Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 24
Found at i:2148311 original size:20 final size:20
Alignment explanation
Indices: 2148286--2148363 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
2148276 TCGCATTGCG
*
2148286 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2148306 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
**
2148326 ATTTTCGTTTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2148346 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2148364 TCAAATGAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2149448 original size:24 final size:24
Alignment explanation
Indices: 2149421--2149474 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2149411 GTATTCGAAA
* *
2149421 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2149445 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2149469 TTTGAT
1 TTTGAT
2149475 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2149666 original size:12 final size:12
Alignment explanation
Indices: 2149649--2149673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2149639 ATATAATCCT
2149649 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2149661 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2149673 G
1 G
2149674 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2152138 original size:14 final size:14
Alignment explanation
Indices: 2152119--2152155 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2152109 CATCAATTAA
2152119 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
2152133 ACAAATTACCTTTT
1 ACAAATCAACTTTT
2152147 ACAAATCAA
1 ACAAATCAA
2152156 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2153579 original size:21 final size:21
Alignment explanation
Indices: 2153513--2153579 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2153503 GTGAATCGGG
*
2153513 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2153533 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2153555 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2153576 CTCT
1 CTCT
2153580 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2154025 original size:91 final size:90
Alignment explanation
Indices: 2153851--2154037 Score: 261
Period size: 91 Copynumber: 2.0 Consensus size: 90
2153841 ATATTTCAAA
* *
2153851 ACTTCAACCAAAAGATAAAACAAAGGCAAATAATAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATAATAACTTCACAGTGTTAAAGAAT--A-AGTTTA
*
2153916 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
*
2153944 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTA
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATAATAACTTCACAGTGTTAA-AGAATAAGTTTA
*
2154007 GCAGCATTGGAAGCAACCGAATAAATTT
63 GCAGAATTGGAAGCAACCGAATAAATTT
2154035 ACT
1 ACT
2154038 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
91 35 0.41
93 20 0.23
95 30 0.35
96 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATAATAACTTCACAGTGTTAAAGAATAAGTTTAGCA
GAATTGGAAGCAACCGAATAAATTT
Found at i:2154240 original size:63 final size:63
Alignment explanation
Indices: 2154181--2154322 Score: 151
Period size: 63 Copynumber: 2.3 Consensus size: 63
2154171 CTTAGAGCGG
* * *
2154181 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** * *
2154244 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGTGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
2154307 CGATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
2154323 GGCATTGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 1 0.01
63 68 0.99
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.20
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:2154323 original size:63 final size:63
Alignment explanation
Indices: 2154204--2154334 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
2154194 TAAAGTAGAC
2154204 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
2154267 ACCTCCACACGCCATGCACCATCGTTATCGTGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
2154330 ACCTC
1 ACCTC
2154335 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:2155817 original size:20 final size:19
Alignment explanation
Indices: 2155788--2155919 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
2155778 CTTTTGGTTG
2155788 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGAGA
* *
2155807 TAATGAGAATCGCAACGCGA
1 -AATGAAAATCGCAACGAGA
**
2155827 AATGACTATCGCAACGAGAGAATGCGA
1 AATGAAAATCGCAAC----G-A---GA
*
2155854 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGAGA
2155873 AATGAAAATCGCAACGAG-
1 AATGAAAATCGCAACGAGA
*
2155891 -A-G--AATCGCAACGGGA
1 AATGAAAATCGCAACGAGA
2155906 AATGAAAATCGCAA
1 AATGAAAATCGCAA
2155920 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
14 11 0.12
16 2 0.02
17 2 0.02
19 40 0.45
20 17 0.19
23 2 0.02
27 15 0.17
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGAGA
Found at i:2155837 original size:19 final size:20
Alignment explanation
Indices: 2155788--2155850 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
2155778 CTTTTGGTTG
*
2155788 AATGAAAATCGCAACGAGAT
1 AATGACAATCGCAACGAGAT
* *
2155808 AATGAGAATCGCAACGCGA-
1 AATGACAATCGCAACGAGAT
* *
2155827 AATGACTATCGCAACGAGAG
1 AATGACAATCGCAACGAGAT
2155847 AATG
1 AATG
2155851 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAT
Found at i:2155875 original size:46 final size:46
Alignment explanation
Indices: 2155808--2155895 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
2155798 GCAACGAGAT
* **
2155808 AATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGCGA
2155854 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAAT
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAAT
2155896 CGCAACGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (46 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGCGA
Found at i:2155942 original size:19 final size:19
Alignment explanation
Indices: 2155920--2155964 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2155910 AAAATCGCAA
*
2155920 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* * *
2155939 TGCGTTTTTTATTTCGTGT
1 TGCGATTTTGATTTCGCGT
2155958 TGCGATT
1 TGCGATT
2155965 CTCTCGTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.53
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:2156542 original size:20 final size:20
Alignment explanation
Indices: 2156517--2156567 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
2156507 GCGCTATGTA
2156517 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2156537 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2156557 TATCTCGTTGC
1 AATCGCGTTGC
2156568 AATTTTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2156681 original size:21 final size:21
Alignment explanation
Indices: 2156641--2156681 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2156631 ACTGTAGACC
**
2156641 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2156662 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2156682 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2173572 original size:15 final size:15
Alignment explanation
Indices: 2173552--2173627 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
2173542 CTATGATATG
2173552 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2173567 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
2173582 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
2173593 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
2173609 GATTTTTAT-TCAAAT
1 AATTTTTATAT-AAAT
2173624 AATT
1 AATT
2173628 AGAATTTCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
11 4 0.09
12 2 0.04
13 1 0.02
14 2 0.04
15 31 0.69
16 5 0.11
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2173596 original size:42 final size:41
Alignment explanation
Indices: 2173549--2173628 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
2173539 CAACTATGAT
*
2173549 ATGAATTTTTATATAAATAATTTTTATTTAAATATATTATCG
1 ATGAATTTTTATATAAATAATTTTTATTCAAATA-ATTATCG
*
2173591 ATGAATTTTTATATAAATGATTTTTATTCAAATAATTA
1 ATGAATTTTTATATAAATAATTTTTATTCAAATAATTA
2173629 GAATTTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (41 bp):
ATGAATTTTTATATAAATAATTTTTATTCAAATAATTATCG
Found at i:2180236 original size:26 final size:26
Alignment explanation
Indices: 2180180--2180236 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2180170 GAAAGTTATG
* *
2180180 GATTTCATACCTAGTTTTATTTATTA
1 GATTTCATACCTAGTTTTATTAATAA
2180206 GATTTCATACCTAGTGTTT-TTAATAA
1 GATTTCATACCTAGT-TTTATTAATAA
*
2180232 TATTT
1 GATTT
2180237 TTAAGCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (26 bp):
GATTTCATACCTAGTTTTATTAATAA
Found at i:2182255 original size:28 final size:27
Alignment explanation
Indices: 2182224--2182311 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
2182214 AAATTTAATA
2182224 ATAAAATTAATTAAAATAATAAACCAAC
1 ATAAAATTAATTAAAATAATAAA-CAAC
*
2182252 ATAAAATTAATTAAACTAATAAATCAAC
1 ATAAAATTAATTAAAATAATAAA-CAAC
*
2182280 A-AATAA-TAA-AAAAAGTAA-AAACAAC
1 ATAA-AATTAATTAAAA-TAATAAACAAC
2182305 ATAAAAT
1 ATAAAAT
2182312 AAAAAAAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.13
26 8 0.15
27 8 0.15
28 29 0.56
ACGTcount: A:0.67, C:0.09, G:0.01, T:0.23
Consensus pattern (27 bp):
ATAAAATTAATTAAAATAATAAACAAC
Found at i:2182316 original size:16 final size:17
Alignment explanation
Indices: 2182290--2182322 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2182280 AAATAATAAA
*
2182290 AAAAGTAAAAACAACAT
1 AAAAGTAAAAAAAACAT
2182307 AAAA-TAAAAAAAACAT
1 AAAAGTAAAAAAAACAT
2182323 CAATACAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAGTAAAAAAAACAT
Found at i:2184277 original size:28 final size:29
Alignment explanation
Indices: 2184217--2184288 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
2184207 TCGAAATTTC
2184217 TTTT-TTTCTTTTTTTTTCAACGAGAAGAA
1 TTTTCTTT-TTTTTTTTTCAACGAGAAGAA
*
2184246 -TTTCTTTTTTTTTTTTCGAAC-ATAA-AA
1 TTTTCTTTTTTTTTTTTC-AACGAGAAGAA
2184273 TTTTCTTTTTTTTTTT
1 TTTTCTTTTTTTTTTT
2184289 GGAACAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 2 0.05
28 31 0.79
29 6 0.15
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (29 bp):
TTTTCTTTTTTTTTTTTCAACGAGAAGAA
Found at i:2191753 original size:40 final size:39
Alignment explanation
Indices: 2191692--2191770 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 39
2191682 TCTAACGGTA
2191692 TAGCCATAATTTTCAGCACCTAGAACCCCTCAACAAAAT
1 TAGCCATAATTTTCAGCACCTAGAACCCCTCAACAAAAT
2191731 TAGCCATAATTTTTCAGCACCTAGAACCCCTCAACAAAAT
1 TAGCCATAA-TTTTCAGCACCTAGAACCCCTCAACAAAAT
