29
Alignment explanation
Indices: 16180233--16180324 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
16180223 AATATTTTTC
* ***
16180233 TTGTCTTAAATTAAG-CCAAACATATTTTC
1 TTGTC-TAAATTAAGACCAAACATGTTAAG
***
16180262 TTGTCTAAATTAAGACCAAACATGTTTTT
1 TTGTCTAAATTAAGACCAAACATGTTAAG
*
16180291 TTGTCTGAATTAAGA-CAAACATGTTAAAG
1 TTGTCTAAATTAAGACCAAACATGTT-AAG
16180320 TTGTC
1 TTGTC
16180325 ATTTTTGTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.35
29 36 0.65
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (29 bp):
TTGTCTAAATTAAGACCAAACATGTTAAG
Found at i:16184571 original size:15 final size:15
Alignment explanation
Indices: 16184526--16184571 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
16184516 AGATCAGAGA
16184526 TTTTGGTTTTAAAG-
1 TTTTGGTTTTAAAGT
*
16184540 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
16184556 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
16184571 T
1 T
16184572 GTTTTAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 5 0.18
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:16195744 original size:20 final size:20
Alignment explanation
Indices: 16195701--16195742 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
16195691 CCACCCATAC
16195701 AAAGAAAGTGAAGAGAAAAG
1 AAAGAAAGTGAAGAGAAAAG
16195721 AAAGAAA-TGAATGA-AAAAG
1 AAAGAAAGTGAA-GAGAAAAG
16195740 AAA
1 AAA
16195743 AGTCAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (20 bp):
AAAGAAAGTGAAGAGAAAAG
Found at i:16196000 original size:4 final size:4
Alignment explanation
Indices: 16195983--16196074 Score: 75
Period size: 4 Copynumber: 23.2 Consensus size: 4
16195973 AGATAGGGTT
* * * * *
16195983 GAAA GAAA GGAA GAAA GAAT GAAT GAAA GAAA G-AA GAAA G-GA GAAGG
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A
*
16196030 GAAA GGAAA GGGAA GAAA GAAA GAAA G-AA -AAA GAAA GAAA GAAA G
1 GAAA -GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
16196075 GAAAAGCATG
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
3 9 0.12
4 52 0.72
5 11 0.15
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:16196062 original size:14 final size:14
Alignment explanation
Indices: 16196045--16196073 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16196035 GAAAGGGAAG
16196045 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
16196059 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
16196073 A
1 A
16196074 GGAAAAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:16196080 original size:14 final size:13
Alignment explanation
Indices: 16196045--16196078 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
16196035 GAAAGGGAAG
16196045 AAAGAAAGAAAGAA
1 AAAGAAAGAAAG-A
16196059 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
*
16196072 AAGGAAA
1 AAAGAAA
16196079 AGCATGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:16199686 original size:34 final size:34
Alignment explanation
Indices: 16199579--16199696 Score: 128
Period size: 35 Copynumber: 3.4 Consensus size: 34
16199569 GAAAAGTTAG
* * *
16199579 TGTGGGTTGTGCTTTCTCCCATTAAAAGGCAATCG
1 TGTGGGTTATGCTTACTCCCATTAAAAGGCAAT-T
* * *
16199614 TGTGGGTTATGCTTGCTCCCATTTTAAAGGCAAAT
1 TGTGGGTTATGCTTACTCCCA-TTAAAAGGCAATT
* * *
16199649 TGTGGTTTATGCTTACTTCCATGAAAAGGCAATT
1 TGTGGGTTATGCTTACTCCCATTAAAAGGCAATT
*
16199683 TGTGGGTTACGCTT
1 TGTGGGTTATGCTT
16199697 GAGCTTGGCA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
34 22 0.32
35 37 0.54
36 10 0.14
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (34 bp):
TGTGGGTTATGCTTACTCCCATTAAAAGGCAATT
Found at i:16209618 original size:33 final size:33
Alignment explanation
Indices: 16209193--16209607 Score: 758
Period size: 33 Copynumber: 12.5 Consensus size: 33
16209183 GTGGACGGCG
*
16209193 GAGAGAGAGGGGCAGACCCACGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
*
16209226 GAGAGAGAGGGGCAGACCCACGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209259 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209292 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209325 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209358 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209391 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209424 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209457 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209490 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
16209523 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
1 GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
* * *
16209556 GAGAGAGAGGGGCAGACCCACCGGTGAGAGCAGTT
1 GAGAGAGAGGGGCAGACCCA-TGG-GTGAGCGGTT
*
16209591 GAGAGAGAGGGGAAGAC
1 GAGAGAGAGGGGCAGAC
16209608 AAGTGAGAGA
Statistics
Matches: 375, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
33 349 0.93
34 2 0.01
35 24 0.06
ACGTcount: A:0.25, C:0.16, G:0.48, T:0.11
Consensus pattern (33 bp):
GAGAGAGAGGGGCAGACCCATGGGTGAGCGGTT
Found at i:16209653 original size:56 final size:56
Alignment explanation
Indices: 16209555--16209662 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
16209545 GGTGAGCGGT
* * * *
16209555 TGAGAGAGAGGGGCAGACCCACCGGTGAGAGCAGTTGAGAGAGAGGGGAAGACAAG
1 TGAGAGAGAGGGGAAGACCCACAGGTGAGAGCAGTGGAGAGAGAGAGGAAGACAAG
* * *
16209611 TGAGAGAGAGGGGAAGACCCACAGTTGAGA-TAGTGGCTGAGAGAGAGGAAGA
1 TGAGAGAGAGGGGAAGACCCACAGGTGAGAGCAGTGG-AGAGAGAGAGGAAGA
16209663 AGACCGATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 4 0.09
56 40 0.91
ACGTcount: A:0.35, C:0.12, G:0.44, T:0.09
Consensus pattern (56 bp):
TGAGAGAGAGGGGAAGACCCACAGGTGAGAGCAGTGGAGAGAGAGAGGAAGACAAG
Found at i:16211123 original size:18 final size:18
Alignment explanation
Indices: 16211096--16211130 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16211086 TTTTCCAACA
16211096 TAATTATTTGAACAAACT
1 TAATTATTTGAACAAACT
*
16211114 TAATTGTTTGAACAAAC
1 TAATTATTTGAACAAAC
16211131 ATAACTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
TAATTATTTGAACAAACT
Found at i:16211997 original size:13 final size:12
Alignment explanation
Indices: 16211970--16212014 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
16211960 TTCCATAACT
16211970 TAAAA-CACTTAA
1 TAAAACCAC-TAA
16211982 TAAAACCACTATA
1 TAAAACCACTA-A
*
16211995 TAAAACCATTAA
1 TAAAACCACTAA
16212007 TAAAACCA
1 TAAAACCA
16212015 TTGATAGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 16 0.53
13 14 0.47
ACGTcount: A:0.58, C:0.20, G:0.00, T:0.22
Consensus pattern (12 bp):
TAAAACCACTAA
Found at i:16212013 original size:12 final size:12
Alignment explanation
Indices: 16211978--16212016 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
16211968 CTTAAAACAC
16211978 TTAATAAAACCA
1 TTAATAAAACCA
*
16211990 CTATATAAAACCA
1 TTA-ATAAAACCA
16212003 TTAATAAAACCA
1 TTAATAAAACCA
16212015 TT
1 TT
16212017 GATAGTGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAATAAAACCA
