Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 26 of 208
Found at i:7409871 original size:16 final size:16
Alignment explanation
Indices: 7409850--7409881 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7409840 TTTTGAATTT
*
7409850 TTCATTATTTTTTTTG
1 TTCATTATTATTTTTG
7409866 TTCATTATTATTTTTG
1 TTCATTATTATTTTTG
7409882 ATTTTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (16 bp):
TTCATTATTATTTTTG
Found at i:7423298 original size:23 final size:23
Alignment explanation
Indices: 7423268--7423313 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
7423258 CTTTCTTATT
*
7423268 GTAGTAATTTTCGGGGTATTACA
1 GTAGTAATTTTCGGGATATTACA
7423291 GTAGTAATTTTCGGGATATTACA
1 GTAGTAATTTTCGGGATATTACA
7423314 TTTTTCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTACA
Found at i:7426151 original size:87 final size:87
Alignment explanation
Indices: 7426044--7426307 Score: 465
Period size: 87 Copynumber: 3.0 Consensus size: 87
7426034 GGCTATAGAC
*
7426044 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATCGTCTTTAACTAAATGTTTGA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTAACTAAATGTTTGA
7426109 ACTATGTTTCAATACTTGAGCA
66 ACTATGTTTCAATACTTGAGCA
* *
7426131 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTCACTAAATGTTTAA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTAACTAAATGTTTGA
7426196 ACTATGTTTCAATACTTGAGCA
66 ACTATGTTTCAATACTTGAGCA
* * *
7426218 CTCTTACTTTCCGTCAATGTTAGGTTCTGACTTAGCTTCAAAATTTTCTTTAACTAAATGTTTGA
1 CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTAACTAAATGTTTGA
*
7426283 ACTATGTTTCAATACTTGAGAA
66 ACTATGTTTCAATACTTGAGCA
7426305 CTC
1 CTC
7426308 CAAAAAGATT
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 168 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (87 bp):
CTCTTACTTTCTGTCAATGTTAGGTTCTGACTTAGTTTCAAAATTGTCTTTAACTAAATGTTTGA
ACTATGTTTCAATACTTGAGCA
Found at i:7438579 original size:43 final size:43
Alignment explanation
Indices: 7438516--7438709 Score: 316
Period size: 43 Copynumber: 4.5 Consensus size: 43
7438506 TGTCCCAGAC
* * **
7438516 ATGGTCTTACATGGGAATCTCGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
7438560 ATGGTCTTACACGAAATCTCAAATCGATGGCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
7438603 ATGGCCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
7438646 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
7438689 ATGGTCTTACTCGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
7438710 CCTTGAAAGT
Statistics
Matches: 141, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
43 130 0.92
44 11 0.08
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:7438911 original size:37 final size:31
Alignment explanation
Indices: 7438830--7438936 Score: 155
Period size: 31 Copynumber: 3.5 Consensus size: 31
7438820 TGCTCAAATC
7438830 AATTCGGCAATATATATCCATAAACAATTCA
1 AATTCGGCAATATATATCCATAAACAATTCA
*
7438861 AATTCGGCAATATATATTCATAAACAATTCA
1 AATTCGGCAATATATATCCATAAACAATTCA
* * *
7438892 AATTCGGCAATGTATAT--ATATACAAATCA
1 AATTCGGCAATATATATCCATAAACAATTCA
*
7438921 AATTCGGCAATGTATA
1 AATTCGGCAATATATA
7438937 AAACATATAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 26 0.36
31 46 0.64
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
AATTCGGCAATATATATCCATAAACAATTCA
Found at i:7438955 original size:60 final size:61
Alignment explanation
Indices: 7438830--7438956 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 61
7438820 TGCTCAAATC
* **
7438830 AATTCGGCAATATATATCCATAAACAATTCAAATTCGGCAATATATATTCATAAACAATTCA
1 AATTCGGCAATATATAT-CATAAACAAATCAAATTCGGCAATATATAAACATAAACAATTCA
* * * * *
7438892 AATTCGGCAATGTATAT-ATATACAAATCAAATTCGGCAATGTATAAAACATATAC-ATTTA
1 AATTCGGCAATATATATCATAAACAAATCAAATTCGGCAATATAT-AAACATAAACAATTCA
7438952 AATTC
1 AATTC
7438957 AAAAACATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 33 0.59
61 7 0.12
62 16 0.29
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (61 bp):