2191771 GGAGTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 9 0.23
40 30 0.77
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.24
Consensus pattern (39 bp):
TAGCCATAATTTTCAGCACCTAGAACCCCTCAACAAAAT
Found at i:2194143 original size:19 final size:21
Alignment explanation
Indices: 2194119--2194178 Score: 88
Period size: 23 Copynumber: 2.9 Consensus size: 21
2194109 TTTTGGTGTA
2194119 GAGGGAACCGA-TCCCCC-TT
1 GAGGGAACCGATTCCCCCTTT
2194138 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTTT
2194159 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
2194179 CACAGGGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.30
20 6 0.16
21 3 0.08
22 1 0.03
23 16 0.43
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTTT
Found at i:2201729 original size:2 final size:2
Alignment explanation
Indices: 2201717--2201755 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
2201707 AAGAATGATG
2201717 AT AT CAT 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
2201756 TGTATGATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2202424 original size:28 final size:28
Alignment explanation
Indices: 2202381--2202452 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
2202371 TTTTATCTAA
2202381 GTACCTAAAGTAATTTTTAATCAAAATAC
1 GTACCTAAAGT-ATTTTTAATCAAAATAC
* ** *
2202410 GTATCTAAAGTATTTTTTGTCAAAATAT
1 GTACCTAAAGTATTTTTAATCAAAATAC
2202438 GTACCTAAAGTATTT
1 GTACCTAAAGTATTT
2202453 AATGTTTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 28 0.74
29 10 0.26
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (28 bp):
GTACCTAAAGTATTTTTAATCAAAATAC
Found at i:2202570 original size:28 final size:28
Alignment explanation
Indices: 2202534--2202591 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
2202524 GAAAAAATTG
* * *
2202534 AATAGTTTAAGTTCTTATTTTGACATAA
1 AATACTTTAAGTACCTATTTTGACATAA
* *
2202562 AATACTTTAGGTACCTATTTTGACCTAA
1 AATACTTTAAGTACCTATTTTGACATAA
2202590 AA
1 AA
2202592 GAAAATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (28 bp):
AATACTTTAAGTACCTATTTTGACATAA
Found at i:2204383 original size:2 final size:2
Alignment explanation
Indices: 2204376--2204402 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2204366 ATTATTTCTA
2204376 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2204403 ATTTATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2205703 original size:16 final size:16
Alignment explanation
Indices: 2205661--2205705 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2205651 GATTTTGGGC
2205661 TTGGATTTGGGTTTAAT
1 TTGGATTTGGG-TTAAT
**
2205678 TTGGGGTTGGGTTAAT
1 TTGGATTTGGGTTAAT
*
2205694 TTGGTTTTGGGT
1 TTGGATTTGGGT
2205706 CTGTTTGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.11, C:0.00, G:0.38, T:0.51
Consensus pattern (16 bp):
TTGGATTTGGGTTAAT
Found at i:2206283 original size:136 final size:136
Alignment explanation
Indices: 2205974--2206745 Score: 1071
Period size: 136 Copynumber: 5.7 Consensus size: 136
2205964 GTTATAAATT
* * * ** *
2205974 GAGCAATAGGTCGAACAAGTTCTTCTCATCATGAACTTCTTCTCCCTTTTTCAAATGAGTTTTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
** * * ** *
2206039 TCATTATGAACTCTTAATTGGAAATGTCAATCCTTCAGGCGA-GCATTATTGATTCGAAGTGTGG
66 TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAGTATGG
2206103 TGAATC
131 TGAATC
* * *
2206109 GAGCAATAGGTCGAAAAAGTTCTTCTTATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* * * * *
2206174 TCATTATGAACTCTCAATTGAAAATGTCAATCTCTCAAGTGAGGCATTGCTGATTCAAAGTATGG
66 TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAGTATGG
2206239 TGAATC
131 TGAATC
* *
2206245 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGCGTTATTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* * * * *
2206310 TCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGCGAGGCGTTGCTAAGTCGAAATATGG
66 TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAGTATGG
2206375 TGAATC
131 TGAATC
* * *
2206381 GAGCAATAGGTCGAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTCTGTCGGATGAGCTCTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* * * **
2206446 TCATTATGAACTCTCCATCGGAAATGTCAATCCCTCAAGCGAGACATTGCTGATTCGAAGTGTTA
66 TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAGTATGG
2206511 TGAATC
131 TGAATC
* * * * *
2206517 GAGCAGTAGATCGAATAAGTTTTTCTCATTGTGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* * * * *
2206582 TCATTATGAACTCTCCATCGAAAATGTCAATCCCTCAAGCGAGGCGTT-ATGGATTCGAAGTATT
66 TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCT-GATTCGAAGTATG
2206646 GTGAATC
130 GTGAATC
* *
2206653 GAGCAATAGGTCAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTC
1 GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
* *
2206718 GCATTATGAACTCTCTATTGGAAATGTC
66 TCATTATGAACTCTCCATTGGAAATGTC
2206746 GATCGGTTCA
Statistics
Matches: 564, Mismatches: 71, Indels: 3
0.88 0.11 0.00
Matches are distributed among these distances:
135 94 0.17
136 470 0.83
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (136 bp):
GAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTC
TCATTATGAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATTGCTGATTCGAAGTATGG
TGAATC
Found at i:2207599 original size:5 final size:5
Alignment explanation
Indices: 2207585--2207650 Score: 68
Period size: 5 Copynumber: 13.8 Consensus size: 5
2207575 GAACCTCTCA
* *
2207585 TTTT- TTTTC TTTTC TTTT- TCTTC TTTT- TCTTC TTTTC TTTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
2207631 TTTTC TTTCTT TTTTC TTTT
1 TTTTC TTT-TC TTTTC TTTT
2207651 TTCCTTCTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
4 14 0.27
5 33 0.65
6 4 0.08
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:2207608 original size:9 final size:8
Alignment explanation
Indices: 2207599--2207652 Score: 65
Period size: 9 Copynumber: 6.5 Consensus size: 8
2207589 TTTTCTTTTC
2207599 TTTTTCTT
1 TTTTTCTT
2207607 CTTTTTCTT
1 -TTTTTCTT
*
2207616 CTTTTCTT
1 TTTTTCTT
2207624 TTCTTTCTT
1 TT-TTTCTT
2207633 TTCTTTC-T
1 TT-TTTCTT
2207641 TTTTTCTT
1 TTTTTCTT
2207649 TTTT
1 TTTT
2207653 CCTTCTTAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
7 4 0.10
8 16 0.39
9 21 0.51
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2207608 original size:14 final size:13
Alignment explanation
Indices: 2207586--2207650 Score: 80
Period size: 13 Copynumber: 4.9 Consensus size: 13
2207576 AACCTCTCAT
2207586 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
2207599 TTTTTCTTCTTTTTC
1 TTTTT-TTC-TTTTC
*
2207614 TTCTTTTCTTTTC
1 TTTTTTTCTTTTC
2207627 TTTCTTTTC-TTTC
1 TTT-TTTTCTTTTC
2207640 -TTTTTTCTTTT
1 TTTTTTTCTTTT
2207651 TTCCTTCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
11 5 0.11
12 5 0.11
13 16 0.35
14 11 0.24
15 9 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:2207611 original size:23 final size:23
Alignment explanation
Indices: 2207585--2207643 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2207575 GAACCTCTCA
2207585 TTTTTTTTCTTTTCTTTT-TCTTC
1 TTTTTTTTCTTTTCTTTTCT-TTC
*
2207608 TTTTTCTTCTTTTCTTTTCTTTC
1 TTTTTTTTCTTTTCTTTTCTTTC
*
2207631 TTTTCTTTCTTTT
1 TTTTTTTTCTTTT
2207644 TTCTTTTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTTCTTTTCTTTTCTTTC
Found at i:2207619 original size:18 final size:16
Alignment explanation
Indices: 2207599--2207652 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
2207589 TTTTCTTTTC
2207599 TTTTTCTTCTTTTTCTT
1 TTTTTCTT-TTTTTCTT
*
2207616 CTTTTCTTTTCTTTCTT
1 TTTTTCTTTT-TTTCTT
2207633 TTCTTTC-TTTTTTCTT
1 TT-TTTCTTTTTTTCTT
2207649 TTTT
1 TTTT
2207653 CCTTCTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 10 0.30
17 17 0.52
18 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTTCTT
Found at i:2207653 original size:14 final size:14
Alignment explanation
Indices: 2207587--2207653 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 14
2207577 ACCTCTCATT
2207587 TTTTTTCTTTTCTT-
1 TTTTTTCTTTT-TTC
*
2207601 TTTCTTC-TTTTTC
1 TTTTTTCTTTTTTC
2207614 TTCTTTTCTTTTCTTTC
1 TT-TTTTC-TTT-TTTC
2207631 TTTTCTTTCTTTTTTC
1 -TTT-TTTCTTTTTTC
2207647 TTTTTTC
1 TTTTTTC
2207654 CTTCTTAGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
12 2 0.05
13 5 0.11
14 14 0.32
15 3 0.07
16 6 0.14
17 8 0.18
18 6 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Found at i:2216839 original size:20 final size:20
Alignment explanation
Indices: 2216815--2216868 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
2216805 TTAATTAAAA
* *
2216815 AAAAATAAACAATAACCATAT
1 AAAAATAAA-AATAACAACAT
2216836 AAAAATAGAAAA-AACAACAT
1 AAAAATA-AAAATAACAACAT
2216856 -AAAATAAAAATAA
1 AAAAATAAAAATAA
2216869 AATAAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 4 0.14
19 8 0.28
20 6 0.21
21 9 0.31
22 2 0.07
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (20 bp):
AAAAATAAAAATAACAACAT
Found at i:2216880 original size:11 final size:11
Alignment explanation
Indices: 2216810--2216874 Score: 51
Period size: 11 Copynumber: 5.4 Consensus size: 11
2216800 TAAACTTAAT
2216810 TAAAAA-AAAA
1 TAAAAATAAAA
2216820 TAAACAATAACCATA
1 TAAA-AATAA--A-A
2216835 TAAAAATAGAAA
1 TAAAAATA-AAA
*
2216847 AAACAACATAAAA
1 TAA-AA-ATAAAA
2216860 TAAAAATAAAA
1 TAAAAATAAAA
2216871 TAAA
1 TAAA
2216875 CCTAAATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
10 4 0.09
11 12 0.27
12 7 0.16
13 8 0.18
14 8 0.18
15 6 0.13
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:2218900 original size:136 final size:136
Alignment explanation
Indices: 2218706--2219497 Score: 1068
Period size: 136 Copynumber: 5.8 Consensus size: 136
2218696 GAGGTGTCGA
* * * *
2218706 TGATTCGAAGTCTTGTGAATCGAGCAATAGGTCGACCAAGTTCTTCTCATCATGAACTTCTTCTC
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * * * *
2218771 CTTCTATCGGATGAGATCTTATCATTATGAACTATCCATTGGAAATGTCAATACTTCAAGCGAGG
66 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAGG
2218836 CATTGC
131 CATTGC
* * *
2218842 TGATTTGAAGTGTGGTGAATCGAGAAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTTTC
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * *
2218907 CCTCTGTCGGATGAGTTTTTCTCATTATGAACTATCAATTGGAAATGTCAATCCCTCAAGCGAGG
66 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAGG
2218972 CATTGC
131 CATTGC
* * *
2218978 TGATTTGAAGTGTGGTGAATCGAGCAATAGGCCGAACAAGTTCTTCTCATTATGAAATT-TTC-C
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * * ** ** *
2219041 CCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTGGATCCCTCAAGAAAGA
66 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAGG
* *
2219106 TATTAC
131 CATTGC
* * * * *