Found at i:16214261 original size:9 final size:9
Alignment explanation
Indices: 16214241--16214271 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
16214231 AATCTATCAA
16214241 AAAGGTAAAG
1 AAAGG-AAAG
16214251 AAAGGAAAG
1 AAAGGAAAG
16214260 AAAGGAAAG
1 AAAGGAAAG
16214269 AAA
1 AAA
16214272 AAGTCATGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (9 bp):
AAAGGAAAG
Found at i:16217652 original size:31 final size:31
Alignment explanation
Indices: 16217614--16217877 Score: 431
Period size: 31 Copynumber: 8.5 Consensus size: 31
16217604 CACGACATGG
*
16217614 GTTATATGCATGGCGTGTTACAACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* * *
16217645 GTTATATGCATGGTGTGTTACAACATTTAAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
*
16217676 GTTATATGCATGGCGTGTTACCACATTTTTC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
16217707 GTTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
16217738 GTTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
*
16217769 GTTATATGCATGGCGTGTTACCACATTTTAT
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
16217800 GTTATTTGCATGGCGTGTTAGCACA-TTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
* *
16217830 GTTATATGCATAGCGTGTTACTACATTTTAC
1 GTTATATGCATGGCGTGTTACCACATTTTAC
16217861 GTTATATGCATGGCGTG
1 GTTATATGCATGGCGTG
16217878 AAACATGACT
Statistics
Matches: 216, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
30 25 0.12
31 191 0.88
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (31 bp):
GTTATATGCATGGCGTGTTACCACATTTTAC
Found at i:16222750 original size:31 final size:31
Alignment explanation
Indices: 16222427--16222743 Score: 411
Period size: 31 Copynumber: 10.2 Consensus size: 31
16222417 AATAAGGAAT
* *
16222427 AAATGTTGTGACATGCCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16222458 AAATGTTGTGACACGCCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16222489 AAATGTTGTGACACGCCATGCATAACAAGTC
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
16222520 AAATGTTGTGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * **
16222551 AAATATTGTGACACGTCGTGCATATTAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
16222582 AAATGTTGTGGCACGTCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
16222613 AAATGTTGTGACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
16222644 AAATTTTGTGACATGCCATGCATAACAAGTT
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
16222675 AAATGTTCTGACACGTCATGCATAATAAGTG
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
16222706 AAATGTTGTCACACGCCATGCATATA-AAGTG
1 AAATGTTGTGACACGCCATGCATA-ACAAGTA
16222737 AAATGTT
1 AAATGTT
16222744 ATCACACTGA
Statistics
Matches: 257, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
31 256 1.00
32 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:16223818 original size:14 final size:14
Alignment explanation
Indices: 16223799--16223868 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
16223789 GAATTAATTC
* *
16223799 TGTATACAATGAAT
1 TGTATAAAATAAAT
16223813 TGTATAAAATAAATT
1 TGTATAAAATAAA-T
*
16223828 GTGTATACAAAAAAATT
1 -TGTATA-AAATAAA-T
* *
16223845 ATATATAAAATTAAT
1 -TGTATAAAATAAAT
16223860 TGTATAAAA
1 TGTATAAAA
16223869 ATAATTCTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
14 19 0.42
15 2 0.04
16 11 0.24
17 13 0.29
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (14 bp):
TGTATAAAATAAAT
Found at i:16223832 original size:16 final size:16
Alignment explanation
Indices: 16223815--16223881 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
16223805 CAATGAATTG
*
16223815 TATAAAATAAATTGTG
1 TATAAAATAAATTGTA
* *
16223831 TATACAAAAAAATTATA
1 TATA-AAATAAATTGTA
*
16223848 TATAAAATTAATTGTA
1 TATAAAATAAATTGTA
*
16223864 TA-AAAAT-AATTCTA
1 TATAAAATAAATTGTA
16223878 TATA
1 TATA
16223882 CAAAAAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
14 8 0.19
15 6 0.14
16 15 0.36
17 13 0.31
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (16 bp):
TATAAAATAAATTGTA
Found at i:16223842 original size:54 final size:54
Alignment explanation
Indices: 16223710--16223842 Score: 155
Period size: 52 Copynumber: 2.4 Consensus size: 54
16223700 GTATTAAATT
*
16223710 AAATATATTGTGTATACCAAAGAAAAAAAATTCTCGGTATAAAATTAATTGTGTAAA
1 AAATATATTGTGTATA-CAAA-AAAAAAAATTCTC-GTATAAAATGAATTGTGTAAA
** * *
16223767 AAATATATTGTGTATACAAAAAGAATTAATTCT-GTATACAATGAA-T-TGTATA
1 AAATATATTGTGTATACAAAAA-AAAAAATTCTCGTATAAAATGAATTGTGTAAA
*
16223819 AAATAAATTGTGTATACAAAAAAA
1 AAATATATTGTGTATACAAAAAAA
16223843 TTATATATAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
51 2 0.03
52 26 0.38
53 1 0.01
54 10 0.14
55 2 0.03
56 12 0.17
57 16 0.23
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.32
Consensus pattern (54 bp):
AAATATATTGTGTATACAAAAAAAAAAATTCTCGTATAAAATGAATTGTGTAAA
Found at i:16223864 original size:47 final size:47
Alignment explanation
Indices: 16223747--16223894 Score: 145
Period size: 47 Copynumber: 3.0 Consensus size: 47
16223737 AAATTCTCGG
* * *
16223747 TATAAAATTAATTGTGTAAAAAATATATTGTGTATACAAAAAGAATTAATTCTG
1 TATAAAATTAA-T-TGTATAAAATAAATTGTGTATACAAAAA-AATT-A---TA
* *
16223801 TATACAATGAATTGTATAAAATAAATTGTGTATACAAAAAAATTATA
1 TATAAAATTAATTGTATAAAATAAATTGTGTATACAAAAAAATTATA
* * *
16223848 TATAAAATTAATTGTATAAAA-ATAATTCTATATACAAAAAAACTATA
1 TATAAAATTAATTGTATAAAATA-AATTGTGTATACAAAAAAATTATA
16223895 CAAACAAGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
46 1 0.01
47 41 0.49
50 1 0.01
51 4 0.05
52 26 0.31
53 1 0.01
54 9 0.11
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (47 bp):
TATAAAATTAATTGTATAAAATAAATTGTGTATACAAAAAAATTATA
Found at i:16223873 original size:14 final size:15
Alignment explanation
Indices: 16223829--16223879 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
16223819 AAATAAATTG
*
16223829 TGTATACAAAAAAAT
1 TGTATACAAAATAAT
* *
16223844 TATATATAAAATTAAT
1 TGTATACAAAA-TAAT
16223860 TGTATA-AAAATAAT
1 TGTATACAAAATAAT
*
16223874 TCTATA
1 TGTATA
16223880 TACAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 9 0.30
15 13 0.43
16 8 0.27
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (15 bp):
TGTATACAAAATAAT
Found at i:16225457 original size:31 final size:31
Alignment explanation
Indices: 16225415--16225718 Score: 421
Period size: 31 Copynumber: 9.8 Consensus size: 31
16225405 TACCACAAAC
*
16225415 CATAACTAGTAAAATGTTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* *
16225446 CACAACAAGTAAAATGTTGTCG-CACACCATG
1 CATAACAAGTAAAATGTTGT-GACACGCCATG
16225477 CATAACAAGTAAAATGTTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* * *
16225508 GATAACAAGTAAAACGCTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* *
16225539 CATAACAAGCAAAATGTTCTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
*
16225570 CATAACAAGTAAAATATTGTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* * *
16225601 GATAACAAGCAAAATGTTCTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* * * *
16225632 CATAACAAGTTAAACGTTGTGACATGCCATT
1 CATAACAAGTAAAATGTTGTGACACGCCATG
* *
16225663 CATAACAAGTAAATTGTTCTGACACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATG
*
16225694 CATAACAAGTAAAATGTTGTCACAC
1 CATAACAAGTAAAATGTTGTGACAC
16225719 ACTAACGTTG
Statistics
Matches: 235, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
30 1 0.00
31 233 0.99
32 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (31 bp):
CATAACAAGTAAAATGTTGTGACACGCCATG
Found at i:16227943 original size:31 final size:31
Alignment explanation
Indices: 16227908--16228109 Score: 223
Period size: 31 Copynumber: 6.5 Consensus size: 31
16227898 AATAAAGAAT
* *
16227908 AAATGTTGTGAAACACCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGCA
16227939 AAATGTTGTGACACGCCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAGCA
*
16227970 AAATGTTGTGACACGCCATGCATATCAAGTC-
1 AAATGTTGTGACACGCCATGCATAACAAG-CA
* *
16228001 AAATGTTGTGACACGCCATGCATATCGAGTC-
1 AAATGTTGTGACACGCCATGCATAACAAG-CA
* * *
16228032 AAATGTTGTCACATGCCATGCATATCAAGTC-
1 AAATGTTGTGACACGCCATGCATAACAAG-CA
* * * *
16228063 AAATATTGTCACACGCCCTGCATATCAAGTC-
1 AAATGTTGTGACACGCCATGCATAACAAG-CA
*
16228094 AAATGTTGTCACACGC
1 AAATGTTGTGACACGC
16228110 TAACGTTGGC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
31 158 0.99
32 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGCA
Found at i:16228005 original size:62 final size:62
Alignment explanation
Indices: 16227908--16228109 Score: 273
Period size: 62 Copynumber: 3.3 Consensus size: 62
16227898 AATAAAGAAT
* * * * *
16227908 AAATGTTGTGAAACACCATGCATAACAAG-CAAAATGTTGTGACACGCCATGCATAACAAG-C
1 AAATGTTGTCACACGCCATGCATATCAAGTC-AAATGTTGTGACACGCCATGCATATCAAGTC
* *
16227969 AAAATGTTGTGACACGCCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCGAGTC
1 -AAATGTTGTCACACGCCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTC
* * * *
16228032 AAATGTTGTCACATGCCATGCATATCAAGTCAAATATTGTCACACGCCCTGCATATCAAGTC
1 AAATGTTGTCACACGCCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTC
16228094 AAATGTTGTCACACGC
1 AAATGTTGTCACACGC
16228110 TAACGTTGGC
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
62 124 0.98
63 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (62 bp):
AAATGTTGTCACACGCCATGCATATCAAGTCAAATGTTGTGACACGCCATGCATATCAAGTC
Found at i:16228077 original size:93 final size:93
Alignment explanation
Indices: 16227908--16228109 Score: 273
Period size: 93 Copynumber: 2.2 Consensus size: 93
16227898 AATAAAGAAT
* * *
16227908 AAATGTTGTGAAACACCATGCATAACAAGCAAAATGTTGTGACACGCCATGCATAACAAGCAAAA
1 AAATGTTGTGACACGCCATGCATAACAAGCAAAATGTTGTCACACGCCATGCATAACAAGCAAAA
* *
16227973 TGTTGTGACACGCCATGCATATCAAGTC
66 TATTGTCACACGCCATGCATATCAAGTC
* * * *
16228001 AAATGTTGTGACACGCCATGCATATCGAGTC-AAATGTTGTCACATGCCATGCATATCAAGTC-A
1 AAATGTTGTGACACGCCATGCATAACAAG-CAAAATGTTGTCACACGCCATGCATAACAAG-CAA
*
16228064 AATATTGTCACACGCCCTGCATATCAAGTC
64 AATATTGTCACACGCCATGCATATCAAGTC
*
16228094 AAATGTTGTCACACGC
1 AAATGTTGTGACACGC
16228110 TAACGTTGGC
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
93 94 0.98
94 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (93 bp):
AAATGTTGTGACACGCCATGCATAACAAGCAAAATGTTGTCACACGCCATGCATAACAAGCAAAA
TATTGTCACACGCCATGCATATCAAGTC
Found at i:16228684 original size:24 final size:24
Alignment explanation
Indices: 16228652--16228733 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
16228642 ACTCTAAACG
16228652 TGGCGTGTCACCAACTCTGAACTC
1 TGGCGTGTCACCAACTCTGAACTC
* * **
16228676 TGGCTTGTCA-CAGCT-T-CCCTCC
1 TGGCGTGTCACCAACTCTGAACT-C
*
16228698 ATGGCATGTCACCAACTCTGAACTC
1 -TGGCGTGTCACCAACTCTGAACTC
*
16228723 TGACGTGTCAC
1 TGGCGTGTCAC
16228734 AGATTCCCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 13 0.30
24 22 0.51
25 2 0.05
26 2 0.05
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.27
Consensus pattern (24 bp):
TGGCGTGTCACCAACTCTGAACTC
Found at i:16228709 original size:47 final size:47
Alignment explanation
Indices: 16228652--16228954 Score: 410
Period size: 47 Copynumber: 6.4 Consensus size: 47
16228642 ACTCTAAACG
* * *
16228652 TGGCGTGTCACCAACTCTGAACTCTGGCTTGTCACAGCTTCCCTCCA
1 TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
*
16228699 TGGCATGTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTCCA
1 TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
* * *
16228746 TGGCATCTCACGAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCA
1 TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
* **
16228793 TGCCATGTCACCAACTCTGAACTCTATCGTGTCACAGATTCCCTCCA
1 TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
* * * * *
16228840 TGG-ATTCTCACCAACTCTGAACGCTGGCATGTCACAAATTCCCACCA
1 TGGCA-TGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
* ***
16228887 TGGCATGTCACCAACTCTTAACTCTTATGTGTCACAGATTCCCTCCA
1 TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
*
16228934 TGGCATCTCACCAACTCTGAA
1 TGGCATGTCACCAACTCTGAA
16228955 TGCTAGTGTG
Statistics
Matches: 221, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
46 1 0.00
47 219 0.99
48 1 0.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.26
Consensus pattern (47 bp):
TGGCATGTCACCAACTCTGAACTCTGGCGTGTCACAGATTCCCTCCA
Found at i:16228967 original size:94 final size:94
Alignment explanation
Indices: 16228659--16228968 Score: 462
Period size: 94 Copynumber: 3.3 Consensus size: 94
16228649 ACGTGGCGTG
* * *
16228659 TCACCAACTCTGAACTCTGGCTTGTCACAGCTTCCCTCCATGGCATGTCACCAACTCTGAACTCT
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGGCATGTCACCAACTCTGAACTCT
* *
16228724 GACGTGTCACAGATTCCCTCCATGGCATC
66 TATGTGTCACAGATTCCCTCCATGGCATC
* *
16228753 TCACGAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGCCATGTCACCAACTCTGAACTC-
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGGCATGTCACCAACTCTGAACTCT
16228817 TATCGTGTCACAGATTCCCTCCATGG-ATTC
66 TAT-GTGTCACAGATTCCCTCCATGGCA-TC
* * * *
16228847 TCACCAACTCTGAACGCTGGCATGTCACAAATTCCCACCATGGCATGTCACCAACTCTTAACTCT
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGGCATGTCACCAACTCTGAACTCT
16228912 TATGTGTCACAGATTCCCTCCATGGCATC
66 TATGTGTCACAGATTCCCTCCATGGCATC
* * *
16228941 TCACCAACTCTGAATGCTAGTGTGTCAC
1 TCACCAACTCTGAACGCTGGCGTGTCAC
16228969 GGTCGTGTCA
Statistics
Matches: 195, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
93 2 0.01
94 189 0.97
95 4 0.02
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (94 bp):
TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGGCATGTCACCAACTCTGAACTCT
TATGTGTCACAGATTCCCTCCATGGCATC
Found at i:16231601 original size:21 final size:21
Alignment explanation
Indices: 16231581--16231618 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
16231571 CAAATAAGTT
*
16231581 TTAT-ATAATTTAA-CAAAAG
1 TTATAATAATCTAATCAAAAG