AATTCGGCAATATATATCATAAACAAATCAAATTCGGCAATATATAAACATAAACAATTCA
Found at i:7439926 original size:11 final size:11
Alignment explanation
Indices: 7439910--7439937 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
7439900 TCTAAATAGC
7439910 TCATTTATATA
1 TCATTTATATA
7439921 TCATTTATATA
1 TCATTTATATA
7439932 TCATTT
1 TCATTT
7439938 GTTCATTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (11 bp):
TCATTTATATA
Found at i:7440969 original size:14 final size:14
Alignment explanation
Indices: 7440950--7440976 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7440940 CATAAAATTC
7440950 TTTTGCTTTTCCCA
1 TTTTGCTTTTCCCA
7440964 TTTTGCTTTTCCC
1 TTTTGCTTTTCCC
7440977 CTTTATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.30, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTGCTTTTCCCA
Found at i:7441262 original size:2 final size:2
Alignment explanation
Indices: 7441255--7441288 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
7441245 AAGAGTTCAC
*
7441255 AT AT AT AT GT 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
7441289 GATTTATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7446211 original size:26 final size:24
Alignment explanation
Indices: 7446165--7446237 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 24
7446155 AGCATTATTA
*
7446165 TTTAAAAATAATATATTAATATGATTACT
1 TTTAAAAATAATA-A--AATAT-A-TAAT
7446194 TTTAAAAATAATAAAATATATAAT
1 TTTAAAAATAATAAAATATATAAT
7446218 TTTATTAAAATAA-AAAATAT
1 TTTA--AAAATAATAAAATAT
7446238 TTAAGTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 7 0.17
25 8 0.20
26 12 0.29
28 1 0.02
29 13 0.32
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (24 bp):
TTTAAAAATAATAAAATATATAAT
Found at i:7446253 original size:25 final size:26
Alignment explanation
Indices: 7446198--7446252 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
7446188 ATTACTTTTA
* *
7446198 AAAATAATAAAATATATAATTTTATT
1 AAAATAATAAAATATATAAGTATATT
*
7446224 AAAATAA-AAAATATTTAAGTATATAT
1 AAAATAATAAAATATATAAGTATAT-T
7446250 AAA
1 AAA
7446253 TTAGTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
AAAATAATAAAATATATAAGTATATT
Found at i:7446823 original size:26 final size:26
Alignment explanation
Indices: 7446773--7446825 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
7446763 AATATTAAGA
*
7446773 TAAACAATATTTATCTTAATAATAAT
1 TAAACAATATTTATATTAATAATAAT
* * *
7446799 TAAATAATATTTATATTTATGATAAT
1 TAAACAATATTTATATTAATAATAAT
7446825 T
1 T
7446826 TATATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAACAATATTTATATTAATAATAAT
Found at i:7447469 original size:44 final size:43
Alignment explanation
Indices: 7447421--7447563 Score: 171
Period size: 43 Copynumber: 3.3 Consensus size: 43
7447411 ATTAGTTAAA
** *
7447421 AATTAAAATAAAATAGAAGTTGTGATAATTATACATTTAAAAAT
1 AATTAAAATTTAATAGAAATTGTGATAATTATACA-TTAAAAAT
* **
7447465 AATTATAATTTAATAGAAACCGTGATAATTATACATTAAAAAT
1 AATTAAAATTTAATAGAAATTGTGATAATTATACATTAAAAAT
* * *
7447508 AATTATAGTTTAATAGAAATTGTGATAATTACACAGTTAAAAA-
1 AATTAAAATTTAATAGAAATTGTGATAATTATACA-TTAAAAAT
*
7447551 AATTCAAATTTAA
1 AATTAAAATTTAA
7447564 ATTACAATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 49 0.58
44 36 0.42
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (43 bp):
AATTAAAATTTAATAGAAATTGTGATAATTATACATTAAAAAT
Found at i:7451426 original size:25 final size:24
Alignment explanation
Indices: 7451398--7451454 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
7451388 GAAGCTTAAA
7451398 AGAGCCATTAATAGGGAAGCTCATG
1 AGAGCCATTAATA-GGAAGCTCATG
* *
7451423 AGAGCTAATTATTAGGAAGCTCATG
1 AGAGC-CATTAATAGGAAGCTCATG
7451448 AGAGCCA
1 AGAGCCA
7451455 AATATCGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.75
26 6 0.21
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (24 bp):
AGAGCCATTAATAGGAAGCTCATG
Found at i:7451469 original size:25 final size:25
Alignment explanation