2219112 TGATTCAAAGTTTGGTGAATCAAGCAATAGGTCGAACAAGTTCATCTCATTATGAACTTATTCTC
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * * * * *
2219177 CCTCTGTCGGATGAATTCTTCTCATTATGAACTCTCCATCGAAAATGTTAATCCCTCAAGCGAGG
66 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAGG
* *
2219242 CGTTAC
131 CATTGC
* * ** *
2219248 AGATTCTAAGTGTTTTGAATCGAGCAATAGGTC-AGACAATTTCTTCTCATTATGAACTTCTTCT
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGA-ACAAGTTCTTCTCATTATGAACTTCTTCT
* ** * *
2219312 CCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATCAGAAATGTCAATCGCTCAAGCAAG
65 CCCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAG
2219377 GCATTGC
130 GCATTGC
* * *
2219384 TGATTCGAAGTGTTGTAAATCGAGCAATAGGTCGAACAAGTTCTACTCATTATGAACTTCTTCTC
1 TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
2219449 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTC
66 CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTC
2219498 TATCTGTTCA
Statistics
Matches: 577, Mismatches: 75, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
134 113 0.20
135 6 0.01
136 457 0.79
137 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (136 bp):
TGATTCGAAGTGTGGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTC
CCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTCAATCCCTCAAGCGAGG
CATTGC
Found at i:2219325 original size:406 final size:408
Alignment explanation
Indices: 2218706--2219496 Score: 1144
Period size: 406 Copynumber: 1.9 Consensus size: 408
2218696 GAGGTGTCGA
* * * * *
2218706 TGATTCGAAGTCTTGTGAATCGAGCAATAGGTCGACCAAGTTCTTCTCATCATGAACTTCTTCTC
1 TGATTCAAAGTCTTGTGAATCAAGCAATAGGTCGAACAAGTTCATCTCATCATGAACTTATTCTC
* * * *
2218771 CTTCTATCGGATGAGATCTTATCATTATGAACTATCCATTGGAAATGTCAATACTTCAAGCGAGG
66 CCTCTATCGGATGAGATCTTATCATTATGAACTATCCATCGAAAATGTCAATACCTCAAGCGAGG
* *
2218836 CATTGCTGATTTGAAGTGTGGTGAATCGAGAAATAGGTCGAACAAGTTCTTCTCATTATGAACTT
131 CATTACAGATTTGAAGTGTGGTGAATCGAGAAATAGGTCGAACAAGTTCTTCTCATTATGAACTT
* * * **
2218901 CTTTTCCCTCTGTCGGATGAGTTTTTCTCATTATGAACTATCAATTGGAAATGTCAATCCCTCAA
196 CTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTATCAATCAGAAATGTCAATCCCTCAA
* * * *
2218966 GCGAGGCATTGCTGATTTGAAGTGTGGTGAATCGAGCAATAGGCCGAACAAGTTCTTCTCATTAT
261 GCAAGGCATTGCTGATTCGAAGTGTGGTAAATCGAGCAATAGGCCGAACAAGTTCTACTCATTAT
* *
2219031 GAAATT-TTC-CCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTGGATC
326 GAAATTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTGGATC
2219094 CCTCAAGAAAGATATTAC
391 CCTCAAGAAAGATATTAC
*
2219112 TGATTCAAAGT-TTGGTGAATCAAGCAATAGGTCGAACAAGTTCATCTCATTATGAACTTATTCT
1 TGATTCAAAGTCTT-GTGAATCAAGCAATAGGTCGAACAAGTTCATCTCATCATGAACTTATTCT
* * * * *
2219176 CCCTCTGTCGGATGA-ATTCTTCTCATTATGAACTCTCCATCGAAAATGTTAATCCCTCAAGCGA
65 CCCTCTATCGGATGAGA-TCTTATCATTATGAACTATCCATCGAAAATGTCAATACCTCAAGCGA
* ** * *
2219240 GGCGTTACAGATTCT-AAGTGTTTTGAATCGAGCAATAGGTC-AGACAATTTCTTCTCATTATGA
129 GGCATTACAGATT-TGAAGTGTGGTGAATCGAGAAATAGGTCGA-ACAAGTTCTTCTCATTATGA
* * *
2219303 ACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCATCAGAAATGTCAATCGC
192 ACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTATCAATCAGAAATGTCAATCCC
* *
2219368 TCAAGCAAGGCATTGCTGATTCGAAGTGTTGTAAATCGAGCAATAGGTCGAACAAGTTCTACTCA
257 TCAAGCAAGGCATTGCTGATTCGAAGTGTGGTAAATCGAGCAATAGGCCGAACAAGTTCTACTCA
* *
2219433 TTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGT
322 TTATGAAATTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGT
2219497 CTATCTGTTC
Statistics
Matches: 339, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
405 4 0.01
406 285 0.84
407 4 0.01
408 46 0.14
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (408 bp):
TGATTCAAAGTCTTGTGAATCAAGCAATAGGTCGAACAAGTTCATCTCATCATGAACTTATTCTC
CCTCTATCGGATGAGATCTTATCATTATGAACTATCCATCGAAAATGTCAATACCTCAAGCGAGG
CATTACAGATTTGAAGTGTGGTGAATCGAGAAATAGGTCGAACAAGTTCTTCTCATTATGAACTT
CTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTATCAATCAGAAATGTCAATCCCTCAA
GCAAGGCATTGCTGATTCGAAGTGTGGTAAATCGAGCAATAGGCCGAACAAGTTCTACTCATTAT
GAAATTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTATCCATTGGAAATGTGGATC
CCTCAAGAAAGATATTAC
Found at i:2220467 original size:16 final size:15
Alignment explanation
Indices: 2220444--2220480 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
2220434 TTTCCTTTTA
*
2220444 TTTTTCTTTTTTCTT
1 TTTTTCTTTTTTATT
2220459 TTCTTTCTTTTTTATT
1 TT-TTTCTTTTTTATT
2220475 TTTTTC
1 TTTTTC
2220481 CTTCTTAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTATT
Found at i:2223984 original size:7 final size:7
Alignment explanation
Indices: 2223972--2224001 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2223962 TATTGGAATG
2223972 TAAAGAA
1 TAAAGAA
2223979 TAAAGAA
1 TAAAGAA
*
2223986 TATAGAA
1 TAAAGAA
2223993 TAAAGAA
1 TAAAGAA
2224000 TA
1 TA
2224002 CGATGCAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (7 bp):
TAAAGAA
Found at i:2229903 original size:13 final size:13
Alignment explanation
Indices: 2229885--2229931 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
2229875 TTTGATATAG
2229885 CTTTTAAAATGAA
1 CTTTTAAAATGAA
2229898 CTTTTAAAAATG--
1 CTTTT-AAAATGAA
*
2229910 CTTTAAAAATGAA
1 CTTTTAAAATGAA
2229923 CTTTTAAAA
1 CTTTTAAAA
2229932 GAAAGTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 13 0.45
14 6 0.21
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (13 bp):
CTTTTAAAATGAA
Found at i:2229918 original size:25 final size:25
Alignment explanation
Indices: 2229884--2229931 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2229874 GTTTGATATA
*
2229884 GCTTTTAAAATGAACTTTTAAAAAT
1 GCTTTAAAAATGAACTTTTAAAAAT
2229909 GCTTTAAAAATGAACTTTTAAAA
1 GCTTTAAAAATGAACTTTTAAAA
2229932 GAAAGTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (25 bp):
GCTTTAAAAATGAACTTTTAAAAAT
Found at i:2230278 original size:25 final size:28
Alignment explanation
Indices: 2230250--2230303 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
2230240 AAATTTTATT
2230250 TATTTTAAAT-A-ATTAA-AATAAATTA
1 TATTTTAAATGATATTAATAATAAATTA
* *
2230275 TATTTTTAATGATATTAATATTAAATTA
1 TATTTTAAATGATATTAATAATAAATTA
2230303 T
1 T
2230304 TGAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 1 0.04
27 5 0.21
28 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTTTAAATGATATTAATAATAAATTA
Found at i:2240653 original size:21 final size:21
Alignment explanation
Indices: 2240602--2240658 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
2240592 TCGATTTTGA
* *
2240602 AATTTCTCCTGTGAAGCGACT
1 AATTTCTCTTGAGAAGCGACT
*
2240623 AA-CTCTTCTTGAGAAGCGACT
1 AATTTC-TCTTGAGAAGCGACT
*
2240644 AATTTCTCTTAAGAA
1 AATTTCTCTTGAGAA
2240659 ATCGCCAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (21 bp):
AATTTCTCTTGAGAAGCGACT
Found at i:2245871 original size:2 final size:2
Alignment explanation
Indices: 2245864--2245892 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2245854 TACGTGGATC
2245864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2245893 AAAGTTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2257191 original size:21 final size:21
Alignment explanation
Indices: 2257170--2257264 Score: 147
Period size: 21 Copynumber: 4.5 Consensus size: 21
2257160 CCATACCAAG
*
2257170 GACGAGAAGACCATTCACAAG
1 GACGAGAAGACCATTCACAAA
*
2257191 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCACAAA
*
2257212 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCACAAA
2257233 GACGAGAAGACCATTCACAAA
1 GACGAGAAGACCATTCACAAA
2257254 GAC-ATGAAGAC
1 GACGA-GAAGAC
2257265 TATTTTGCAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 1 0.01
21 69 0.99
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (21 bp):
GACGAGAAGACCATTCACAAA
Found at i:2257515 original size:6 final size:6
Alignment explanation
Indices: 2257504--2257553 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
2257494 ATTAACACCT
* *
2257504 TTTGCA TTTGCA TTTAGCA TTTACA TTTAGCA TTTGCA TTTTCA -TTGCA
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA
2257553 T
1 T
2257554 GTATTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 22 0.59
7 11 0.30
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:2257525 original size:13 final size:13
Alignment explanation
Indices: 2257507--2257544 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2257497 AACACCTTTT
2257507 GCATTTGCATTTA
1 GCATTTGCATTTA
*
2257520 GCATTTACATTTA
1 GCATTTGCATTTA
2257533 GCATTTGCATTT
1 GCATTTGCATTT
2257545 TCATTGCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (13 bp):
GCATTTGCATTTA
Found at i:2257542 original size:19 final size:19
Alignment explanation
Indices: 2257508--2257553 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2257498 ACACCTTTTG
2257508 CATTTGCATTTAGCATTTA
1 CATTTGCATTTAGCATTTA
*
2257527 CATTTAGCATTT-GCATTTT
1 CATTT-GCATTTAGCATTTA
2257546 CA-TTGCAT
1 CATTTGCAT
2257554 GTATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 2 0.08
19 13 0.52
20 6 0.24
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (19 bp):
CATTTGCATTTAGCATTTA
Found at i:2259638 original size:2 final size:2
Alignment explanation
Indices: 2259631--2259681 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2259621 ATACCCAACA
2259631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2259673 AT AT A- AT AT
1 AT AT AT AT AT
2259682 GTGTATACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2260940 original size:253 final size:253
Alignment explanation
Indices: 2260492--2260997 Score: 1012
Period size: 253 Copynumber: 2.0 Consensus size: 253
2260482 TGAAAGATCC
2260492 TTGAAGTTGGTGCGGCTCATTGTGCCTCCATTGGAGAAGAAGAATAAGCAATGTCGGGACACGAA
1 TTGAAGTTGGTGCGGCTCATTGTGCCTCCATTGGAGAAGAAGAATAAGCAATGTCGGGACACGAA
2260557 GAATTCCACAATCTTGAAGCAGATGGTCCGAGAGATCAGAATGGATGAAGGATAGAACTGGTAAG
66 GAATTCCACAATCTTGAAGCAGATGGTCCGAGAGATCAGAATGGATGAAGGATAGAACTGGTAAG
2260622 ATTTCCTTGTGACGTTGTCAGTAACCCATCAAGAAGAAGATGTTCTCATCATTCAGAAGAGACAC
131 ATTTCCTTGTGACGTTGTCAGTAACCCATCAAGAAGAAGATGTTCTCATCATTCAGAAGAGACAC
2260687 ATATTACAACTTGTATAAAAATGCTAGATAATTTGTTTGAAGAATTGATCACTCTGTA
196 ATATTACAACTTGTATAAAAATGCTAGATAATTTGTTTGAAGAATTGATCACTCTGTA
2260745 TTGAAGTTGGTGCGGCTCATTGTGCCTCCATTGGAGAAGAAGAATAAGCAATGTCGGGACACGAA
1 TTGAAGTTGGTGCGGCTCATTGTGCCTCCATTGGAGAAGAAGAATAAGCAATGTCGGGACACGAA
2260810 GAATTCCACAATCTTGAAGCAGATGGTCCGAGAGATCAGAATGGATGAAGGATAGAACTGGTAAG
66 GAATTCCACAATCTTGAAGCAGATGGTCCGAGAGATCAGAATGGATGAAGGATAGAACTGGTAAG
2260875 ATTTCCTTGTGACGTTGTCAGTAACCCATCAAGAAGAAGATGTTCTCATCATTCAGAAGAGACAC