16231600 TTATAATAATCTAATCAAA
1 TTATAATAATCTAATCAAA
16231619 TAAGAGGCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.37
Consensus pattern (21 bp):
TTATAATAATCTAATCAAAAG
Found at i:16232827 original size:37 final size:36
Alignment explanation
Indices: 16232780--16232895 Score: 196
Period size: 37 Copynumber: 3.2 Consensus size: 36
16232770 ACATACATTG
16232780 TCATCATGTGTGCACTCCCTACTCGCACACTCTATCA
1 TCATCATGTGTGCACTCCCTACTCGCACACTC-ATCA
16232817 TCATCATGTGTGCACTCCCTACTCGCACACTCCATCA
1 TCATCATGTGTGCACTCCCTACTCGCACACT-CATCA
* *
16232854 TCATCATGTGTGCACTCCCTACTCGCACAGTCAACA
1 TCATCATGTGTGCACTCCCTACTCGCACACTCATCA
16232890 TCATCA
1 TCATCA
16232896 CCCAACATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
36 10 0.13
37 65 0.86
38 1 0.01
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (36 bp):
TCATCATGTGTGCACTCCCTACTCGCACACTCATCA
Found at i:16234223 original size:65 final size:67
Alignment explanation
Indices: 16234079--16234244 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 67
16234069 TAATCCCCCT
* * *
16234079 ATGAGAATATGTATGTGATGT-TATTCCATATACTACATGAGATGATTAAGTATGCATGATTAAT
1 ATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGCAAGCATGA-TAAT
16234143 GCC
65 GCC
* * * *
16234146 ATGAGAACATGTATATGATGTATATTTCATGTACTACATGAGATGATTGAGCAAGCAT-A-AATG
1 ATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGCAAGCATGATAATG
16234209 CC
66 CC
* * *
16234211 ATGAGATTATGTATATGATGTAAATTCTATATAC
1 ATGAGAATATGTATATGATGTATATTCCATATAC
16234245 CTTATGAGAT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 34 0.40
67 20 0.24
68 31 0.36
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (67 bp):
ATGAGAATATGTATATGATGTATATTCCATATACTACATGAGATGATTAAGCAAGCATGATAATG
CC
Found at i:16234428 original size:31 final size:31
Alignment explanation
Indices: 16234383--16234452 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
16234373 ATCATAAAAT
* *
16234383 GCCCAA-GAGCAATGGGGATATACGTTGCCA
1 GCCCAAGGTGCAATGGGGATATACATTGCCA
*
16234413 GCCCAAGGTGCAATGGGGATGTACATTGCCA
1 GCCCAAGGTGCAATGGGGATATACATTGCCA
16234444 GCCCAAGGT
1 GCCCAAGGT
16234453 TGATGGGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.17
Consensus pattern (31 bp):
GCCCAAGGTGCAATGGGGATATACATTGCCA
Found at i:16234461 original size:30 final size:30
Alignment explanation
Indices: 16234393--16234462 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
16234383 GCCCAAGAGC
*
16234393 AATGGGGATATACGTTGCCAGCCCAAGGTG
1 AATGGGGATATACATTGCCAGCCCAAGGTG
*
16234423 CAATGGGGATGTACATTGCCAGCCCAAGGTTG
1 -AATGGGGATATACATTGCCAGCCCAAGG-TG
16234455 -ATGGGGAT
1 AATGGGGAT
16234463 CAAACCATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 8 0.22
31 26 0.72
32 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (30 bp):
AATGGGGATATACATTGCCAGCCCAAGGTG
Found at i:16234894 original size:15 final size:16
Alignment explanation
Indices: 16234874--16234903 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16234864 GAATTTGATG
16234874 AGGATTT-TAAAGGTA
1 AGGATTTCTAAAGGTA
16234889 AGGATTTCTAAAGGT
1 AGGATTTCTAAAGGT
16234904 TTATATAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (16 bp):
AGGATTTCTAAAGGTA
Found at i:16237237 original size:36 final size:36
Alignment explanation
Indices: 16237171--16237278 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
16237161 TCTAAACACA
* *
16237171 TGTGGTATTCTTACCCCCCACATCTGGGCCATATT-T
1 TGTGGTATTCTTA-CCCTCACATCTAGGCCATATTCT
* *
16237207 GTGTGGTATTTTTACCCTCACATTTAGGCCATATTCT
1 -TGTGGTATTCTTACCCTCACATCTAGGCCATATTCT
*
16237244 TGTGGTATTCTTA-CCTCCACATCTAGACCATATTC
1 TGTGGTATTCTTACCCT-CACATCTAGGCCATATTC
16237279 ATAAATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
35 3 0.05
36 46 0.74
37 13 0.21
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (36 bp):
TGTGGTATTCTTACCCTCACATCTAGGCCATATTCT
Found at i:16239597 original size:37 final size:37
Alignment explanation
Indices: 16239517--16239589 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
16239507 ACAAATTGAA
* * *
16239517 AAAAATGCCCTTAGGATTACACAAGATATTTAATGAC
1 AAAAATACTCTTAGGATTACACAAGATATTAAATGAC
*
16239554 AAAAATACTCTTAGGATTACA-TAGCATATTAAATGA
1 AAAAATACTCTTAGGATTACACAAG-ATATTAAATGA
16239590 TGAAAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.06
37 29 0.94
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (37 bp):
AAAAATACTCTTAGGATTACACAAGATATTAAATGAC
Found at i:16252956 original size:23 final size:23
Alignment explanation
Indices: 16252930--16252983 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
16252920 GAAAAAAGAG
* *
16252930 AAAAAG-GAAAGAAAAAGAGAGGT
1 AAAAAGAGAAACAAAAA-ACAGGT
16252953 AAAAAGAGAAACAAAAAACAGGT
1 AAAAAGAGAAACAAAAAACAGGT
16252976 AAAAAGAG
1 AAAAAGAG
16252984 GCCGTGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.69, C:0.04, G:0.24, T:0.04
Consensus pattern (23 bp):
AAAAAGAGAAACAAAAAACAGGT
Found at i:16261208 original size:26 final size:26
Alignment explanation
Indices: 16261175--16261245 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
16261165 TTCATCCACT
* *
16261175 TCTT-GTGGTAAAATTATCCATCTAC
1 TCTTGGTGGCAAAATTATCCATCAAC
16261200 TCTTGGTGGCAAAATTATCCATCAAC
1 TCTTGGTGGCAAAATTATCCATCAAC
16261226 T-TCTGGTGGCAAAATTATCC
1 TCT-TGGTGGCAAAATTATCC
16261246 TTAGATTCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
25 5 0.12
26 37 0.88
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (26 bp):
TCTTGGTGGCAAAATTATCCATCAAC
Found at i:16262755 original size:39 final size:39
Alignment explanation
Indices: 16262696--16262796 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
16262686 ATAGGAAATA
* *
16262696 AAACAGAAAGTTTTTTGCTGCAGCGAAATTGTGACCCAG
1 AAACAGAAAGTTTCTTGCTGCAGCGAAATTGTAACCCAG
* * *
16262735 AAACAGAATGTTTCTCGCTGCAGCGAAATTTTAACCCAG
1 AAACAGAAAGTTTCTTGCTGCAGCGAAATTGTAACCCAG
*
16262774 AAACAAAAAGTTTCTTGCTGCAG
1 AAACAGAAAGTTTCTTGCTGCAG
16262797 GGAGAATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (39 bp):
AAACAGAAAGTTTCTTGCTGCAGCGAAATTGTAACCCAG
Found at i:16262936 original size:21 final size:21
Alignment explanation
Indices: 16262911--16262967 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
16262901 CGAGAGTTTC
* *
16262911 TCGCTACAGCGAGAATGATTT
1 TCGCTGCAGCGAGAATAATTT
*
16262932 TCGCTGCAACGAGAATAATTT
1 TCGCTGCAGCGAGAATAATTT
* *
16262953 TTGCTGTAGCGAGAA
1 TCGCTGCAGCGAGAA
16262968 ACAGGGCACC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (21 bp):
TCGCTGCAGCGAGAATAATTT
Found at i:16263260 original size:43 final size:43
Alignment explanation
Indices: 16263213--16263327 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
16263203 CAGCTCATAT
** * * *
16263213 GCACTCCCTACTCGCACATGGTTGGGTCATCAC-CGGGTTATGC
1 GCACTCCCTACTCGCACATAATCGAGTCATC-CTCGGCTTATGC
16263256 GCACTCCCTACTCGCACATAATCGAGTCATCCTCGGCTTATGC
1 GCACTCCCTACTCGCACATAATCGAGTCATCCTCGGCTTATGC