Indices: 7451411--7451501 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
7451401 GCCATTAATA
* *
7451411 GGGAAGCTCATGAGAGCTAATTATT
1 GGGAAGCTCATGAGAGCTAAATATC
* *
7451436 AGGAAGCTCATGAGAGCCAAATATC
1 GGGAAGCTCATGAGAGCTAAATATC
* * *
7451461 GGGATGCTCATAAGAGCTAAATAAC
1 GGGAAGCTCATGAGAGCTAAATATC
*
7451486 GGGAAGCTCGTGAGAG
1 GGGAAGCTCATGAGAG
7451502 TTGTGGTGCG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (25 bp):
GGGAAGCTCATGAGAGCTAAATATC
Found at i:7458316 original size:25 final size:25
Alignment explanation
Indices: 7458288--7458376 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
7458278 TTCCAAGCCA
*
7458288 TATAACGGGAAGCTCATGTGAGTTG
1 TATAACGGGAAGCTCATGCGAGTTG
** * * *
7458313 TATAATAGGAAGCTCTTGCCAGCTG
1 TATAACGGGAAGCTCATGCGAGTTG
* *
7458338 -AGTATCGGGAAGCTCATACGAGTTG
1 TA-TAACGGGAAGCTCATGCGAGTTG
7458363 TATAACGGGAAGCT
1 TATAACGGGAAGCT
7458377 TAAGAGAGCC
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
24 1 0.02
25 46 0.96
26 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (25 bp):
TATAACGGGAAGCTCATGCGAGTTG
Found at i:7458486 original size:25 final size:25
Alignment explanation
Indices: 7458396--7458485 Score: 108
Period size: 25 Copynumber: 3.6 Consensus size: 25
7458386 CATTAATTGA
*
7458396 GAAGCTCATGAGAGCCAATTATCGG
1 GAAGCTCATGAGAGCCAAATATCGG
*
7458421 GAAGCTCATGCGAGCCAAATATCGG
1 GAAGCTCATGAGAGCCAAATATCGG
* * * * *
7458446 GATGTTCATAAGAGCTAAATAACGG
1 GAAGCTCATGAGAGCCAAATATCGG
*
7458471 GAAGCTCGTGAGAGC
1 GAAGCTCATGAGAGC
7458486 TGTGGTGTGT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAAATATCGG
Found at i:7467213 original size:4 final size:4
Alignment explanation
Indices: 7467206--7467243 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
7467196 TTTTTCTTTC
*
7467206 AATA AATA AATA AATA AAT- AA-A AATA AATA AATT AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
7467244 TTTAAGTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 4 0.13
4 26 0.87
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:7467232 original size:18 final size:18
Alignment explanation
Indices: 7467209--7467243 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7467199 TTCTTTCAAT
7467209 AAATAAATAAATAAATAA
1 AAATAAATAAATAAATAA
*
7467227 AAATAAATAAATTAATA
1 AAATAAATAAATAAATA
7467244 TTTAAGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAATAAATAAATAA
Found at i:7480211 original size:4 final size:4
Alignment explanation
Indices: 7480204--7480237 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
7480194 ATATATAGAT
7480204 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
7480238 GGTCATGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:7488138 original size:23 final size:21
Alignment explanation
Indices: 7488112--7488156 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
7488102 GAGAATCGAG
7488112 ACCAACTACAGTGATATCGCGAT
1 ACCAACTA-A-TGATATCGCGAT
* *
7488135 ACCAAGTAATGGTATCGCGAT
1 ACCAACTAATGATATCGCGAT
7488156 A
1 A
7488157 TCGAGACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (21 bp):
ACCAACTAATGATATCGCGAT
Found at i:7516060 original size:2 final size:2
Alignment explanation
Indices: 7516053--7516084 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7516043 TAGCTTTTGC
7516053 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
7516085 TGGTGAACTC
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:7519436 original size:18 final size:18
Alignment explanation
Indices: 7519413--7519449 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
7519403 TACACGAGTC
7519413 TAGCTATACATGCCATTA
1 TAGCTATACATGCCATTA
7519431 TAGCTATACATGCCATTA
1 TAGCTATACATGCCATTA
7519449 T
1 T
7519450 CCAACCGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (18 bp):
TAGCTATACATGCCATTA
Found at i:7520907 original size:18 final size:18
Alignment explanation
Indices: 7520873--7520907 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7520863 ACCTCTCTTT
*
7520873 TTTTTTTTTAAACACAAA