131 ATTTCCTTGTGACGTTGTCAGTAACCCATCAAGAAGAAGATGTTCTCATCATTCAGAAGAGACAC
2260940 ATATTACAACTTGTATAAAAATGCTAGATAATTTGTTTGAAGAATTGATCACTCTGTA
196 ATATTACAACTTGTATAAAAATGCTAGATAATTTGTTTGAAGAATTGATCACTCTGTA
2260998 AGTGTTTGTG
Statistics
Matches: 253, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 253 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (253 bp):
TTGAAGTTGGTGCGGCTCATTGTGCCTCCATTGGAGAAGAAGAATAAGCAATGTCGGGACACGAA
GAATTCCACAATCTTGAAGCAGATGGTCCGAGAGATCAGAATGGATGAAGGATAGAACTGGTAAG
ATTTCCTTGTGACGTTGTCAGTAACCCATCAAGAAGAAGATGTTCTCATCATTCAGAAGAGACAC
ATATTACAACTTGTATAAAAATGCTAGATAATTTGTTTGAAGAATTGATCACTCTGTA
Found at i:2262907 original size:54 final size:54
Alignment explanation
Indices: 2262813--2263926 Score: 1063
Period size: 54 Copynumber: 20.8 Consensus size: 54
2262803 ACTGAAGCAA
* * * *
2262813 AAGAAGATGTTTGAGTTCTATACTCTCTGAAGAAAGAGGGAGCGAACCCGTTTA
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * *
2262867 AATAAGACGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCAAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * * ** *
2262921 CAGAATATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAGCGGGTTTT
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2262975 CAGAAGATCATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGAT-GTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTG
*
2263031 CAA-AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
1 -AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2263086 CAA-AAGATTTTTGAGTCCTATACTCCCTAAAGAAAGAGGGAGC-AAGCCCGTCT-
1 -AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAA-CCCGTTTG
* ** * *
2263139 ATATAATTTTTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 A-AGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2263194 AAGAAGATGTCCGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCATCTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * * **
2263248 CAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAACGAACCCATAAG
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
2263303 AAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCGTTTA
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* *
2263357 AAGAAGATG-TCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTTC-GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* ** *
2263411 AAGAAGATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGTAAACCCATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTG
* * * ** *
2263466 CAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGAAAACCTGTTT-
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* ** *
2263520 --GAAGATGTTCGAGTTCCATA----C------AAGAGGGAGTAAACCCATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * ** *
2263562 CAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGAAAACCTGTTT-
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2263616 --GAAGATGTTCGAGTTCCATACTCCCTATAGAAAGAGGGAGAGAACTCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * * * *
2263668 AAGGAGATTTTCGAGTTCCATACTCCATAGAGAAAGATGGAGCGAACCCATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * **
2263722 AAGAATATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCAATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTG
* * * *
2263777 CAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTT-
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
*
2263831 --GAAGATGTTCAAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCG-TTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
* * * * * *
2263882 ATAGAAGATTATTTGAGTCCTATACTCTCTAAAGGAATAGGGAGC
1 A-AGAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGC
2263927 AGACATGTTT
Statistics
Matches: 888, Mismatches: 134, Indels: 75
0.81 0.12 0.07
Matches are distributed among these distances:
41 17 0.02
44 5 0.01
45 13 0.01
47 1 0.00
49 1 0.00
50 2 0.00
51 92 0.10
52 16 0.02
53 5 0.01
54 408 0.46
55 245 0.28
56 81 0.09
57 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG
Found at i:2263609 original size:96 final size:96
Alignment explanation
Indices: 2263445--2263636 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
2263435 CCCTGAAAGA
2263445 AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGA
1 AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGA
2263510 AAACCTGTTTGAAGATGTTCGAGTTCCATAC
66 AAACCTGTTTGAAGATGTTCGAGTTCCATAC
2263541 AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGA
1 AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGA
2263606 AAACCTGTTTGAAGATGTTCGAGTTCCATAC
66 AAACCTGTTTGAAGATGTTCGAGTTCCATAC
2263637 TCCCTATAGA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (96 bp):
AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGA
AAACCTGTTTGAAGATGTTCGAGTTCCATAC
Found at i:2263641 original size:51 final size:51
Alignment explanation
Indices: 2263572--2263877 Score: 342
Period size: 51 Copynumber: 5.8 Consensus size: 51
2263562 CAGAAGATTA
** **
2263572 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGAAAACCTGTTTGAAGATG
1 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATG
* * * * * *
2263623 TTCGAGTTCCATACTCCCTATAGAAAGAGGGAGAGAACTCGTTTGAAGGAGATT
1 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTG-A--AGATG
* * *
2263677 TTCGAGTTCCATACTCCATAGAGAAAGATGGAGCGAACCCATTTGAAGAATATG
1 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAG---ATG
* * * *
2263731 TCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCAATTTGCAGAAGATTA
1 TTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCATTT---GAAGA-TG
2263787 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATG
1 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATG
* *
2263838 TTCAAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC
1 TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCC
2263878 GTTGATAGAA
Statistics
Matches: 218, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
51 81 0.37
52 6 0.03
53 1 0.00
54 61 0.28
55 46 0.21
56 19 0.09
58 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (51 bp):
TTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATG
Found at i:2263793 original size:311 final size:310
Alignment explanation
Indices: 2262899--2263851 Score: 1089
Period size: 311 Copynumber: 3.0 Consensus size: 310
2262889 CTCCCTAAAG
* *
2262899 AAAGAGGGAGCAAACCCGTTTGCAGAATATT-TTCGAGTTCTATACTCCCT-GAAGAAAGAGGGA
1 AAAGAGGGAGCAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAG-AGAAAGAGGGA
** * ** * * * *
2262962 GCGAGCGGGTTTTCAGAAGATCATTCAAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCAG
65 GAAAACCTG-TTT--GAAGAT-GTTCGAGTTCCATACTTCCT-AAAGAAAGAGGGAGAGAACC-G
* *
2263027 TTTGCAA-AAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAA-A
124 TTTG-AAGAAGATT-TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-AAGA
* ** * * * ** * * *
2263090 AGATTTTTGAGTCCTATACTCCCT-AAAGAAAGAGGGAGCAAGCCCGTCTATATAA-TTTTTTCG
186 AGATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCAA-CCCATTTGCAGAAGATTATTCG
*
2263153 AGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCCATACT
250 AGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTCGAGTTCCATA--
2263218 CCC
310 --C
* *
2263221 TAAAGAAAGAGGGAGCGAACCCATCTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGA
1 -----AAAGAGGGAGCAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGA
* ** * *
2263286 GGGA-ACGAACCCATAAG-AAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAA
61 GGGAGA--AAACC-T--GTTTGAAGATGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGAGAGAA
* *
2263349 CCCGTTTAAAGAAGA-TGTCTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
121 -CCGTTTGAAGAAGATTTTC-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA
*
2263413 GAAGATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGTAAACCCATTTGCAGAAGATTATT
184 GAAGATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAG-CAACCCATTTGCAGAAGATTATT
** *
2263478 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGAAAACCTGTTTGAAGATGTTCGAGTTCCATAC
248 CGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
*
2263541 -AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAG
1 AAAGAGGGAGCAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAG
* *
2263605 AAAACCTGTTTGAAGATGTTCGAGTTCCATACTCCCTATAGAAAGAGGGAGAGAACTCGTTTGAA
66 AAAACCTGTTTGAAGATGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGAGAGAAC-CGTTTGAA
* * * * *
2263670 GGAGATTTTCGAGTTCCATACTCCATAGAGAAAGATGGAGCGAACCCATTTGAAGAATATGTCCG
130 GAAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCG
*
2263735 AGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCAATTTGCAGAAGATTATTCGAGTTCTATA
195 AGTTCTATACTCCCTGAAAGAAAGAGGGAGC-AACCCATTTGCAGAAGATTATTCGAGTTCTATA
* * *
2263800 CTCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATGTTCAAGTTCTATAC
259 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
2263852 TCCCTAAAGA
Statistics
Matches: 547, Mismatches: 60, Indels: 54
0.83 0.09 0.08
Matches are distributed among these distances:
310 2 0.00
311 211 0.39
312 4 0.01
313 4 0.01
314 60 0.11
315 1 0.00
320 1 0.00
324 23 0.04
325 64 0.12
326 46 0.08
327 91 0.17
328 36 0.07
329 3 0.01
332 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (310 bp):
AAAGAGGGAGCAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAG
AAAACCTGTTTGAAGATGTTCGAGTTCCATACTTCCTAAAGAAAGAGGGAGAGAACCGTTTGAAG
AAGATTTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGA
GTTCTATACTCCCTGAAAGAAAGAGGGAGCAACCCATTTGCAGAAGATTATTCGAGTTCTATACT
CCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
Found at i:2263944 original size:55 final size:55
Alignment explanation
Indices: 2263885--2264059 Score: 201
Period size: 55 Copynumber: 3.2 Consensus size: 55
2263875 CCCGTTGATA
* * *
2263885 GAAGATTATTTGAGTCCTATACTCTCTAAAGGAATAGGGAGCAGACATGTTTGCT
1 GAAGATTATTTGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGTTTACT
* * * *
2263940 GAAGATTATTTAAGTCTTATACTCTCTGAAGGAATTA-GGAGAAGACACGTTTTCT
1 GAAGATTATTTGAGTCTTATACTCTCTAAAGGAA-TAGGGAGCAGACACGTTTACT
* * * * * *
2263995 GAAGATTGTTCGAGTCTTATACTCCCTGAAA-GAATAGAGAGCATACACGTTTATT
1 GAAGATTATTTGAGTCTTATACTCTCT-AAAGGAATAGGGAGCAGACACGTTTACT
2264050 GAAGATTATT
1 GAAGATTATT
2264060 CAAGTTCCAG
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 2 0.02
55 94 0.94
56 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (55 bp):
GAAGATTATTTGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGTTTACT
Found at i:2263963 original size:161 final size:163
Alignment explanation
Indices: 2263541--2263877 Score: 364