* **
16263299 GCACTCCCTACTCACACATAGCCGAGTCA
1 GCACTCCCTACTCGCACATAATCGAGTCA
16263328 ATATAATTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 62 0.98
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (43 bp):
GCACTCCCTACTCGCACATAATCGAGTCATCCTCGGCTTATGC
Found at i:16286898 original size:22 final size:21
Alignment explanation
Indices: 16286856--16286899 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
16286846 GGAACAAAAT
* * *
16286856 AGAAAGATTTTCGCTGTAGCG
1 AGAAAGATTCTCACTGCAGCG
16286877 AGAATAGATTCTCACTGCAGCG
1 AGAA-AGATTCTCACTGCAGCG
16286899 A
1 A
16286900 AATTTCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AGAAAGATTCTCACTGCAGCG
Found at i:16287229 original size:2 final size:2
Alignment explanation
Indices: 16287224--16287248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16287214 TGTGTGTGTG
16287224 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16287249 CAACACAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16292449 original size:43 final size:42
Alignment explanation
Indices: 16292387--16292510 Score: 158
Period size: 43 Copynumber: 2.9 Consensus size: 42
16292377 ATTGACTTGG
**
16292387 CTATGTGCGAGTAGGGAGTGCGCATAAGCTGAGGATGACCCGG
1 CTATGTGCGAGTAGGGAGTGCGCATAAGCTG-GGATGACCCAA
* * *
16292430 TTATGTGCGAGTAGGGAGTGCGCATAACCCTGTGATGACCCAA
1 CTATGTGCGAGTAGGGAGTGCGCATAA-GCTGGGATGACCCAA
* *
16292473 CCATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 CTATGTGCGAGTAGGGAGTGCGCATAAGCTGG-GATGA
16292511 TGATGATGGG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.04
43 63 0.91
44 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTATGTGCGAGTAGGGAGTGCGCATAAGCTGGGATGACCCAA
Found at i:16292963 original size:60 final size:60
Alignment explanation
Indices: 16292867--16293000 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
16292857 CAATAGCTTC
* * *
16292867 TCACTGCAGCGAAATTCATTCTCGCTGCAACAAGAAAC-TTTCTATTTCTGGGTTACAATT
1 TCACTGCAGCGAAATTCAATCTCGCTACAACAAGAAACATTT-TATTTCTGGGTCACAATT
* * * * *
16292927 TCACTGCAGC-AAGATTGAATCTCGCTACAGCGAGAAACATTTTGTTTTTGGGTCACAATT
1 TCACTGCAGCGAA-ATTCAATCTCGCTACAACAAGAAACATTTTATTTCTGGGTCACAATT
*
16292987 TCGCTGCAGCGAAA
1 TCACTGCAGCGAAA
16293001 AACCTTCTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 2 0.03
60 55 0.89
61 5 0.08
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (60 bp):
TCACTGCAGCGAAATTCAATCTCGCTACAACAAGAAACATTTTATTTCTGGGTCACAATT
Found at i:16294326 original size:26 final size:26
Alignment explanation
Indices: 16294290--16294343 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
16294280 ATATCTTGCC
16294290 AAATCTGTCTTTAAACATTAAAACAT
1 AAATCTGTCTTTAAACATTAAAACAT
*
16294316 AAATTTGTCTTTAAACATTAAAACAT
1 AAATCTGTCTTTAAACATTAAAACAT
16294342 AA
1 AA
16294344 TTGCTTTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (26 bp):
AAATCTGTCTTTAAACATTAAAACAT
Found at i:16307074 original size:19 final size:19
Alignment explanation
Indices: 16307050--16307087 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16307040 CCATTTGACT
16307050 TATTGGAATATGATTTGAG
1 TATTGGAATATGATTTGAG
*
16307069 TATTGGAGTATGATTTGAG
1 TATTGGAATATGATTTGAG
16307088 ATTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAATATGATTTGAG
Found at i:16310538 original size:176 final size:176
Alignment explanation
Indices: 16310239--16310589 Score: 542
Period size: 176 Copynumber: 2.0 Consensus size: 176
16310229 TCTAAGTCAA
* * *
16310239 TAGGTTGTAAATAGATTTTTCAAGAAGAAAATCAAAGTTGATGGAACCATTGAGTTTAAAGCTAG
1 TAGGCTGTAAATAGATTTTTCAAGAAGAAAATCAAAGTTGATGGAACCATTGAATTGAAAGCTAG
* *
16310304 ACTAGTGGCCAAGGGCATTACACAAAAAGAAAATGTTGACTATTTCGATACATATGCACTTGTAG
66 ACTACTGGCCAAGGGCACTACACAAAAAGAAAATGTTGACTATTTCGATACATATGCACTTGTAG
* * *
16310369 CAAGAATAGCTATAATTATGTGGCATTTGGTACCTTACAATGCAAC
131 CAAGAATAGCTACAATTAAGTGGCATTTAGTACCTTACAATGCAAC
*
16310415 TAGGCTGTAAATAGATTTTTC-AGAAAGAAAATCAAAGTTGATGGAATCATTGAATTGAAAGCTA
1 TAGGCTGTAAATAGATTTTTCAAG-AAGAAAATCAAAGTTGATGGAACCATTGAATTGAAAGCTA
* * * * * * *
16310479 GGCTACTGGGCAAGGGCCCTACACAAAAGGAAAGTGTTGATTATTTCGGTACATATGCACTTGTA
65 GACTACTGGCCAAGGGCACTACACAAAAAGAAAATGTTGACTATTTCGATACATATGCACTTGTA
16310544 GCAAGAATAGCTACAATTAAGTGGCATTTAGTACCTTACAATGCAA
130 GCAAGAATAGCTACAATTAAGTGGCATTTAGTACCTTACAATGCAA
16310590 TGTAATTGTA
Statistics
Matches: 158, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
175 2 0.01
176 156 0.99
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (176 bp):
TAGGCTGTAAATAGATTTTTCAAGAAGAAAATCAAAGTTGATGGAACCATTGAATTGAAAGCTAG
ACTACTGGCCAAGGGCACTACACAAAAAGAAAATGTTGACTATTTCGATACATATGCACTTGTAG
CAAGAATAGCTACAATTAAGTGGCATTTAGTACCTTACAATGCAAC
Found at i:16310805 original size:33 final size:33
Alignment explanation
Indices: 16310757--16310849 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
16310747 AGAATTACCC
* * *
16310757 TAATGTCATATATTTTATTTTTATTTCTTATTA
1 TAATCTCAGATATTTTATTTTTATTTCTTAATA
* *
16310790 TAATCTTAGATATTTTATTTTCATTTCTTAATA
1 TAATCTCAGATATTTTATTTTTATTTCTTAATA
*
16310823 TAATCTCATATATTTTATATTTTATTT
1 TAATCTCAGATATTTTAT-TTTTATTT
16310850 TAATTTCATT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 44 0.86
34 7 0.14
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (33 bp):
TAATCTCAGATATTTTATTTTTATTTCTTAATA
Found at i:16315738 original size:72 final size:71
Alignment explanation
Indices: 16315613--16315781 Score: 189
Period size: 72 Copynumber: 2.4 Consensus size: 71
16315603 TGACAAGTAG
* * * * *
16315613 GTCTCGATACTTGGACACTTGCTCTTTGGAATTTTAAGTTATGAAGACAAGGTCACAAAACATTG
1 GTCTCAATACTTGG-CACTTGCTCTTTGAAAATTAAAGTTATGAAAACAAGGTCACAAAACATTG
16315678 ATAGCAA
65 ATAGCAA
* * * * *
16315685 GTCTCAATACTTTGGCATTTGCTCTTTGAAAATTAAAGTTCA-GAAAACGAGGTCTCGATACATT
1 GTCTCAATAC-TTGGCACTTGCTCTTTGAAAATTAAAGTT-ATGAAAACAAGGTCACAAAACATT
16315749 GATAGCAA
64 GATAGCAA
*
16315757 GTCTTAATACCTTGGCACTTG-TCTT
1 GTCTCAATA-CTTGGCACTTGCTCTT
16315782 CTAGAATTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
71 4 0.05
72 72 0.88
73 6 0.07
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (71 bp):
GTCTCAATACTTGGCACTTGCTCTTTGAAAATTAAAGTTATGAAAACAAGGTCACAAAACATTGA
TAGCAA
Found at i:16328984 original size:72 final size:72
Alignment explanation
Indices: 16328691--16329012 Score: 280
Period size: 72 Copynumber: 4.5 Consensus size: 72
16328681 ATGCGGCTTG
* * * * * * * **
16328691 GTCTCAATACTTT-GCAGCTTGCTCTCTAGAAATTCATGTTTGGAA-ATGATGTCTCGATAC-TT
1 GTCTCGATACTTTGGCA-CTTGCTTTCTGGAAATTGAAGTTTTGAAGATGAGGTCTTAATACATT
*
16328753 GGCAAGCAA
65 GACAA-CAA
* * * * * * *
16328762 GTCTCGATACTTAGGCAGTTGCTTTTTGGAATTTGAAGGTTTAAAGATGAGGTCTTAATACACTG
1 GTCTCGATACTTTGGCACTTGCTTTCTGGAAATTGAAGTTTTGAAGATGAGGTCTTAATACATTG
16328827 ACAACAA
66 ACAACAA
* * * * ** *
16328834 GTCTCAATATTTTGGCACTTGCTTTCT-GAAATTAAAGTCTTGAAGATGAGGTCTCGATATATTG
1 GTCTCGATACTTTGGCACTTGCTTTCTGGAAATTGAAGTTTTGAAGATGAGGTCTTAATACATTG