1 TTTTTTTTAAAACACAAA
*
7520891 TTTTTTTTAAAATACAA
1 TTTTTTTTAAAACACAA
7520908 GAATTTTAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTTTTAAAACACAAA
Found at i:7520975 original size:18 final size:18
Alignment explanation
Indices: 7520952--7520988 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7520942 ACCACGAAAA
7520952 TTTTG-AAACACGAGATTT
1 TTTTGAAAACACGA-ATTT
7520970 TTTTGAAAACACGAATTT
1 TTTTGAAAACACGAATTT
7520988 T
1 T
7520989 CTTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (18 bp):
TTTTGAAAACACGAATTT
Found at i:7520995 original size:21 final size:21
Alignment explanation
Indices: 7520969--7521029 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
7520959 ACACGAGATT
* *
7520969 TTTTTGAAAACACGAATTTTC
1 TTTTTGAAAACACAAAATTTC
*
7520990 TTTTTG-AAACACAAAATTTG
1 TTTTTGAAAACACAAAATTTC
*
7521010 TTTTTGAAAACATAAAATTT
1 TTTTTGAAAACACAAAATTT
7521030 TTGATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (21 bp):
TTTTTGAAAACACAAAATTTC
Found at i:7520999 original size:20 final size:18
Alignment explanation
Indices: 7520952--7521018 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 18
7520942 ACCACGAAAA
7520952 TTTTGAAACACGAGA-TTT
1 TTTTGAAACACGA-ATTTT
7520970 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAA-TTT-T
*
7520991 TTTTGAAACACAAAATTTGT
1 TTTTGAAACAC-GAATTT-T
7521011 TTTTGAAA
1 TTTTGAAA
7521019 ACATAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.14
19 8 0.19
20 20 0.48
21 8 0.19
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (18 bp):
TTTTGAAACACGAATTTT
Found at i:7521118 original size:18 final size:18
Alignment explanation
Indices: 7521095--7521280 Score: 96
Period size: 17 Copynumber: 10.3 Consensus size: 18
7521085 GGTCAATTTT
7521095 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
7521113 TTTTTGAAAGATGA-GAATTT
1 TTTTTGAAA-A-CACGAA-AA
** *
7521133 TTTTTGAAAATTCGGAAA
1 TTTTTGAAAACACGAAAA
* * *
7521151 TTTAT-AAAACAGGGAAATT
1 TTTTTGAAAACA-CGAAA-A
* *
7521170 TTTTCTGAAAACAAGAAAG
1 TTTT-TGAAAACACGAAAA
*
7521189 TTTTTGAAATACGCG--AA
1 TTTTTGAAA-ACACGAAAA
**
7521206 TTTTTGAAAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
7521224 TTATTGAAAACGCGAAAA
1 TTTTTGAAAACACGAAAA
7521242 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
7521259 ATTTTG-AAATACGATAA
1 TTTTTGAAAACACGAAAA
7521276 TTTTT
1 TTTTT
7521281 TTTGTTTTAA
Statistics
Matches: 125, Mismatches: 31, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
16 4 0.03
17 42 0.34
18 41 0.33
19 17 0.14
20 15 0.12
21 6 0.05
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:7521132 original size:39 final size:36
Alignment explanation
Indices: 7521054--7521197 Score: 119
Period size: 38 Copynumber: 3.8 Consensus size: 36
7521044 AATACGAGGA
7521054 TTTTTTTG-AAACACGAAAATTTATGAAACACGGTCAATT
1 TTTTTTTGAAAACACGAAAATTTATGAAACA-GG--AA-T
* *
7521093 TTTTTTTGAAAACACGAAAATTTTTGAAAGATGAGAAT
1 TTTTTTTGAAAACACGAAAATTTATGAAACA-G-GAAT
** * *
7521131 TTTTTTTGAAAATTCGGAAATTTATAAAACAGGGAAAT
1 TTTTTTTGAAAACACGAAAATTTATGAAACA-GG-AAT
* * * *
7521169 TTTTTCTGAAAACAAGAAAGTTTTTGAAA
1 TTTTTTTGAAAACACGAAAATTTATGAAA
7521198 TACGCGAATT
Statistics
Matches: 84, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
37 1 0.01
38 51 0.61
39 10 0.12
40 21 0.25
41 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.37
Consensus pattern (36 bp):
TTTTTTTGAAAACACGAAAATTTATGAAACAGGAAT
Found at i:7521211 original size:17 final size:17
Alignment explanation
Indices: 7521189--7521254 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
7521179 AACAAGAAAG
*
7521189 TTTTTGAAATACGCGAA
1 TTTTTGAAACACGCGAA
*
7521206 TTTTTGAAAACACGGGAA
1 TTTTTG-AAACACGCGAA
*
7521224 TTATTGAAA-ACGCGAAAA
1 TTTTTGAAACACGCG--AA
*
7521242 TTTTTAAAACACG
1 TTTTTGAAACACG
7521255 AAAAATTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.10
17 9 0.23
18 23 0.59
19 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGCGAA
Found at i:7521231 original size:35 final size:34
Alignment explanation
Indices: 7521190--7521280 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 34
7521180 ACAAGAAAGT
**
7521190 TTTTGAAATACGCGAATTTTTGAAAACACG-GGAA
1 TTTTGAAATACGCGAATTTTT-AAAACACGAAAAA
7521224 TTATTGAAA-ACGCGAAAATTTTTAAAACACGAAAAA
1 TT-TTGAAATACGCG--AATTTTTAAAACACGAAAAA
**
7521260 TTTTGAAATACGATAATTTTT
1 TTTTGAAATACGCGAATTTTT
7521281 TTTGTTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
34 14 0.29
35 20 0.42
36 14 0.29
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (34 bp):
TTTTGAAATACGCGAATTTTTAAAACACGAAAAA
Found at i:7521905 original size:27 final size:26
Alignment explanation
Indices: 7521865--7521918 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
7521855 GCTTTTTTTT
* * *
7521865 TGCCGGATTTGGGCCTGGAGGGCCTGC
1 TGCCGAATTCGGGCCTAG-GGGCCTGC
7521892 TGCCGAATTCGGGCCTAGGGGCCTGC
1 TGCCGAATTCGGGCCTAGGGGCCTGC
7521918 T
1 T
7521919 TGATCTGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.09, C:0.28, G:0.41, T:0.22
Consensus pattern (26 bp):
TGCCGAATTCGGGCCTAGGGGCCTGC
Found at i:7522110 original size:16 final size:15
Alignment explanation
Indices: 7522080--7522116 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
7522070 CTGTTTGCAG
*
7522080 CGGGTCGACCCGGGT
1 CGGGTCGAACCGGGT
7522095 CGGGTCGGAACCGGGT
1 CGGGTC-GAACCGGGT
7522111 CGGGTC
1 CGGGTC
7522117 AACAGGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.08, C:0.30, G:0.49, T:0.14
Consensus pattern (15 bp):
CGGGTCGAACCGGGT
Found at i:7522160 original size:18 final size:18
Alignment explanation
Indices: 7522137--7522171 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7522127 ATTTACCCTC
*
7522137 TTTTTTTTTCTATTTCTA
1 TTTTTTCTTCTATTTCTA
*
7522155 TTTTTTCTTCTTTTTCT
1 TTTTTTCTTCTATTTCT
7522172 CTCTATTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTCTATTTCTA
Found at i:7523109 original size:14 final size:14
Alignment explanation
Indices: 7523092--7523118 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7523082 ATATATATAT
7523092 ATAAAATAAAATAA
1 ATAAAATAAAATAA
7523106 ATAAAATAAAATA
1 ATAAAATAAAATA
7523119 CGAAAGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAATAAAATAA
Found at i:7523829 original size:240 final size:239
Alignment explanation
Indices: 7523323--7524246 Score: 1326
Period size: 240 Copynumber: 3.8 Consensus size: 239
7523313 GTGTGACCCG
* **
7523323 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAAAAAAAGACAGAAA-TTAAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAA-ACAGAAATTTAAAAATACC
7523387 TCAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAAT
65 TCAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAAT
* *
7523452 TTAAAAAAAAATACCTCAGCGTGCGACCCGATGCTCAACTCACTTCTCGCAATATGAGTTG-GTT
130 TT-AAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTT
7523516 TT-AAAAAAAAACAGAAATTTAAAAAAAATACCTCAGCGTGGTCCA
194 TTGAAAAAAAAACAGAAATTTAAAAAAAATACCTCAGCGTGGTCCA
** *
7523561 AGGCTCAACTCACCTCT---ATATAATGAGTTGATTTTTTGAAAAAAATAGAAATTTAAAAATAC
1 AGGCTCAACTCACCTCTCGCA-AT-ATGAGTTGATTTTTAAAAAAAAACAGAAATTTAAAAATAC
** *
7523623 CTCAGTATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAAACAGA
64 CTCAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAAAACAGA
*
7523688 AATTTAAAAAAAATACCTCAGCGTTCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
127 AATTTAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
* * *
7523753 TTTTGAAAAAAAAATAGAAATTTAAAAAAAATACCTCGGCATGGTCCA
192 TTTTGAAAAAAAAACAGAAATTTAAAAAAAATACCTCAGCGTGGTCCA
* * **
7523801 AGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAAACAGAAATTTAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAACAGAAATTTAAAAATACCT
*
7523865 CAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAAAACAGAA
66 CAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAAAAAACAGAA
*
7523930 ATTTAAAAAAAATACATCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