Period size: 160 Copynumber: 2.1 Consensus size: 163
2263531 AGTTCCATAC
** * * * * * *
2263541 AAGAGGGAGTAAACCCATTTGCAGAAGATTATTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAG
1 AAGAGGGAGCGAACCCATTTGAAGAATA-TGTCCGAGTCCTATACTCCCTGAAAGAAAGAGGGAG
** ** * * * * * *
2263605 AAAACCTGTTT---GAAGA-TGTTCGAGTTCCATACTCCCTATAGAAAGAGGGAGAGAACTCGTT
65 CGAACCAATTTGCAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGAGAACCCATT
* * *
2263666 TGAAGGAGATTTTCGAGTTCCATACTCCATAGAGA
130 TGAA-GAGATGTTCAAGTTCCATACTCCATAAAGA
* *
2263701 AAGATGGAGCGAACCCATTTGAAGAATATGTCCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGC
1 AAGAGGGAGCGAACCCATTTGAAGAATATGTCCGAGTCCTATACTCCCTGAAAGAAAGAGGGAGC
* *
2263766 GAACCAATTTGCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATTT
66 GAACCAATTTGCAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGAGAACCCATTT
* *
2263831 G-A-AGATGTTCAAGTTCTATACTCCCTAAAGA
131 GAAGAGATGTTCAAGTTCCATACTCCATAAAGA
2263862 AAGAGGGAGCGAACCC
1 AAGAGGGAGCGAACCC
2263878 GTTGATAGAA
Statistics
Matches: 148, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
159 19 0.13
160 43 0.29
161 39 0.26
163 6 0.04
164 41 0.28
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (163 bp):
AAGAGGGAGCGAACCCATTTGAAGAATATGTCCGAGTCCTATACTCCCTGAAAGAAAGAGGGAGC
GAACCAATTTGCAGAAGATTATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGAGAACCCATTT
GAAGAGATGTTCAAGTTCCATACTCCATAAAGA
Found at i:2267104 original size:7 final size:7
Alignment explanation
Indices: 2267092--2267199 Score: 175
Period size: 7 Copynumber: 15.7 Consensus size: 7
2267082 TAGAGTAAAT
2267092 GCATGAA
1 GCATGAA
2267099 GCATGAA
1 GCATGAA
2267106 GCATGAA
1 GCATGAA
*
2267113 GCACGAA
1 GCATGAA
*
2267120 GCACGAA
1 GCATGAA
*
2267127 ACATGAA
1 GCATGAA
2267134 GCATGAA
1 GCATGAA
2267141 GC-TGAA
1 GCATGAA
2267147 GCATGAA
1 GCATGAA
2267154 GC-TGAA
1 GCATGAA
2267160 GCATGAA
1 GCATGAA
2267167 GCATGAA
1 GCATGAA
2267174 GCATGAA
1 GCATGAA
2267181 GCATGAA
1 GCATGAA
2267188 GCATGAA
1 GCATGAA
2267195 GCATG
1 GCATG
2267200 CCGCATAGAC
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
6 12 0.13
7 83 0.87
ACGTcount: A:0.42, C:0.17, G:0.29, T:0.13
Consensus pattern (7 bp):
GCATGAA
Found at i:2270275 original size:19 final size:20
Alignment explanation
Indices: 2270250--2270301 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2270240 TAATTAAATT
2270250 AGTATCGATACTAA-AGTGG
1 AGTATCGATACTAAGAGTGG
* * *
2270269 GGTATCGATACCAAGAGTTG
1 AGTATCGATACTAAGAGTGG
2270289 AGTATCGATACTA
1 AGTATCGATACTA
2270302 TTATTAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (20 bp):
AGTATCGATACTAAGAGTGG
Found at i:2270954 original size:22 final size:23
Alignment explanation
Indices: 2270929--2270992 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
2270919 AGTCGAGGGT
*
2270929 TCTATGCAGTCCTTCGGGACA-A
1 TCTATGTAGTCCTTCGGGACATA
*
2270951 TCTATGTAGTCCTTCGGGACATT
1 TCTATGTAGTCCTTCGGGACATA
*
2270974 TCTATGTGGTCCTTCGGGA
1 TCTATGTAGTCCTTCGGGA
2270993 AAAATTCTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 20 0.53
23 18 0.47
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (23 bp):
TCTATGTAGTCCTTCGGGACATA
Found at i:2271008 original size:24 final size:24
Alignment explanation
Indices: 2270959--2271051 Score: 82
Period size: 24 Copynumber: 3.9 Consensus size: 24
2270949 AATCTATGTA
* * * *
2270959 GTCCTTCGGG-ACATTTCTATGTG
1 GTCCTTCGGGAAAAATTCTACGCG
2270982 GTCCTTCGGGAAAAATTCTACGCG
1 GTCCTTCGGGAAAAATTCTACGCG
* *
2271006 GTCCTT-TGGAACAAATTCCACGCG
1 GTCCTTCGGGAA-AAATTCTACGCG
* * *
2271030 GTCCTTTGGGACAAATTATACG
1 GTCCTTCGGGAAAAATTCTACG
2271052 TGGCACTTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
23 14 0.25
24 40 0.70
25 3 0.05
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
GTCCTTCGGGAAAAATTCTACGCG
Found at i:2277400 original size:82 final size:81
Alignment explanation
Indices: 2277221--2277401 Score: 195
Period size: 82 Copynumber: 2.2 Consensus size: 81
2277211 CTAGGGTTAG
*
2277221 AGTATCAATACTCTCAATAGGAGTATCGATACAAGGAATAATTTTAAAACATCAAACCATTTTTG
1 AGTATCAATAC-CTCAATAGGAGTATCGATACAAGGAATAATTTTAAAACATCAAACCAGTTTTG
2277286 GTATCGATACTCAGGGA
65 GTATCGATACTCAGGGA
** * * ** **
2277303 AGTATTGATACCCTC-ATTGAGAGTATCGATAC-TGAGAATTTTTTTAAAACATCAAAGGTAGTT
1 AGTATCAATA-CCTCAATAG-GAGTATCGATACAAG-GAATAATTTTAAAACATCAAA-CCAGTT
* * *
2277366 TTGGTATCGGTACTCGGGGT
62 TTGGTATCGATACTCAGGGA
2277386 AGTATCAATACCTCAA
1 AGTATCAATACCTCAA
2277402 GGCTAATATC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
81 4 0.05
82 46 0.57
83 30 0.38
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (81 bp):
AGTATCAATACCTCAATAGGAGTATCGATACAAGGAATAATTTTAAAACATCAAACCAGTTTTGG
TATCGATACTCAGGGA
Found at i:2283853 original size:91 final size:91
Alignment explanation
Indices: 2283698--2283880 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
2283688 TAAGCAGAAA
2283698 AGTGAAATATTTTGTAATTCATAATCATTGTACATTTCTGTTATTCTTCTCCCCTTTATAGATCT
1 AGTGAAATATTTTGTAATTCATAATCATTGTACATTTCTGTTATTCTTCTCCCCTTTATAGATCT
2283763 TCCAACTTTTATGGGAGGTGCTTTAG
66 TCCAACTTTTATGGGAGGTGCTTTAG
2283789 AGTGAAATATTTTGTAATTCATAATCATTGTACATTTCTGTTATTCTTCTCCCCTTTATAGATCT
1 AGTGAAATATTTTGTAATTCATAATCATTGTACATTTCTGTTATTCTTCTCCCCTTTATAGATCT
2283854 TCCAACTTTTATGGGAGGTGCTTTAG
66 TCCAACTTTTATGGGAGGTGCTTTAG
2283880 A
1 A
2283881 ATTTTCTGTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (91 bp):
AGTGAAATATTTTGTAATTCATAATCATTGTACATTTCTGTTATTCTTCTCCCCTTTATAGATCT
TCCAACTTTTATGGGAGGTGCTTTAG
Found at i:2288897 original size:8 final size:8
Alignment explanation
Indices: 2288884--2289008 Score: 250
Period size: 8 Copynumber: 15.6 Consensus size: 8
2288874 TAACTTATAT
2288884 GCAAATAA
1 GCAAATAA
2288892 GCAAATAA
1 GCAAATAA
2288900 GCAAATAA
1 GCAAATAA
2288908 GCAAATAA
1 GCAAATAA
2288916 GCAAATAA
1 GCAAATAA
2288924 GCAAATAA
1 GCAAATAA
2288932 GCAAATAA
1 GCAAATAA
2288940 GCAAATAA
1 GCAAATAA
2288948 GCAAATAA
1 GCAAATAA
2288956 GCAAATAA
1 GCAAATAA
2288964 GCAAATAA
1 GCAAATAA
2288972 GCAAATAA
1 GCAAATAA
2288980 GCAAATAA
1 GCAAATAA
2288988 GCAAATAA
1 GCAAATAA
2288996 GCAAATAA
1 GCAAATAA
2289004 GCAAA
1 GCAAA
2289009 AGTAATGATT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 117 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.12
Consensus pattern (8 bp):
GCAAATAA
Found at i:2289078 original size:21 final size:22
Alignment explanation
Indices: 2289054--2289102 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2289044 AACTAAAAAT
2289054 ATTAATATAT-AATATGCATAA
1 ATTAATATATCAATATGCATAA
* *
2289075 ATT-ATATATCTATATGCGTAA
1 ATTAATATATCAATATGCATAA
2289096 ATTAATA
1 ATTAATA
2289103 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
ATTAATATATCAATATGCATAA
Found at i:2289278 original size:22 final size:22
Alignment explanation
Indices: 2289236--2289295 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
2289226 TATATAATAT
*
2289236 ATAATATATATAATACACTTA-A
1 ATAATATATAT-ATATACTTATA
*
2289258 ATAATATAATATATATGCTTATA
1 ATAATAT-ATATATATACTTATA
*
2289281 A-AATATGTTATATAT
1 ATAATAT-ATATATAT
2289296 CGTATGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (22 bp):
ATAATATATATATATACTTATA
Found at i:2289537 original size:21 final size:21
Alignment explanation
Indices: 2289512--2289560 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2289502 ATAATTCTAT
2289512 CACTAAAGTTAAAGTATCCGA
1 CACTAAAGTTAAAGTATCCGA
2289533 CACTAAAGTTAAAGTATCCGA
1 CACTAAAGTTAAAGTATCCGA
2289554 CACTAAA
1 CACTAAA
2289561 TATTAAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (21 bp):
CACTAAAGTTAAAGTATCCGA
Found at i:2290193 original size:2 final size:2
Alignment explanation
Indices: 2290186--2290240 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2290176 TTTTAGGCTC
2290186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
2290227 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2290241 TGCATGCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2291312 original size:111 final size:109
Alignment explanation
Indices: 2291003--2291673 Score: 659
Period size: 113 Copynumber: 6.1 Consensus size: 109
2290993 TTCAAGGAAG
* *
2291003 ATTGAATCATGG-TAGACTTGTTCCATTATCACTCATGGAATATCAAATCTTGA-AAGAGAGGGA
1 ATTGAATCA-GGATAGACTTGTTCCACT-T-ACTCAGGGAATATCAAATCTTGATAAGAGA--GA
* *
2291066 TCTGTTCCGCTT-CTTCTG-AGGGAATATTAGATCTGGGAAAGTTAATCT
61 TCTGTTCCGCTTAC-TCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
* *
2291114 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACGT-A-GGAATATCAAATCTTGA-AAGAGAGGGA
1 ATTGAATCAGGATAGACTTGTTCCACT-T-AC-TCAGGGAATATCAAATCTTGATAAGAGA--GA
* * * * *
2291176 TTTGTCCCGCTT-CTTCTG-AGGGAATATCAAATCTGGGAAAATTGATCC
61 TCTGTTCCGCTTAC-TCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
* *
2291224 ATCGAATCAGGGTAGACTTGTTCCACTATCACTCAGGGAATATCAAATCTTGA-AAGAGAGGGAT
1 ATTGAATCAGGATAGACTTGTTCCACT-T-ACTCAGGGAATATCAAATCTTGATAAGAGA--GAT
* *
2291288 CTGTTCTGCTT-CTTCTG-AGGGAATATCAGATCTAGGAAAGTTGATCT
62 CTGTTCCGCTTAC-TCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
* * *
2291335 ATTGAATCAGGATAAACTTGTTCCACTTGCTC----AA-ATC---T-TGGATAAGAGAGA-CATG
1 ATTGAATCAGGATAGACTTGTTCCACTTACTCAGGGAATATCAAATCTTGATAAGAGAGATC-TG
* *
2291390 TTCTGCTTACTCTGAAGGGAATATCAGATCTGGGAGAGTTGATAC-
65 TTCCGCTTACTCTGAAGGGAATATCAGATCTGGGAAAGTTGAT-CT
* *
2291435 ATTGAATCAGGATATACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGAC
1 ATTGAATCAGGATAGACTTGTTCCACTTACTC---AGGGAATATCAAATCTT-GATAAGAGAGAT
**
2291500 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCT
62 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
* *
2291548 ATTGAATCAGGATAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGATAGAC
1 ATTGAATCAGGATAGACTTGTTCCACTTACTC---AGGGAATATCAAATCTT-GATAAGAGAGAT
** ** *
2291613 CTGTTCTACTTACTCTGAAGGGAATATCAGATCTGGGGGATTTGATCT
62 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
2291661 ATTGAATCAGGAT
1 ATTGAATCAGGAT
2291674 CGAACCTGAA
Statistics
Matches: 499, Mismatches: 37, Indels: 46
0.86 0.06 0.08
Matches are distributed among these distances:
98 1 0.00
99 16 0.03
100 60 0.12
101 8 0.02
104 3 0.01
105 2 0.00
107 2 0.00
108 3 0.01
109 4 0.01
110 101 0.20
111 120 0.24
112 3 0.01
113 175 0.35
114 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (109 bp):
ATTGAATCAGGATAGACTTGTTCCACTTACTCAGGGAATATCAAATCTTGATAAGAGAGATCTGT
TCCGCTTACTCTGAAGGGAATATCAGATCTGGGAAAGTTGATCT
Found at i:2296033 original size:4 final size:4
Alignment explanation
Indices: 2296000--2296052 Score: 63
Period size: 4 Copynumber: 12.5 Consensus size: 4