16328898 ACAACAA
66 ACAACAA
* * *
16328905 G-CTTCGATACTTTGGCACTTAAC-TTCTGGAAATTGAAGTTTTGAAGATGAGATCTTAATAGAT
1 GTC-TCGATACTTTGGCACTT-GCTTTCTGGAAATTGAAGTTTTGAAGATGAGGTCTTAATACAT
* *
16328968 TAACAGCAA
64 TGACAACAA
*
16328977 GTCTCGATACTTTGGCACTTGTCTTT-TGGAATTTGA
1 GTCTCGATACTTTGGCACTTG-CTTTCTGGAAATTGA
16329013 GACTTTGGAG
Statistics
Matches: 198, Mismatches: 44, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
70 1 0.01
71 84 0.42
72 105 0.53
73 8 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (72 bp):
GTCTCGATACTTTGGCACTTGCTTTCTGGAAATTGAAGTTTTGAAGATGAGGTCTTAATACATTG
ACAACAA
Found at i:16332758 original size:36 final size:36
Alignment explanation
Indices: 16332718--16332788 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
16332708 ATAGTTTCAC
*
16332718 AATAAAAAATTATGTCTCTTCATATGAAAAATTGTA
1 AATAAAAAATTATATCTCTTCATATGAAAAATTGTA
* * * *
16332754 AATAAAAAGTTATATTTTTTCATATGAAAACTTGT
1 AATAAAAAATTATATCTCTTCATATGAAAAATTGT
16332789 GACCATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (36 bp):
AATAAAAAATTATATCTCTTCATATGAAAAATTGTA
Found at i:16335903 original size:45 final size:46
Alignment explanation
Indices: 16335853--16336053 Score: 182
Period size: 45 Copynumber: 4.3 Consensus size: 46
16335843 CACGTTATGA
*
16335853 TGTTACATGCCATGTACAAAACCATGCTACACA-CCATGGTTAGGT
1 TGTTACATGCCATGTACAAAACCATGTTACACAGCCATGGTTAGGT
* *
16335898 TGTTACATGTCATGTACAAAA--AT-TTATGACAAGCCATGGTTAGGT
1 TGTTACATGCCATGTACAAAACCATGTTA-CAC-AGCCATGGTTAGGT
* *
16335943 TGTTACACGCCATGTACAAAAACC-TGTGACA-AGCCATGGTTAGGT
1 TGTTACATGCCATGTAC-AAAACCATGTTACACAGCCATGGTTAGGT
* * * **
16335988 TGTTGCATGCTATGTTGAAAAAAATACTGTTGTTACAC-GCCATGGTTAGGT
1 TGTTACATGCCATG-T---ACAAA-AC-CATGTTACACAGCCATGGTTAGGT
16336039 TGTTACATGCCATGT
1 TGTTACATGCCATGT
16336054 TAAAAAAAAA
Statistics
Matches: 126, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.03
44 1 0.01
45 72 0.57
46 5 0.04
47 2 0.02
48 5 0.04
49 3 0.02
50 1 0.01
51 31 0.25
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (46 bp):
TGTTACATGCCATGTACAAAACCATGTTACACAGCCATGGTTAGGT
Found at i:16336009 original size:90 final size:93
Alignment explanation
Indices: 16335853--16336053 Score: 231
Period size: 90 Copynumber: 2.2 Consensus size: 93
16335843 CACGTTATGA
16335853 TGTTACATGCCATGTACAAAACCATGCTACACACCATGGTTAGGTTGTTACATGTCATGTAC-AA
1 TGTTACATGCCATGTACAAAACCATGCTACACACCATGGTTAGGTTGTTACATGTCATGTACAAA
16335917 AAAT-T-TATG-ACAAGCCATGGTTAGGT
66 AAATATGT-TGTACAAGCCATGGTTAGGT
* *
16335943 TGTTACACGCCATGTACAAAAACC-TG-TGACA-AGCCATGGTTAGGTTGTTGCATG-CTATGTT
1 TGTTACATGCCATGTAC-AAAACCATGCT-ACACA-CCATGGTTAGGTTGTTACATGTC-ATG-T
*
16336004 GA-AAAAAATACTGTTGTTACACGCCATGGTTAGGT
61 -ACAAAAAATA-TGTTG-TACAAGCCATGGTTAGGT
16336039 TGTTACATGCCATGT
1 TGTTACATGCCATGT
16336054 TAAAAAAAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 18
0.81 0.03 0.15
Matches are distributed among these distances:
89 3 0.03
90 44 0.46
91 7 0.07
92 7 0.07
94 3 0.03
95 1 0.01
96 30 0.32
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (93 bp):
TGTTACATGCCATGTACAAAACCATGCTACACACCATGGTTAGGTTGTTACATGTCATGTACAAA
AAATATGTTGTACAAGCCATGGTTAGGT
Found at i:16336031 original size:51 final size:52
Alignment explanation
Indices: 16335930--16336082 Score: 187
Period size: 51 Copynumber: 3.1 Consensus size: 52
16335920 TTTATGACAA
* * * *
16335930 GCCATGGTTAGGTTGTTACACGCCATG-T--ACAAAAA-CCTG-TG--ACAA
1 GCCATGGTTAGGTTGTTACATGCCATGTTAAAAAAAAATACTGTTGTTACAC
* * *
16335975 GCCATGGTTAGGTTGTTGCATGCTATGTT-GAAAAAAATACTGTTGTTACAC
1 GCCATGGTTAGGTTGTTACATGCCATGTTAAAAAAAAATACTGTTGTTACAC
16336026 GCCATGGTTAGGTTGTTACATGCCATGTTAAAAAAAAATACTGTTGTTACAC
1 GCCATGGTTAGGTTGTTACATGCCATGTTAAAAAAAAATACTGTTGTTACAC
16336078 GCCAT
1 GCCAT
16336083 ATACAAAAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
45 24 0.26
46 1 0.01
47 6 0.07
48 3 0.03
49 2 0.02
51 30 0.33
52 26 0.28
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (52 bp):
GCCATGGTTAGGTTGTTACATGCCATGTTAAAAAAAAATACTGTTGTTACAC
Found at i:16336123 original size:26 final size:26
Alignment explanation
Indices: 16336068--16336174 Score: 76
Period size: 26 Copynumber: 4.0 Consensus size: 26
16336058 AAAAAATACT
* *
16336068 GTTGTTACACGCCAT-AT-ACAAAAA
1 GTTGTTACACGCCATGTTGAAAAAAA
** *
16336092 CATGTTACACGTCATGGTT-AAAAAAA
1 GTTGTTACACGCCAT-GTTGAAAAAAA
*
16336118 GTTGTTACGCGCCATGTTGAAAAAAAATA
1 GTTGTTACACGCCATGTTG--AAAAAA-A
*
16336147 TTATTGTTACACGCCATGTTGAAAAAAA
1 --GTTGTTACACGCCATGTTGAAAAAAA
16336175 AATATTGTTG
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
24 12 0.19
25 3 0.05
26 18 0.28
28 7 0.11
29 7 0.11
31 17 0.27
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (26 bp):
GTTGTTACACGCCATGTTGAAAAAAA
Found at i:16336178 original size:32 final size:31
Alignment explanation
Indices: 16336119--16336220 Score: 127
Period size: 32 Copynumber: 3.3 Consensus size: 31
16336109 TTAAAAAAAG
*
16336119 TTGTTACGCGCCATGTTGAAAAAAAATATTA
1 TTGTTACACGCCATGTTGAAAAAAAATATTA
*
16336150 TTGTTACACGCCATGTTGAAAAAAAAATATTG
1 TTGTTACACGCCATGTTG-AAAAAAAATATTA
* **
16336182 TTGTTATACGGTATGTTG--AAAAAATATTA
1 TTGTTACACGCCATGTTGAAAAAAAATATTA
*
16336211 TTGTTGCACG
1 TTGTTACACG
16336221 ACATATTCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 18 0.29
31 17 0.27
32 27 0.44
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (31 bp):
TTGTTACACGCCATGTTGAAAAAAAATATTA
Found at i:16336667 original size:23 final size:23
Alignment explanation
Indices: 16336623--16336668 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16336613 CTTGGTGTCT
*
16336623 TGAAAACGCAAGAAATAAAAATC
1 TGAAAACGCAAGAAAGAAAAATC
* * *
16336646 TGAAAACGCGAGAGAGAGAAATC
1 TGAAAACGCAAGAAAGAAAAATC
16336669 GGAAGCATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.13, G:0.22, T:0.11
Consensus pattern (23 bp):
TGAAAACGCAAGAAAGAAAAATC
Found at i:16346820 original size:660 final size:657
Alignment explanation
Indices: 16345860--16347156 Score: 2283
Period size: 658 Copynumber: 2.0 Consensus size: 657
16345850 AAACAGAAGC
* * * *
16345860 TGTAAAGCATTACAGGTAAGAAGCTTTAAACAGCATTTATTGTAATGTGGCAACCAGCATGGGTC
1 TGTAAAGCATTACAGGGAAGAAGCTTTAAACAACATTTATTATAATGTGGCAACCAGCATAGGTC
* *
16345925 CTTGCTGATAACTATACATTCTGTGCGATTTCTAAGACCGTGTTTGGCCTGATTTTTTTCTAACT
66 CTTGCTGATAACTATACATTCTGTGCAATTTCTAAGACCATGTTTGGCCTGATTTTTTTCTAACT
*
16345990 TAAAAGCTATTATAAAGCTTTTATGAAAAATAATAGCTTTTAAAATTAAGTTAAAGTTATTTGAT
131 TAAAAGCTATTATAAAGCTTTTATGAAAAATAATAGCTTTTAAAATTAAGCTAAAG-T-TTTGAT
16346055 AAATTTACTTTTTATAAGCTCTTTTTTATAGATAAGTTGTTTGACAAAACAACTTATATAAACTC
194 AAATTTACTTTTTATAAGCTCTTTTTTATAGATAAGTTGTTTGACAAAACAACTTATATAAACTC
16346120 TAATTTTAGTTAAAATTACTATAAAAGATATTTAATAAATAACATTTTATTAATCGCGAATTTCT
259 TAATTTTAGTTAAAATTACTATAAAAGATATTTAATAAATAAC-TTTTATTAATCGCGAATTTCT
*