128 ATTTAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
* * *
7523995 TTTG-AAAAAAAACAGAAATTAAAAAAAAATACCTCAGCGTGCGACCCG
193 TTTGAAAAAAAAACAGAAATTTAAAAAAAATACCTCAGCGTG-G-TCCA
* *
7524043 AGACTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAAAAACAGAAATTTAAAATAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAAAAACAGAAA-TT----T-AA-
*
7524108 AAATACCTCAGCGTGCGACCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAAA
58 AAATACCTCAGCGT--GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
* * *
7524173 AACAGAAATTT-AAAAAAATACCTCAGCGTGCGACCCGAGTCTCAACTCACTTCTCGCATTATAA
121 AACAGAAATTTAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGA
7524237 GTTGATTTTT
186 GTTGATTTTT
7524247 TTTGAAAAAC
Statistics
Matches: 624, Mismatches: 39, Indels: 35
0.89 0.06 0.05
Matches are distributed among these distances:
235 1 0.00
236 8 0.01
237 71 0.11
238 78 0.12
239 20 0.03
240 180 0.29
241 82 0.13
242 18 0.03
243 17 0.03
244 13 0.02
245 2 0.00
249 60 0.10
250 18 0.03
251 14 0.02
252 6 0.01
253 36 0.06
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (239 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAAAACAGAAATTTAAAAATACCT
CAGCGTGACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATT
TAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT
GAAAAAAAAACAGAAATTTAAAAAAAATACCTCAGCGTGGTCCA
Found at i:7524142 original size:87 final size:82
Alignment explanation
Indices: 7523299--7524269 Score: 1217
Period size: 82 Copynumber: 12.0 Consensus size: 82
7523289 ATAGAAATTG
* **
7523299 AAAAATACCTC-GACGTGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTAAAAA
1 AAAAATACCTCAG-CGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAA
7523363 AAAAAGACAGAAA-TT---
65 AAAAA-ACAGAAATTTAAA
* * *
7523378 AAAAATACCTCAGCGT--GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
7523440 AAAAACAGAAATTTAAAA
66 AAAAACAGAAATTT-AAA
* *
7523458 AAAAATACCTCAGCGTGCGACCCGATGCTCAACTCACTTCTCGCAATATGAGTTG-GTTTTAAAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
7523522 AAAAACAGAAATTTAAA
66 AAAAACAGAAATTTAAA
* * * **
7523539 AAAAATACCTCAGCGTG-G-TCCAAGGCTCAACTCAC--CTC-TATATAATGAGTTGATTTTTTG
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCA-AT-ATGAGTTGATTTTTAA
*
7523599 AAAAAAATAGAAATTT---
64 AAAAAAACAGAAATTTAAA
** * *
7523615 AAAAATACCTCA--GTATGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTAAA
7523678 AAAAAACAGAAATTTAAA
65 AAAAAACAGAAATTTAAA
*
7523696 AAAAATACCTCAGCGTTCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-AAA
*
7523761 AAAAAATAGAAATTTAAA
65 AAAAAACAGAAATTTAAA
* * * * * * * **
7523779 AAAAATACCTCGGCATG-G-TCCAAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
7523841 AAAAACAGAAATTT---
66 AAAAACAGAAATTTAAA
*
7523855 AAAAATACCTCAGCGT--GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTT-AA
7523918 AAAAAAACAGAAATTTAAA
64 AAAAAAACAGAAATTTAAA
* *
7523937 AAAAATACATCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
*
7524002 AAAAACAGAAATTAAAA
66 AAAAACAGAAATTTAAA
*
7524019 AAAAATACCTCAGCGTGCGACCCGAGACTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-AAA
7524084 AAAAAACAGAAATTTAAAATA
65 AAAAAACAGAAATTT--AA-A
* *
7524105 AATAAATACCTCAGCGTGCGACCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT-GA
1 AA-AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAA
7524169 AAAAAACAGAAATTT-AA
65 AAAAAACAGAAATTTAAA
* * * ****
7524186 AAAAATACCTCAGCGTGCGACCCGAGTCTCAACTCACTTCTCGCATTATAAGTTGATTTTTTTTG
1 AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
*
7524251 AAAAACAGAAATTGAAA
66 AAAAACAGAAATTTAAA
7524268 AA
1 AA
7524270 TGTAATTCTT
Statistics
Matches: 784, Mismatches: 68, Indels: 77
0.84 0.07 0.08
Matches are distributed among these distances:
74 2 0.00
75 9 0.01
76 69 0.09
77 65 0.08
78 38 0.05
79 79 0.10
80 90 0.11
81 70 0.09
82 154 0.20
83 93 0.12
84 37 0.05
85 18 0.02
86 3 0.00
87 57 0.07
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (82 bp):
AAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAA
AAAAACAGAAATTTAAA
Found at i:7525137 original size:1 final size:1
Alignment explanation
Indices: 7525123--7525228 Score: 59
Period size: 1 Copynumber: 106.0 Consensus size: 1
7525113 TTCATCTTGA
* * * ** * * * *
7525123 TTTTTCTTTCTTTTTTCTTTTTTCCTTTTTTTTGTTTTTTTTTTGTTTTTTTTGTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * *
7525188 TTTGTCTGTTTTTTTGTTTTGTCTTTTTGTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7525229 AAGCATAATA
Statistics
Matches: 73, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (1 bp):
T
Found at i:7525143 original size:17 final size:16
Alignment explanation
Indices: 7525123--7525226 Score: 104
Period size: 17 Copynumber: 6.3 Consensus size: 16
7525113 TTCATCTTGA
*
7525123 TTTTTCTTTCTTTTTTCT
1 TTTTTCTTT-TTTTTT-G
*
7525141 TTTTTCCTTTTTTTTG
1 TTTTTCTTTTTTTTTG
*
7525157 TTTTT-TTTTTGTTT-
1 TTTTTCTTTTTTTTTG
*
7525171 TTTTTGTTTTTTTTTG
1 TTTTTCTTTTTTTTTG
*
7525187 TTTTGTCTGTTTTTTTG
1 TTTT-TCTTTTTTTTTG
7525204 TTTTGTCTTTTTGTTTTG
1 TTTT-TCTTTTT-TTTTG
7525222 TTTTT
1 TTTTT
7525227 TTAAGCATAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
14 5 0.07
15 15 0.20
16 9 0.12
17 28 0.38
18 17 0.23
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTG
Found at i:7525164 original size:13 final size:13
Alignment explanation
Indices: 7525148--7525228 Score: 78
Period size: 13 Copynumber: 6.2 Consensus size: 13
7525138 TCTTTTTTCC
7525148 TTTTTTTTG--TT
1 TTTTTTTTGTTTT
7525159 TTTTTTTTGTTTT
1 TTTTTTTTGTTTT
7525172 TTTTGTTTT-TTTT
1 TTTT-TTTTGTTTT
*
7525185 TGTTTTGTCTGTTTT
1 T-TTTT-TTTGTTTT
* *
7525200 TTTGTTTTGTCTT
1 TTTTTTTTGTTTT
*
7525213 TTTGTTTTGTTTT
1 TTTTTTTTGTTTT
7525226 TTT
1 TTT
7525229 AAGCATAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
11 9 0.15
13 33 0.56
14 12 0.20
15 5 0.08
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTTTT
Found at i:7525165 original size:20 final size:19
Alignment explanation
Indices: 7525123--7525226 Score: 86
Period size: 19 Copynumber: 5.3 Consensus size: 19
7525113 TTCATCTTGA
*
7525123 TTTTTCTTTCTTTTT-TCTT
1 TTTTTCTTT-TTTTTGTTTT
*
7525142 TTTTCCTTTTTTTTGTTTTT
1 TTTTTCTTTTTTTTG-TTTT
*
7525162 TTTTTGTTTTTTTTGTTTT
1 TTTTTCTTTTTTTTGTTTT
* * *
7525181 TTTTTGTTTTGTCTGTTTT
1 TTTTTCTTTTTTTTGTTTT
7525200 TTTGTT-TTGTCTTTTTGTTTT
1 TTT-TTCTT-T-TTTTTGTTTT
7525221 GTTTTT
1 -TTTTT
7525227 TTAAGCATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
18 5 0.07
19 34 0.48
20 19 0.27
21 10 0.14
22 3 0.04
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTTTTTGTTTT
Found at i:7525181 original size:54 final size:54
Alignment explanation
Indices: 7525123--7525228 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
7525113 TTCATCTTGA
* * *
7525123 TTTTTCTTTCTTTTTTCTTTTTTCCTTTTTTTTGT-TTTTT-TTTTGTTTTTTTTG
1 TTTTTCTTTCTTTTGTCTGTTTT--TTTGTTTTGTCTTTTTGTTTTGTTTTTTTTG
* *
7525177 TTTTTTTTTGTTTTGTCTGTTTTTTTGTTTTGTCTTTTTGTTTTGTTTTTTT
1 TTTTTCTTTCTTTTGTCTGTTTTTTTGTTTTGTCTTTTTGTTTTGTTTTTTT
7525229 AAGCATAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
52 9 0.20
53 5 0.11
54 31 0.69
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (54 bp):
TTTTTCTTTCTTTTGTCTGTTTTTTTGTTTTGTCTTTTTGTTTTGTTTTTTTTG
Found at i:7525182 original size:30 final size:31
Alignment explanation
Indices: 7525124--7525228 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 31
7525114 TCATCTTGAT
* * *
7525124 TTTTCTTTCTTTTTTCTTTTTTCCTTTTTTTTG
1 TTTT-TTT-TTTTTTGTTTTGTCTTTTTTTTTG
*
7525157 TTTTTTTTTTGTTT-TTTT-TGTTTTTTTTTG
1 TTTTTTTTTT-TTTGTTTTGTCTTTTTTTTTG
7525187 TTTTGTCTGTTTTTTTGTTTTGTCTTTTTGTTTTG
1 TTTT-T-T-TTTTTTTGTTTTGTCTTTTT-TTTTG
7525222 TTTTTTT
1 TTTTTTT
7525229 AAGCATAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
30 14 0.23
31 8 0.13
32 11 0.18
33 13 0.21
34 7 0.11
35 9 0.15
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.84
Consensus pattern (31 bp):