2295990 TCCCATATCA
2296000 AAAT AGAAT GAAAT -AAT AATAT ATAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT A-AAT -AAAT AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
2296047 AAAT AA
1 AAAT AA
2296053 GGAGAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 27 0.61
5 12 0.27
6 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2301933 original size:122 final size:122
Alignment explanation
Indices: 2301716--2301956 Score: 482
Period size: 122 Copynumber: 2.0 Consensus size: 122
2301706 TAATAACTAG
2301716 GTGATCTGGGAATCAGTACCGTTTATGAAATGATATGATATGATAATGATACATGCAATCAGGAT
1 GTGATCTGGGAATCAGTACCGTTTATGAAATGATATGATATGATAATGATACATGCAATCAGGAT
2301781 ACAAAACAATAAGTTAGTGATATTAGAATAATTCAAATAATCAAAGAATAATTATAA
66 ACAAAACAATAAGTTAGTGATATTAGAATAATTCAAATAATCAAAGAATAATTATAA
2301838 GTGATCTGGGAATCAGTACCGTTTATGAAATGATATGATATGATAATGATACATGCAATCAGGAT
1 GTGATCTGGGAATCAGTACCGTTTATGAAATGATATGATATGATAATGATACATGCAATCAGGAT
2301903 ACAAAACAATAAGTTAGTGATATTAGAATAATTCAAATAATCAAAGAATAATTA
66 ACAAAACAATAAGTTAGTGATATTAGAATAATTCAAATAATCAAAGAATAATTA
2301957 ATAAAAATTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (122 bp):
GTGATCTGGGAATCAGTACCGTTTATGAAATGATATGATATGATAATGATACATGCAATCAGGAT
ACAAAACAATAAGTTAGTGATATTAGAATAATTCAAATAATCAAAGAATAATTATAA
Found at i:2303947 original size:8 final size:8
Alignment explanation
Indices: 2303934--2304066 Score: 266
Period size: 8 Copynumber: 16.6 Consensus size: 8
2303924 TAACTTATAT
2303934 GCAAATAA
1 GCAAATAA
2303942 GCAAATAA
1 GCAAATAA
2303950 GCAAATAA
1 GCAAATAA
2303958 GCAAATAA
1 GCAAATAA
2303966 GCAAATAA
1 GCAAATAA
2303974 GCAAATAA
1 GCAAATAA
2303982 GCAAATAA
1 GCAAATAA
2303990 GCAAATAA
1 GCAAATAA
2303998 GCAAATAA
1 GCAAATAA
2304006 GCAAATAA
1 GCAAATAA
2304014 GCAAATAA
1 GCAAATAA
2304022 GCAAATAA
1 GCAAATAA
2304030 GCAAATAA
1 GCAAATAA
2304038 GCAAATAA
1 GCAAATAA
2304046 GCAAATAA
1 GCAAATAA
2304054 GCAAATAA
1 GCAAATAA
2304062 GCAAA
1 GCAAA
2304067 AGTAATGATT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 125 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.12
Consensus pattern (8 bp):
GCAAATAA
Found at i:2304136 original size:21 final size:22
Alignment explanation
Indices: 2304112--2304160 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2304102 AACTAAAAAT
2304112 ATTAATATAT-AATATGCATAA
1 ATTAATATATCAATATGCATAA
* *
2304133 ATT-ATATATCTATATGCGTAA
1 ATTAATATATCAATATGCATAA
2304154 ATTAATA
1 ATTAATA
2304161 AAAATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
ATTAATATATCAATATGCATAA
Found at i:2304588 original size:21 final size:21
Alignment explanation
Indices: 2304563--2304611 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2304553 ACAATTCTAT
2304563 CACTAAAGTTAAAGTATCCGA
1 CACTAAAGTTAAAGTATCCGA
2304584 CACTAAAGTTAAAGTATCCGA
1 CACTAAAGTTAAAGTATCCGA
2304605 CACTAAA
1 CACTAAA
2304612 TATTAAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (21 bp):
CACTAAAGTTAAAGTATCCGA
Found at i:2305246 original size:2 final size:2
Alignment explanation
Indices: 2305239--2305270 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2305229 AGACTCACAG
2305239 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
2305271 GCATGCAAAG
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:2305509 original size:18 final size:18
Alignment explanation
Indices: 2305486--2305532 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2305476 TGAAATCACG
2305486 GGTTTGTCTTGGTCTTGA
1 GGTTTGTCTTGGTCTTGA
2305504 GGTTTGTCTTGGTCTTGA
1 GGTTTGTCTTGGTCTTGA
* *
2305522 TGTTTGACTTG
1 GGTTTGTCTTG
2305533 TGAATCCAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.06, C:0.11, G:0.32, T:0.51
Consensus pattern (18 bp):
GGTTTGTCTTGGTCTTGA
Found at i:2306156 original size:2 final size:2
Alignment explanation
Indices: 2306149--2306176 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2306139 TTAAGACCTG
2306149 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
2306177 CACGAATGCA
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):
TA
Found at i:2306377 original size:2 final size:2
Alignment explanation
Indices: 2306370--2306407 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2306360 TTTATTTGAG
2306370 TA TA TA TA 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 TA TA TA TA
2306408 ATGAACAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2310616 original size:27 final size:27
Alignment explanation
Indices: 2310585--2310648 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
2310575 AGTAAAATGA
*
2310585 CCTTATGGGCTAAAATTACCAAATTTC
1 CCTTATGGGCTAAAATTACCAAATTGC
2310612 CCTTATGGGCTAAAATTACCAAATTGC
1 CCTTATGGGCTAAAATTACCAAATTGC
2310639 CCTTATGGGC
1 CCTTATGGGC
2310649 CTAAGTGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (27 bp):
CCTTATGGGCTAAAATTACCAAATTGC
Found at i:2316864 original size:36 final size:37
Alignment explanation
Indices: 2316794--2316865 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
2316784 TCCCTGGTAA
* *
2316794 ATAGAAGGGAAAAGACCTGTACAAATAATCATTATAT
1 ATAGAAGGGAAAAGACATGTAAAAATAATCATTATAT
*
2316831 ATAGAAGGGAAAA-ACATGTAAAAATAATTATTATA
1 ATAGAAGGGAAAAGACATGTAAAAATAATCATTATA
2316866 ATGTATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (37 bp):
ATAGAAGGGAAAAGACATGTAAAAATAATCATTATAT
Found at i:2321213 original size:9 final size:8
Alignment explanation
Indices: 2321169--2321226 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
2321159 TCTTTTCTAA
2321169 TATTTTAAT
1 TATTTT-AT
2321178 T-TTTTA-
1 TATTTTAT
2321184 TATGTTTAT
1 TAT-TTTAT
*
2321193 TATTATAT
1 TATTTTAT
2321201 T-TTTTAT
1 TATTTTAT
2321208 TATTTTACT
1 TATTTTA-T
2321217 TATTTTAT
1 TATTTTAT
2321225 TA
1 TA
2321227 AATACTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 1 0.02
7 8 0.19
8 21 0.50
9 12 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (8 bp):
TATTTTAT
Found at i:2321225 original size:24 final size:23
Alignment explanation
Indices: 2321169--2321225 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
2321159 TCTTTTCTAA
2321169 TATTTTAATTTTTTATATGTTTAT
1 TATTTT-ATTTTTTATATGTTTAT
*
2321193 TATTATATTTTTTATTAT-TTTACT
1 TATTTTATTTTTTA-TATGTTTA-T
2321217 TATTTTATT
1 TATTTTATT
2321226 AAATACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTTATTTTTTATATGTTTAT
Found at i:2321264 original size:20 final size:20
Alignment explanation
Indices: 2321219--2321266 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2321209 ATTTTACTTA
2321219 TTTTATTAAATACTATATCT
1 TTTTATTAAATACTATATCT
* * *
2321239 TATTATATATATA-TATATTT
1 TTTTAT-TAAATACTATATCT
2321259 TTTTATTA
1 TTTTATTA
2321267 TTTCTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.09
20 16 0.70
21 5 0.22
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTAAATACTATATCT
Found at i:2325820 original size:84 final size:84
Alignment explanation
Indices: 2325714--2326537 Score: 823
Period size: 84 Copynumber: 9.9 Consensus size: 84
2325704 TGACCAAAAC
* * *
2325714 ACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
2325779 GGTTATCTGCCAACCAAAG
66 GGTTATCTGCCAACCAAAG
* *
2325798 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
*
2325863 GGCTATCTG----CCAAAG
66 GGTTATCTGCCAACCAAAG
* * * * * * * * * *
2325878 ACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATCATTTACAGCATAACTCAAGGCTAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAGCTTAAGTCGAGAA
* ** *
2325943 GGGTTATATG-TGACCAAAAT
65 GGGTTATCTGCCAACC-AAAG
* * * * *
2325963 ACCTTCGAGTTCGACAACGCTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
2326028 GGTTATCTGCCAACCAAAG
66 GGTTATCTGCCAACCAAAG
* * * *
2326047 ACCTTCGAGTTCGACTATGCTCAGCTCCATGGCACATCATTTACAGTATAGCTTAAGTCGAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
2326112 GGTTATCTG----CCAAAG
66 GGTTATCTGCCAACCAAAG
* * * * * * * *
2326127 ACCCTCGAGTTTGATTACACTCAGCTTCGAGATCACATCATTTGCAGCATAACTTAAGTCGAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTGCAGCATAGCTTAAGTCGAGAA
2326192 GGGTTATCTGCCAACCAAAG
65 GGGTTATCTGCCAACCAAAG
* * * *
2326212 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAAGAAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* *
2326277 GGCTATCTGCCAA-AAAAG
66 GGTTATCTGCCAACCAAAG
* * * * * * *
2326295 ACCTTCAAGCTCGACTACGCTCAGCT-CAACGACACATTATTTGCAACATAGCTTAAGGCAAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
*
2326359 GGGCTATCT----ACCAAAG
65 GGGTTATCTGCCAACCAAAG
* * * * * * * * * * *
2326375 ACCTTTGAGTTCCATTACACTTAGCTCAAAGGCACATCAATCGCAGCATAGCTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* * *
2326440 TGTTATATGCCAACAAAAG
66 GGTTATCTGCCAACCAAAG
* * * * * * * * * *
2326459 ACATGCGAGTTAGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAG
1 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
*
2326524 GGTTATCTGTCAAC
66 GGTTATCTGCCAAC
2326538 AAAATTGTCG
Statistics
Matches: 609, Mismatches: 113, Indels: 36
0.80 0.15 0.05
Matches are distributed among these distances:
79 1 0.00
80 117 0.19
81 75 0.12
82 3 0.00
83 64 0.11
84 289 0.47
85 60 0.10
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAG
GGTTATCTGCCAACCAAAG
Found at i:2325989 original size:165 final size:165
Alignment explanation
Indices: 2325690--2326532 Score: 788
Period size: 165 Copynumber: 5.1 Consensus size: 165
2325680 ACTCAAGGAT
* * * * *
2325690 AGAAGGGTTATTTGTGACCAAAACACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTA--TCTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
* *
2325755 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCT
63 TGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCC-ACCAAAAGACCTTCGAGTTCGACTACGCT
*
2325819 CAGCTCCAAGACATATCATTTGCAGCATAGCTTAAGTCG
127 CAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
2325858 AGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATCATTTA
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAG-GCACATCATTTG
* * * * ** * *
2325922 CAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAATACCTTCGAGTTCGACAACGCTCAG
65 CAGCATAGCTTAAGTCGAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * *
2325987 CTCTAAGGCATATCATTTGCAGCATAACTTAAGTTG
130 CTCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
* * *
2326023 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCATGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
* * * * * * *
2326088 TACAGTATAGCTTAAGTCGAGAAGGGTTATCTG---CC-AAAGACCCTCGAGTTTGATTACACTC
63 TGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTC
* * *
2326149 AGCTTCGAGATCACATCATTTGCAGCATAACTTAAGTCG