16346185 TTGTTCAAAATAAAAAAATTAATTTTATTTTTTTATCTATTTAAAATAAATTTTTGAAAATATTA
323 TTGTTCAAAATAAAAAAATTAATTTTA-TTTGTTATCTATTTAAAATAAATTTTTGAAAATATTA
16346250 AAAGGATTTTTATATAACATAAAGTTTATAATTAATAATAAATCATAAAAAAAAGTTCCACAAAT
387 AAAGGATTTTTATATAACATAAAGTTTATAATTAATAATAAATCATAAAAAAAAGTTCCACAAAT
*
16346315 AATTGATAAATAACGCATAATTCATAAATAATTTTTTATTGAATAATAATAAATAAATAAAATCA
452 AATTGATAAATAACACATAATTCATAAATAA-TTTTTATTGAA-AATAATAAATAAATAAAATCA
*
16346380 AGAGAAAAAAATTGAATCAAATAAAAAAAAATGAGAGATGAAAGAAAGCAGTGAGTCGACTACTG
515 AGAGAAAAAAATTGAATCAAATAAAAAAAAACGAGAGATGAAAGAAAGCAGTGAGTCGACTACTG
*
16346445 GAACTCATAACCCTAAGAATGGAGGAGAA-CCAAAAAAGAAGAAAAGAAGTCTAAGCTGGTAATG
580 AAACTCATAACCCTAAGAATGGAGGAGAACCCAAAAAAGAAGAAAAGAAGTCTAAGCTGGTAATG
16346509 ATAATTCAGGAGT
645 ATAATTCAGGAGT
*
16346522 TGTAAAGCATTATAGGGAAGAAGCTTTAAACAACATTTATTATAATGTGGCAACCAGCATAGGTC
1 TGTAAAGCATTACAGGGAAGAAGCTTTAAACAACATTTATTATAATGTGGCAACCAGCATAGGTC
* * * *
16346587 CTTGCTGATAACTATACATTCTGTGCAATTTCTAAGAGCATGTTTGGCTTGGTTTTTTTTTTAAC
66 CTTGCTGATAACTATACATTCTGTGCAATTTCTAAGACCATGTTTGGCCT-GATTTTTTTCTAAC
*
16346652 TTAAAAGCTATTATAAAGCTTTTATGAAAAATAATAGTTTTTAAAATTAAGCTAAAG-TTTGATA
130 TTAAAAGCTATTATAAAGCTTTTATGAAAAATAATAGCTTTTAAAATTAAGCTAAAGTTTTGATA
*
16346716 AATTTACTTTTTATAAGCTCTTTTTTATAGATAAGTTGTTTGGCAAAACAACTTATATAAACTCT
195 AATTTACTTTTTATAAGCTCTTTTTTATAGATAAGTTGTTTGACAAAACAACTTATATAAACTCT
* *
16346781 AATTTTAGTTAAAATTACTATAAAGGGTATTTAATAAATAACTTTTATTAATCGCGAATTTCTTT
260 AATTTTAGTTAAAATTACTATAAAAGATATTTAATAAATAACTTTTATTAATCGCGAATTTCTTT
16346846 GTTCAAAATAAAAAAATTAATTTTATTTGTTATCTATTTAAAATAAATTTTTGAAAATATTAAAA
325 GTTCAAAATAAAAAAATTAATTTTATTTGTTATCTATTTAAAATAAATTTTTGAAAATATTAAAA
*
16346911 GGATTTTTATATAACATAAAGTTTATAATTAATAATAAATCATAAAAAAAAGTTTCACAAATAAT
390 GGATTTTTATATAACATAAAGTTTATAATTAATAATAAATCATAAAAAAAAGTTCCACAAATAAT
* *
16346976 TTATAAGTAACACATAATTCATAAATAATTTTTATTGAAAATAATAAATAAATAAAATCAAGAGA
455 TGATAAATAACACATAATTCATAAATAATTTTTATTGAAAATAATAAATAAATAAAATCAAGAGA
* *
16347041 AAAAAATTGAATCAAATAAAAATAAACGAGAGATGAAAGAAAGCAGTGAGTTGACTACTGAAACT
520 AAAAAATTGAATCAAATAAAAAAAAACGAGAGATGAAAGAAAGCAGTGAGTCGACTACTGAAACT
*
16347106 CATAACCCTAAGAATGGAGGAGAACCCAAAAAAGAAGAAGAGAAGTCTAAG
585 CATAACCCTAAGAATGGAGGAGAACCCAAAAAAGAAGAAAAGAAGTCTAAG
16347157 GTAATAATAA
Statistics
Matches: 607, Mismatches: 26, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
656 111 0.18
657 36 0.06
658 128 0.21
659 48 0.08
660 111 0.18
662 106 0.17
663 67 0.11
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (657 bp):
TGTAAAGCATTACAGGGAAGAAGCTTTAAACAACATTTATTATAATGTGGCAACCAGCATAGGTC
CTTGCTGATAACTATACATTCTGTGCAATTTCTAAGACCATGTTTGGCCTGATTTTTTTCTAACT
TAAAAGCTATTATAAAGCTTTTATGAAAAATAATAGCTTTTAAAATTAAGCTAAAGTTTTGATAA
ATTTACTTTTTATAAGCTCTTTTTTATAGATAAGTTGTTTGACAAAACAACTTATATAAACTCTA
ATTTTAGTTAAAATTACTATAAAAGATATTTAATAAATAACTTTTATTAATCGCGAATTTCTTTG
TTCAAAATAAAAAAATTAATTTTATTTGTTATCTATTTAAAATAAATTTTTGAAAATATTAAAAG
GATTTTTATATAACATAAAGTTTATAATTAATAATAAATCATAAAAAAAAGTTCCACAAATAATT
GATAAATAACACATAATTCATAAATAATTTTTATTGAAAATAATAAATAAATAAAATCAAGAGAA
AAAAATTGAATCAAATAAAAAAAAACGAGAGATGAAAGAAAGCAGTGAGTCGACTACTGAAACTC
ATAACCCTAAGAATGGAGGAGAACCCAAAAAAGAAGAAAAGAAGTCTAAGCTGGTAATGATAATT
CAGGAGT
Found at i:16354962 original size:2 final size:2
Alignment explanation
Indices: 16354955--16354982 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16354945 TGAAAACCAA
16354955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16354983 TTTAATTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16365361 original size:42 final size:42
Alignment explanation
Indices: 16365302--16365385 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
16365292 GTAATGATAT
*
16365302 TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCTGATGC
1 TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCCGATGC
* *
16365344 TGACCC-GACTATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
1 TGACCCAG-CTATGTGCGAGTAGGAGTGAGCATAAGCCGATGC
16365386 ATATGAGCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.20
Consensus pattern (42 bp):
TGACCCAGCTATGTGCGAGTAGGAGTGAGCATAAGCCGATGC
Found at i:16365557 original size:15 final size:15
Alignment explanation
Indices: 16365537--16365569 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16365527 ATTTTGTCAT
16365537 TGCTCTGTTTCTCAC
1 TGCTCTGTTTCTCAC
*
16365552 TGCTCTGTTTCTCTC
1 TGCTCTGTTTCTCAC
16365567 TGC
1 TGC
16365570 AACGAGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.33, G:0.15, T:0.48
Consensus pattern (15 bp):
TGCTCTGTTTCTCAC
Found at i:16376726 original size:2 final size:2
Alignment explanation
Indices: 16376719--16376743 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16376709 ATCACATATA
16376719 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
16376744 TATTCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16400865 original size:13 final size:13
Alignment explanation
Indices: 16400847--16400871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16400837 GAAGAAATTG
16400847 TGATTTTATAAAA
1 TGATTTTATAAAA
16400860 TGATTTTATAAA
1 TGATTTTATAAA
16400872 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:16407703 original size:42 final size:42
Alignment explanation
Indices: 16407652--16407740 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
16407642 GCATAAGTCG
*
16407652 ATGCAGACCCGGCTATGTGCGAGTGGGAGTGCACAAAAGCCA
1 ATGCAGACCCGGCTATCTGCGAGTGGGAGTGCACAAAAGCCA
* *
16407694 ATGCTGACCCGGCTATCTGCGAGTGGGAGTGCACATAAGCCA
1 ATGCAGACCCGGCTATCTGCGAGTGGGAGTGCACAAAAGCCA
16407736 ATGCA
1 ATGCA
16407741 TATAAGCTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.31, T:0.17
Consensus pattern (42 bp):
ATGCAGACCCGGCTATCTGCGAGTGGGAGTGCACAAAAGCCA
Found at i:16407785 original size:2 final size:2
Alignment explanation
Indices: 16407780--16407831 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
16407770 ATGATGATTG
16407780 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16407821 AT AT AT GAT AT
1 AT AT AT -AT AT
16407832 GTGGTTGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16408164 original size:164 final size:163
Alignment explanation
Indices: 16407893--16408220 Score: 620
Period size: 164 Copynumber: 2.0 Consensus size: 163
16407883 TTATGTGTTT
16407893 TATGTTGATTATGTTATTTCAACAGGATGGCTTTTTCTTGAAAGGAAGGAAACTTTTTTTCTCAC
1 TATGTTGATTATGTTATTTCAACAGGATGGCTTTTTCTTGAAAGGAAGGAAACTTTTTTTCTCAC
* *
16407958 TGCTCTATTTCTCGCTGCAACAAAATTCATTCACGCTACAGCGAGAAACTCTCTGGTTGGAGGGG
66 TGCTCTATTTCTCGCTGCAACAAAATTCATTCACGCTACAGCGAGAAACTCTCGGGTTAGAGGGG
16408023 TAAGGTTGGCCAAAAATCTCGCTGCAACGAGAA
131 TAAGGTTGGCCAAAAATCTCGCTGCAACGAGAA
16408056 NTATGTTGATTATGTTATTTCAACAGGATGGCTTTTTCTTGAAAGGAAGGAAACTTTTTTTCTCA
1 -TATGTTGATTATGTTATTTCAACAGGATGGCTTTTTCTTGAAAGGAAGGAAACTTTTTTTCTCA
16408121 CTGCTCTATTTCTCGCTGCAACAAAATTCATTCACGCTACAGCGAGAAACTCTCGGGTTAGAGGG