128 AGCTCCAAGA-CACATCATTTGCAGCATAGCTTAAGTCG
* *
2326188 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
* * * * * * * *
2326253 TGCAGTATAGCTTAAGTCAAGAAAGGCTATCTGCCA-AAAAAGACCTTCAAGCTCGACTACGCTC
63 TGCAGCATAGCTTAAGTCGAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTC
* * * *
2326317 AGCT-CAACGACACATTATTTGCAACATAGCTTAAGGCA
128 AGCTCCAA-GACACATCATTTGCAGCATAGCTTAAGTCG
* * * * * * * *
2326355 AGAAGGGCTATCT-ACCAAAGACCTTTGAGTTCCATTACACTTAGC-TCAAAGGCACATCAATCG
1 AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTG
* * * * * * * * * *
2326418 CAGCATAGCTCAAGGCTAGAAGTGTTATATGCCAACAAAAGACATGCGAGTTAGATTACACTCAG
65 CAGCATAGCTTAAGTCGAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * * *
2326483 CTCAAAGGCACATCATTTACAGCATAGCTCAAGGCA
130 CTCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
2326519 AGAAGGGTTATCTG
1 AGAAGGGTTATCTG
2326533 TCAACAAAAT
Statistics
Matches: 559, Mismatches: 100, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
162 1 0.00
163 67 0.12
164 118 0.21
165 231 0.41
166 3 0.01
167 37 0.07
168 72 0.13
169 30 0.05
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (165 bp):
AGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGC
AGCATAGCTTAAGTCGAGAAGGGTTATATGCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC
TCCAAGACACATCATTTGCAGCATAGCTTAAGTCG
Found at i:2326112 original size:249 final size:249
Alignment explanation
Indices: 2325668--2326537 Score: 1084
Period size: 249 Copynumber: 3.5 Consensus size: 249
2325658 AAAAAAAACT
* * * * * *
2325668 ATTTATAGCATAACTCAAGGATAGAAGGGTTATTTGTGACCAAAACACCTTCGAGTTCGACTATG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGCGACCAAAAGACCTTCGAGTTCGACTACG
* *
2325733 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAG
*
2325798 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACATATCATTTGCAGCATAGCTTAAGTCGAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAG
2325863 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATC
196 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATC
* * *
2325917 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTGACCAAAATACCTTCGAGTTCGACAACG
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGCGACCAAAAGACCTTCGAGTTCGACTACG
* * **
2325982 CTCAGCTCTAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAG
* * * * *
2326047 ACCTTCGAGTTCGACTATGCTCAGCTCCATGGCACATCATTTACAGTATAGCTTAAGTCGAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAG
* * *
2326112 GGTTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGATCACATC
196 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATC
* * * * * * *
2326166 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTAC
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATG-CGACCAAAAGACCTTCGAGTTCGACTAC
* * * * *
2326230 GCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCAAGAAAGGCTATCTGCCAA-AAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAA
* * * * * *
2326294 GACCTTCAAGCTCGACTACGCTCAGCT-CAACGACACATTATTTGCAACATAGCTTAAGGCAAGA
130 GACCTTCGAGTTCGACTACGCTCAGCTCCAA-GACACATCATTTGCAGCATAGCTTAAGTCGAGA
* * * * * *
2326358 AGGGCTATCTACCAAAGACCTTTGAGTTCCATTACACTTAGC-TC-AAAGGCACATC
194 AGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGA-GCACATC
* ** * * * * * * * * *
2326413 AATCGCAGCATAGCTCAAGGCTAGAAGTGTTATATGCCAACAAAAGACATGCGAGTTAGATTACA
1 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGCGACCAAAAGACCTTCGAGTTCGACTACG
* * * * * *
2326478 CTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGTTATCTGTCAAC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAC
2326538 AAAATTGTCG
Statistics
Matches: 536, Mismatches: 80, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
246 5 0.01
247 106 0.20
248 88 0.16
249 334 0.62
250 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (249 bp):
ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGCGACCAAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAGAAG
GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATC
Found at i:2328038 original size:23 final size:24
Alignment explanation
Indices: 2327995--2328044 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2327985 TAATATTTTA
*
2327995 ATTTTTATATATGTTTGTTATTAT
1 ATTTTTATATATGTTTCTTATTAT
*
2328019 ATTTTTAT-TAT-TTTACTTATTTT
1 ATTTTTATATATGTTT-CTTATTAT
2328042 ATT
1 ATT
2328045 AAATACTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 12 0.52
24 8 0.35
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
ATTTTTATATATGTTTCTTATTAT
Found at i:2328077 original size:17 final size:17
Alignment explanation
Indices: 2328039--2328080 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2328029 TTTTACTTAT
2328039 TTTATTA-AATACTATA
1 TTTATTATAATACTATA
2328055 TCTTATTATATATA-TATA
1 T-TTATTATA-ATACTATA
2328073 TTTATTAT
1 TTTATTAT
2328081 TTATTATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 13 0.57
18 6 0.26
19 3 0.13
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATTATAATACTATA
Found at i:2328228 original size:35 final size:34
Alignment explanation
Indices: 2328172--2328237 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
2328162 TCATAACGAT
* *
2328172 TTATATATATATTTTTATCTTTGTTTTGTTTTGTA
1 TTATATATATAATTTTATCTTTATTTT-TTTTGTA
2328207 TTATATATATTAATTTT-TCTTTATTTTTTTT
1 TTATATATA-TAATTTTATCTTTATTTTTTTT
2328238 ATTCATCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 4 0.14
35 18 0.64
36 6 0.21
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (34 bp):
TTATATATATAATTTTATCTTTATTTTTTTTGTA
Found at i:2329794 original size:19 final size:18
Alignment explanation
Indices: 2329770--2329809 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2329760 ATGAGAGTAC
* *
2329770 ATGTGTTATATGTTATGGT
1 ATGTGTTACATGATAT-GT
2329789 ATGTGTTACATGATATGT
1 ATGTGTTACATGATATGT
2329807 ATG
1 ATG
2329810 AATACATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (18 bp):
ATGTGTTACATGATATGT
Found at i:2330952 original size:21 final size:21
Alignment explanation
Indices: 2330923--2330966 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2330913 GTCGAGGGTT
* *
2330923 ATATGTGGTCCTTTGAGACAA
1 ATATATGGTCCTTCGAGACAA
* *
2330944 ATATATGGTTCTTCGGGACAA
1 ATATATGGTCCTTCGAGACAA
2330965 AT
1 AT
2330967 CCTATGTGCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
ATATATGGTCCTTCGAGACAA
Found at i:2332054 original size:21 final size:21
Alignment explanation
Indices: 2332024--2332077 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2332014 CTGAACCTAG
2332024 AGTATCGATACTCCTTACATA
1 AGTATCGATACTCCTTACATA
* *
2332045 AGTATTGATACTCCTTACATG
1 AGTATCGATACTCCTTACATA
*
2332066 AGTATCAATACT
1 AGTATCGATACT
2332078 TCCACCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTCCTTACATA
Found at i:2338972 original size:20 final size:21
Alignment explanation
Indices: 2338929--2338973 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2338919 TGGAGAATTC
*
2338929 AATGCTGAAATTTAATTATGG
1 AATGCTGAAATTTAATTATAG
*
2338950 AATGCTGAATTTTAATT-TAG
1 AATGCTGAAATTTAATTATAG
2338970 AATG
1 AATG
2338974 TTGATTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (21 bp):
AATGCTGAAATTTAATTATAG
Found at i:2340043 original size:11 final size:11
Alignment explanation
Indices: 2340027--2340088 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
2340017 AAAATTACAT
2340027 TATTAAAAATA
1 TATTAAAAATA
2340038 TATTAAAAATA
1 TATTAAAAATA
* ***
2340049 CATTATTGATA
1 TATTAAAAATA
2340060 -ATTATAAAAT-
1 TATTA-AAAATA
2340070 T-TTAAAAATA
1 TATTAAAAATA
2340080 TATTAAAAA
1 TATTAAAAA
2340089 CTCTATAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 27 0.68
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2340216 original size:7 final size:7
Alignment explanation
Indices: 2340200--2340274 Score: 105
Period size: 7 Copynumber: 10.7 Consensus size: 7
2340190 GTAATTAACA
*
2340200 CTAAGCC
1 CTAAACC
*
2340207 CTAAAAC
1 CTAAACC
2340214 CTAAACC
1 CTAAACC
*
2340221 ATAAACC
1 CTAAACC
2340228 CTAAACC
1 CTAAACC
2340235 CTAAACC
1 CTAAACC
2340242 CTAAACC
1 CTAAACC
*
2340249 TTAAACC
1 CTAAACC
2340256 CTAAACC
1 CTAAACC
*
2340263 ATAAACC
1 CTAAACC
2340270 CTAAA
1 CTAAA
2340275 TCCGATTATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.47, C:0.36, G:0.01, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:2346747 original size:19 final size:19
Alignment explanation
Indices: 2346712--2346749 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2346702 CCCCCTTTGA
*
2346712 AGGGGAACTGATTCCCCCT
1 AGGGGAACTGATACCCCCT
2346731 AGGGGAA-TCGATACCCCCT
1 AGGGGAACT-GATACCCCCT
2346750 GGTGTTCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.24, C:0.32, G:0.26, T:0.18
Consensus pattern (19 bp):
AGGGGAACTGATACCCCCT
Found at i:2349065 original size:13 final size:13
Alignment explanation
Indices: 2349047--2349116 Score: 94
Period size: 13 Copynumber: 5.7 Consensus size: 13
2349037 AGGGGGAGTA
2349047 ATTTCAAAACTTG
1 ATTTCAAAACTTG
*
2349060 ATTTCAAAA--TC
1 ATTTCAAAACTTG
2349071 ATTTCAAAACTTG
1 ATTTCAAAACTTG
*
2349084 ATTTCAAAA--TC
1 ATTTCAAAACTTG
2349095 ATTTCAAAACTTG
1 ATTTCAAAACTTG
2349108 ATTTCAAAA
1 ATTTCAAAA
2349117 TCTTAAAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 20 0.41
13 29 0.59
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (13 bp):
ATTTCAAAACTTG
Found at i:2349076 original size:11 final size:11
Alignment explanation
Indices: 2349060--2349118 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
2349050 TCAAAACTTG
2349060 ATTTCAAAATC
1 ATTTCAAAATC
*
2349071 ATTTCAAAACTTG
1 ATTTCAAAA--TC
2349084 ATTTCAAAATC
1 ATTTCAAAATC
*
2349095 ATTTCAAAACTTG
1 ATTTCAAAA--TC
2349108 ATTTCAAAATC
1 ATTTCAAAATC
2349119 TTAAAATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 20 0.50
13 20 0.50
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.37
Consensus pattern (11 bp):
ATTTCAAAATC
Found at i:2349079 original size:24 final size:24
Alignment explanation
Indices: 2349047--2349118 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
2349037 AGGGGGAGTA
2349047 ATTTCAAAACTTGATTTCAAAATC
1 ATTTCAAAACTTGATTTCAAAATC
2349071 ATTTCAAAACTTGATTTCAAAATC
1 ATTTCAAAACTTGATTTCAAAATC
2349095 ATTTCAAAACTTGATTTCAAAATC
1 ATTTCAAAACTTGATTTCAAAATC
2349119 TTAAAATTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTCAAAACTTGATTTCAAAATC
Found at i:2356412 original size:21 final size:21
Alignment explanation
Indices: 2356386--2356466 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 21
2356376 TATTAATTGT
2356386 TATATTTATTATAAAATTTTA
1 TATATTTATTATAAAATTTTA
* *
2356407 TATATTTA-TA-ATAATATTA
1 TATATTTATTATAAAATTTTA
2356426 TA-ATGTTATTTATAATAATTTTA
1 TATAT-TTA-TTATAA-AATTTTA
*
2356449 -ATAATT-TT-TAAAATTTTA
1 TATATTTATTATAAAATTTTA
2356467 ATAATTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
18 9 0.18
19 15 0.31
20 4 0.08
21 10 0.20
22 4 0.08
23 7 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (21 bp):
TATATTTATTATAAAATTTTA
Found at i:2356423 original size:12 final size:12
Alignment explanation
Indices: 2356387--2356453 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
2356377 ATTAATTGTT
*
2356387 ATATTTATTATA
1 ATATTTATAATA
*
2356399 AAATTT-T-AT-
1 ATATTTATAATA
2356408 ATATTTATAATA
1 ATATTTATAATA
*
2356420 ATA-TTATAATG
1 ATATTTATAATA
*
2356431 TTATTTATAATA
1 ATATTTATAATA
2356443 AT-TTTAATAAT
1 ATATTT-ATAAT
2356454 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.11
10 3 0.07
11 15 0.34
12 21 0.48
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (12 bp):
ATATTTATAATA
Found at i:2356436 original size:23 final size:24
Alignment explanation
Indices: 2356409--2356453 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2356399 AAATTTTATA
2356409 TATTTATAATAATATT-ATAATGT
1 TATTTATAATAATATTAATAATGT
*
2356432 TATTTATAATAATTTTAATAAT
1 TATTTATAATAATATTAATAAT
2356454 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTATAATAATATTAATAATGT
Found at i:2356467 original size:8 final size:9
Alignment explanation
Indices: 2356433--2356472 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2356423 TTATAATGTT
2356433 ATTTATAATA
1 ATTT-TAATA
2356443 ATTTTAATA
1 ATTTTAATA
2356452 ATTTTTAA-A
1 A-TTTTAATA
2356461 ATTTTAATA
1 ATTTTAATA
2356470 ATT
1 ATT
2356473 AAAATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 12 0.43
10 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTTTAATA
Found at i:2356478 original size:27 final size:29
Alignment explanation
Indices: 2356433--2356488 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
2356423 TTATAATGTT
**
2356433 ATTTATAATAATTTTAATAATT-TTTAAA
1 ATTTATAATAATTAAAATAATTATTTAAA
2356461 ATTT-TAATAATTAAAATAATTATTTAAA
1 ATTTATAATAATTAAAATAATTATTTAAA
2356489 TAGAATTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTATAATAATTAAAATAATTATTTAAA
Found at i:2356481 original size:18 final size:19
Alignment explanation
Indices: 2356433--2356481 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
2356423 TTATAATGTT
*
2356433 ATTTATAATAATTTTAATA
1 ATTTAAAATAATTTTAATA
**
2356452 ATTTTTAA-AATTTTAATA
1 ATTTAAAATAATTTTAATA
2356470 A-TTAAAATAATT
1 ATTTAAAATAATT
2356482 ATTTAAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 15 0.58
19 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAAAATAATTTTAATA
Found at i:2357414 original size:15 final size:13
Alignment explanation
Indices: 2357384--2357426 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 13
2357374 AATATTATAG
*
2357384 AAATTAAA-ATAT
1 AAATTAAATAAAT
2357396 AAATTAATACTAAAT
1 AAATTAA-A-TAAAT
2357411 AAATTAAATAAAT
1 AAATTAAATAAAT
2357424 AAA
1 AAA
2357427 ATATTAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 1 0.04
15 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATTAAATAAAT
Found at i:2360471 original size:27 final size:27
Alignment explanation
Indices: 2360429--2360496 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
2360419 ATGTATGAAT
*
2360429 TATAGAG--ATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2360454 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2360481 TATAGAGATATGATTT
1 TATAGAGATATGATTT
2360497 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:2360574 original size:15 final size:15
Alignment explanation
Indices: 2360554--2360589 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2360544 GATTATTATT
2360554 TTTCCTTTCTTAGAG
1 TTTCCTTTCTTAGAG
2360569 TTTCCTTTCTTAGAG
1 TTTCCTTTCTTAGAG
2360584 TTTCCT
1 TTTCCT
2360590 ACTTTAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (15 bp):
TTTCCTTTCTTAGAG
Found at i:2360596 original size:15 final size:15
Alignment explanation
Indices: 2360554--2360598 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
2360544 GATTATTATT
*
2360554 TTTCCTTTCTTAGAG
1 TTTCCTCTCTTAGAG
*
2360569 TTTCCTTTCTTAGAG
1 TTTCCTCTCTTAGAG
2360584 TTTCCTACT-TTAGAG
1 TTTCCT-CTCTTAGAG
2360599 AGAGCTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTCCTCTCTTAGAG
Found at i:2364245 original size:27 final size:27
Alignment explanation
Indices: 2364203--2364270 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
2364193 GTGTAGGAAT
2364203 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2364228 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
2364255 TATAGAGATATGATTT
1 TATAGAGATATGATTT
2364271 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:2368255 original size:14 final size:14
Alignment explanation
Indices: 2368236--2368263 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2368226 AGTATAGCTA
2368236 TGTATAGAGTGTGT
1 TGTATAGAGTGTGT
2368250 TGTATAGAGTGTGT
1 TGTATAGAGTGTGT
2368264 AATATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
TGTATAGAGTGTGT
Found at i:2370482 original size:64 final size:63
Alignment explanation
Indices: 2370409--2370537 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 63
2370399 AATCCTTTAA
*
2370409 GGCAAGCTCGCAAGGATTACTGGGATGGGAGGAGAAGTGGGTTGCTGATCGAATCCAAAGTAAG
1 GGCAAGCTCGCAAGGATTACTGGGATGGGAGGAGAAGTGGGGTGCTGATCGAATCCAAAG-AAG
2370473 GGCAAGCTCGCAAGGATTACTGGGATGGGAGGAGAAGTGGGGTGCTGATCGAATCCAAAGAAG
1 GGCAAGCTCGCAAGGATTACTGGGATGGGAGGAGAAGTGGGGTGCTGATCGAATCCAAAGAAG
2370536 GG
1 GG
2370538 AGAGTCCGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 5 0.08
64 59 0.92
ACGTcount: A:0.29, C:0.14, G:0.40, T:0.17
Consensus pattern (63 bp):
GGCAAGCTCGCAAGGATTACTGGGATGGGAGGAGAAGTGGGGTGCTGATCGAATCCAAAGAAG
Found at i:2373678 original size:28 final size:29
Alignment explanation
Indices: 2373631--2373687 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
2373621 TGGTAATCCT
2373631 TCTCGAAGTTTTGCTGATATAGTTACGGC
1 TCTCGAAGTTTTGCTGATATAGTTACGGC
2373660 TCTCGAAG-TTTGCTGATATAGTTACGGC
1 TCTCGAAGTTTTGCTGATATAGTTACGGC
2373688 GGGAGAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (29 bp):
TCTCGAAGTTTTGCTGATATAGTTACGGC
Found at i:2379513 original size:7 final size:8
Alignment explanation
Indices: 2379497--2379539 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
2379487 GAAATGAGTG
2379497 AAAATGAA
1 AAAATGAA
*
2379505 AAAATAAA
1 AAAATGAA
2379513 AAAAT-AA
1 AAAATGAA
*
2379520 AAAATGGA
1 AAAATGAA
2379528 AAAATGAA
1 AAAATGAA
2379536 AAAA
1 AAAA
2379540 AAAGAAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:2380532 original size:55 final size:55
Alignment explanation
Indices: 2380463--2380962 Score: 817
Period size: 55 Copynumber: 9.1 Consensus size: 55
2380453 AGGTTTCCCA
2380463 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
2380518 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
2380573 ACAATTGTTGAAGATTATTCGAGTCTCATACTCTTTGAAGGAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
2380628 ACGATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCATAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
2380683 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
2380738 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
2380793 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAACAAATAGGGAACAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
2380848 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGGC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
2380903 ACGATTATCG-AGAATCGTTCGAGTCTTATACTCTCTG-A-AAATAGGGAGCAGAC
1 ACGATTGTTGAAG-ATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
2380956 ACGATTG
1 ACGATTG
2380963 ACGAAGATAT
Statistics
Matches: 413, Mismatches: 31, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
53 20 0.05
54 3 0.01
55 390 0.94
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:2385970 original size:27 final size:26
Alignment explanation
Indices: 2385932--2386010 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
2385922 ATACACTCTA
*
2385932 CACCACCTGGGAGTGTTGCTGAAGAAT
1 CACC-CCTGGGAGTGGTGCTGAAGAAT
* *
2385959 CACCGCCTGGGAGTGGGGCTAAAGAAT
1 CACC-CCTGGGAGTGGTGCTGAAGAAT
* *
2385986 CATCCCTTGGGAATGGTGCTGAAGA
1 CA-CCCCTGGGAGTGGTGCTGAAGA
2386011 TGCTGGTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.20
Consensus pattern (26 bp):
CACCCCTGGGAGTGGTGCTGAAGAAT
Found at i:2388689 original size:31 final size:31
Alignment explanation
Indices: 2388654--2388714 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2388644 GGAGGTAGAA
2388654 TTGCTCTTATCAAGTCAGTTTTTTCTAGTCT
1 TTGCTCTTATCAAGTCAGTTTTTTCTAGTCT
* *
2388685 TTGCTCTTATGAAGTCGGTTTTTTCTAGTC
1 TTGCTCTTATCAAGTCAGTTTTTTCTAGTC
2388715 ATCCGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (31 bp):
TTGCTCTTATCAAGTCAGTTTTTTCTAGTCT
Found at i:2394684 original size:16 final size:17
Alignment explanation
Indices: 2394663--2394695 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2394653 TTATTGTTCA
2394663 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
2394679 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
2394696 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:2402352 original size:87 final size:87
Alignment explanation
Indices: 2402249--2402422 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
2402239 TGTCATTTTT
*
2402249 AAAACGAAAAAATTTAAAAGAAAAATGTGATTAACCACTCTGGTTGTTTCGTGTGGTATTCTGAT
1 AAAACGAAAAAATTTAAAAGAAAAATGTGATTAACCACTCTGGTGGTTTCGTGTGGTATTCTGAT
2402314 CCGTCGACTATGTGTCGTACTG
66 CCGTCGACTATGTGTCGTACTG
2402336 AAAACGAAAAAATTTAAAAGAAAAATGTGATTAACCACTCTGGTGGTTTCGTGTGGTATTCTGAT
1 AAAACGAAAAAATTTAAAAGAAAAATGTGATTAACCACTCTGGTGGTTTCGTGTGGTATTCTGAT
2402401 CCGTCGACTATGTGTCGTACTG
66 CCGTCGACTATGTGTCGTACTG
2402423 GTTTAAGGTG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (87 bp):
AAAACGAAAAAATTTAAAAGAAAAATGTGATTAACCACTCTGGTGGTTTCGTGTGGTATTCTGAT
CCGTCGACTATGTGTCGTACTG
Found at i:2404166 original size:20 final size:22
Alignment explanation
Indices: 2404117--2404167 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2404107 AAAATATATC
* *
2404117 ATAAACTATAATATGATAAATT
1 ATAAATTATTATATGATAAATT
2404139 ATAAATTATTATAT-ATAAA-T
1 ATAAATTATTATATGATAAATT
*
2404159 ATATATTAT
1 ATAAATTAT
2404168 ACATAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 5 0.19
22 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAATTATTATATGATAAATT
Done.