65 CTGCTCTATTTCTCGCTGCAACAAAATTCATTCACGCTACAGCGAGAAACTCTCGGGTTAGAGGG
*
16408186 GTAAGGTTGGCCAAAAATCTCGCTGCAGCGAGAA
130 GTAAGGTTGGCCAAAAATCTCGCTGCAACGAGAA
16408220 T
1 T
16408221 GTTACTGTAG
Statistics
Matches: 161, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
163 1 0.01
164 160 0.99
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (163 bp):
TATGTTGATTATGTTATTTCAACAGGATGGCTTTTTCTTGAAAGGAAGGAAACTTTTTTTCTCAC
TGCTCTATTTCTCGCTGCAACAAAATTCATTCACGCTACAGCGAGAAACTCTCGGGTTAGAGGGG
TAAGGTTGGCCAAAAATCTCGCTGCAACGAGAA
Found at i:16414596 original size:22 final size:22
Alignment explanation
Indices: 16414558--16414674 Score: 110
Period size: 22 Copynumber: 5.2 Consensus size: 22
16414548 TGGCTTAGTG
*
16414558 TATTTGGTTTGCATGCCTTAGCA
1 TATTTGG-TTACATGCCTTAGCA
* * * * *
16414581 TGTGTGATTATATGCCTTAGCG
1 TATTTGGTTACATGCCTTAGCA
*
16414603 TATTTAGGTTACATGTCTTAGCA
1 TATTT-GGTTACATGCCTTAGCA
* *
16414626 TGA-ATGGTTATATGCCTTAGCA
1 T-ATTTGGTTACATGCCTTAGCA
16414648 TATTTGGTTGACATGCCTTAGCA
1 TATTTGGTT-ACATGCCTTAGCA
16414671 TATT
1 TATT
16414675 CATTTACATA
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
21 1 0.01
22 36 0.49
23 35 0.48
24 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (22 bp):
TATTTGGTTACATGCCTTAGCA
Found at i:16414600 original size:45 final size:44
Alignment explanation
Indices: 16414544--16414671 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 44
16414534 ATGTTTCAAA
* * **
16414544 TATATGGCTTAGTGTATTTGGTTTGCATGCCTTAGCATGTGTGAT
1 TATATGCCTTAGCGTATTTGG-TTGCATGCCTTAGCATGAATGAT
* * *
16414589 TATATGCCTTAGCGTATTTAGGTTACATGTCTTAGCATGAATGGT
1 TATATGCCTTAGCGTATTT-GGTTGCATGCCTTAGCATGAATGAT
*
16414634 TATATGCCTTAGCATATTTGGTTGACATGCCTTAGCAT
1 TATATGCCTTAGCGTATTTGGTTG-CATGCCTTAGCAT
16414672 ATTCATTTAC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
44 4 0.06
45 65 0.92
46 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (44 bp):
TATATGCCTTAGCGTATTTGGTTGCATGCCTTAGCATGAATGAT
Found at i:16415143 original size:74 final size:75
Alignment explanation
Indices: 16415057--16415210 Score: 215
Period size: 75 Copynumber: 2.1 Consensus size: 75
16415047 TCCTAAGAAA
16415057 TAAAGGGTCGATC-CCTTTAAAATA-AAGTGCTTCAA-AATTGTGTTTTATGTTGAAAGGATCAA
1 TAAAGGGTCGATCTCCTTTAAAATAGAA-TGCTT-AAGAATTGTGTTTTATGTTGAAAGGATCAA
*
16415119 CCCTTCTTTCAT
64 CCCCTCTTTCAT
** * **
16415131 TAAAGGGTCGATCTTTTTTGAAATAGAATGCTTAAGAATTGTGTTTTATGTTGAAAGGATTGACC
1 TAAAGGGTCGATCTCCTTTAAAATAGAATGCTTAAGAATTGTGTTTTATGTTGAAAGGATCAACC
16415196 CCTCTTTCAT
66 CCTCTTTCAT
16415206 TAAAG
1 TAAAG
16415211 AGCCGACCTC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
74 15 0.21
75 54 0.76
76 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (75 bp):
TAAAGGGTCGATCTCCTTTAAAATAGAATGCTTAAGAATTGTGTTTTATGTTGAAAGGATCAACC
CCTCTTTCAT
Found at i:16418342 original size:32 final size:32
Alignment explanation
Indices: 16418249--16418347 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
16418239 AAAAGTTGGT
*
16418249 TGTTGGGTTTTGGTTGATCCCGAT-AAAAACCAT
1 TGTTGGGTTTTGGTTGAT-CCG-TGAAAAACCAC
* * *
16418282 TGTTGTAGGTTATGGTTGAGCCTTTGAAAAACCAC
1 TGTTG--GGTTTTGGTTGATCC-GTGAAAAACCAC
16418317 T-TTGGGTTTTGGTTGATCTCGTGAAAAACCA
1 TGTTGGGTTTTGGTTGATC-CGTGAAAAACCA
16418348 TTGCTAAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
32 22 0.41
33 6 0.11
34 6 0.11
35 20 0.37
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (32 bp):
TGTTGGGTTTTGGTTGATCCGTGAAAAACCAC
Found at i:16418378 original size:67 final size:67
Alignment explanation
Indices: 16418251--16418378 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
16418241 AAGTTGGTTG
* ** * **
16418251 TTGGGTTTTGGTTGATCCCGATAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGATCCCGATAAAAACCATTGCTAAAGGTTATGGCTGAGCCTGCGAAAAACCA
16418316 CT
66 CT
* *
16418318 TTGGGTTTTGGTTGATCTCG-TGAAAAACCATTGCTAAAGGTTGTGGCTGAGCCTGCGAAAA
1 TTGGGTTTTGGTTGATCCCGAT-AAAAACCATTGCTAAAGGTTATGGCTGAGCCTGCGAAAA
16418379 GCCATTGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 1 0.02
67 51 0.98
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.34
Consensus pattern (67 bp):
TTGGGTTTTGGTTGATCCCGATAAAAACCATTGCTAAAGGTTATGGCTGAGCCTGCGAAAAACCA
CT
Found at i:16429543 original size:22 final size:23
Alignment explanation
Indices: 16429476--16429591 Score: 98
Period size: 22 Copynumber: 5.2 Consensus size: 23
16429466 AAGGTCTCAC
*
16429476 AGCATATTTGGTTTACATGCCTT
1 AGCATATTTAGTTTACATGCCTT
** *
16429499 AGC-T-TGAATGTTTATATGCCTT
1 AGCATATTTA-GTTTACATGCCTT
16429521 AGCATATTTAGTTTACATG-CTT
1 AGCATATTTAGTTTACATGCCTT
* * * *
16429543 AACATGTGTAG-TTATATGCCTT
1 AGCATATTTAGTTTACATGCCTT
* *
16429565 AGCATATTTGGTTTACATACCTT
1 AGCATATTTAGTTTACATGCCTT
16429588 -GCAT
1 AGCAT
16429592 GTTTGGAACA
Statistics
Matches: 71, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
21 7 0.10
22 41 0.58
23 21 0.30
24 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (23 bp):
AGCATATTTAGTTTACATGCCTT
Found at i:16429572 original size:44 final size:45
Alignment explanation
Indices: 16429476--16429587 Score: 149
Period size: 44 Copynumber: 2.5 Consensus size: 45
16429466 AAGGTCTCAC
*
16429476 AGCATATTTGGTTTACATGCCTTAGCTTGAATGTTTATATGCCTT
1 AGCATATTTGGTTTACATGCCTTAACTTGAATGTTTATATGCCTT
* *
16429521 AGCATATTTAGTTTACATG-CTTAACATG--TGTAGTTATATGCCTT
1 AGCATATTTGGTTTACATGCCTTAACTTGAATGT--TTATATGCCTT
*
16429565 AGCATATTTGGTTTACATACCTT
1 AGCATATTTGGTTTACATGCCTT
16429588 GCATGTTTGG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.05
44 35 0.59
45 21 0.36
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (45 bp):
AGCATATTTGGTTTACATGCCTTAACTTGAATGTTTATATGCCTT
Found at i:16429973 original size:22 final size:20
Alignment explanation
Indices: 16429943--16429983 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
16429933 AATGTAGGGA
16429943 TCAACCCTTGAGAGAAACAAAG
1 TCAACCCTT-AG-GAAACAAAG
*
16429965 TCAATCCTTAGGAAACAAA
1 TCAACCCTTAGGAAACAAA
16429984 ATGCTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.17
Consensus pattern (20 bp):
TCAACCCTTAGGAAACAAAG
Found at i:16431890 original size:43 final size:42
Alignment explanation
Indices: 16431843--16431992 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 42
16431833 AAATTCAGAG
* *
16431843 TTCTTTTAGAATTGTGGAGTCTCGTAGAAAAAGTATTTTTCAA
1 TTCTTTTA-AATTATGGAGCCTCGTAGAAAAAGTATTTTTCAA
16431886 TTCTTTTAAATGTATGGAGCCTCGTA-AAAAGAGTATTTTTCAA
1 TTCTTTTAAAT-TATGGAGCCTCGTAGAAAA-AGTATTTTTCAA
* * * *
16431929 TTCTTTTAAAGTTATGGAGCCTCGCAGGAAGAGTATTTTACAAA
1 TTCTTTTAAA-TTATGGAGCCTCGTAGAAAAAGTATTTTTC-AA
* *
16431973 AT-TTTTAAGTTATGGAGCCT
1 TTCTTTTAAATTATGGAGCCT
16431993 TATATGAGGA
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
42 18 0.19
43 70 0.74
44 6 0.06
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (42 bp):
TTCTTTTAAATTATGGAGCCTCGTAGAAAAAGTATTTTTCAA
Done.