TTTTTTTTTTTTTGTTTTGTCTTTTTTTTTG
Found at i:7525185 original size:19 final size:19
Alignment explanation
Indices: 7525148--7525226 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 19
7525138 TCTTTTTTCC
7525148 TTTTTTTTGTTTTTTTTTTG
1 TTTTTTTTG-TTTTTTTTTG
7525168 TTTTTTTTGTTTTTTTTTG
1 TTTTTTTTGTTTTTTTTTG
* *
7525187 TTTTGTCTGTTTTTTTGTT-
1 TTTTTTTTGTTTTTTT-TTG
7525206 TTGTCTTTTTGTTTTGTTTTT
1 TT-T-TTTTTGTTTT-TTTTT
7525227 TTAAGCATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
19 26 0.51
20 12 0.24
21 10 0.20
22 3 0.06
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (19 bp):
TTTTTTTTGTTTTTTTTTG
Found at i:7534449 original size:20 final size:19
Alignment explanation
Indices: 7534407--7534449 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
7534397 AACCTCTCTT
* * *
7534407 TTTTTTTTGAAAACACGAT
1 TTTTTTTTAAAAACAAGAA
7534426 TTTTTTTTAAAATACAAGAA
1 TTTTTTTTAAAA-ACAAGAA
7534446 TTTT
1 TTTT
7534450 AGAAACACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (19 bp):
TTTTTTTTAAAAACAAGAA
Found at i:7534456 original size:35 final size:33
Alignment explanation
Indices: 7534411--7534523 Score: 91
Period size: 35 Copynumber: 3.1 Consensus size: 33
7534401 TCTCTTTTTT
7534411 TTTTGAAAACACGATTTTTTTTTAAAATACAAGAA
1 TTTTG-AAACACGATTTTTTTTTAAAA-ACAAGAA
*
7534446 TTTTAGAAACACGAAACTTTTTTTTTAAAAAAACACGAAAA
1 TTTT-GAAACACG--A-TTTTTTTTT--AAAAACA--AGAA
** * *
7534487 TTTTGAAACACGAGATTTTTTTGAAAACACGAA
1 TTTTGAAACACGATTTTTTTTTAAAAACAAGAA
7534520 TTTT
1 TTTT
7534524 CTTTTTGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
33 6 0.09
35 17 0.27
36 1 0.02
37 8 0.12
38 10 0.16
39 3 0.05
40 12 0.19
41 7 0.11
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (33 bp):
TTTTGAAACACGATTTTTTTTTAAAAACAAGAA
Found at i:7534510 original size:18 final size:18
Alignment explanation
Indices: 7534487--7534523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7534477 AACACGAAAA
7534487 TTTTG-AAACACGAGATTT
1 TTTTGAAAACACGA-ATTT
7534505 TTTTGAAAACACGAATTT
1 TTTTGAAAACACGAATTT
7534523 T
1 T
7534524 CTTTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (18 bp):
TTTTGAAAACACGAATTT
Found at i:7534547 original size:16 final size:17
Alignment explanation
Indices: 7534526--7534557 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7534516 CGAATTTTCT
7534526 TTTTG-AAACACAAAAA
1 TTTTGAAAACACAAAAA
7534542 TTTTGAAAACACAAAA
1 TTTTGAAAACACAAAA
7534558 TTTGTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.25
Consensus pattern (17 bp):
TTTTGAAAACACAAAAA
Found at i:7534552 original size:37 final size:37
Alignment explanation
Indices: 7534505--7534582 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
7534495 CACGAGATTT
* *
7534505 TTTTGAAAACACGAATTTTCTTTTTGAAACACA-AAAA
1 TTTTGAAAACACAAAATTTCTTTTTGAAA-ACATAAAA
*
7534542 TTTTGAAAACACAAAATTTGTTTTTGAAAACATAAAA
1 TTTTGAAAACACAAAATTTCTTTTTGAAAACATAAAA
7534579 TTTT
1 TTTT
7534583 TGATAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 3 0.08
37 34 0.92
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (37 bp):
TTTTGAAAACACAAAATTTCTTTTTGAAAACATAAAA
Found at i:7534567 original size:21 final size:20
Alignment explanation
Indices: 7534502--7534583 Score: 82
Period size: 21 Copynumber: 4.2 Consensus size: 20
7534492 AAACACGAGA
* *
7534502 TTTTTTTGAAAACACGAATT
1 TTTTTTTGAAAACACAAAAT
7534522 TTCTTTTTG-AAACACAAAA-
1 TT-TTTTTGAAAACACAAAAT
*
7534541 --ATTTTGAAAACACAAAAT
1 TTTTTTTGAAAACACAAAAT
*
7534559 TTGTTTTTGAAAACATAAAAT
1 TT-TTTTTGAAAACACAAAAT
7534580 TTTT
1 TTTT
7534584 GATAAAATAC
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
16 5 0.10
17 10 0.20
20 12 0.24
21 24 0.47
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTTTTTGAAAACACAAAAT
Found at i:7534658 original size:40 final size:37
Alignment explanation
Indices: 7534606--7534834 Score: 161
Period size: 38 Copynumber: 6.2 Consensus size: 37
7534596 AATACGAGGA
7534606 TTTTTTTG-AAACACGAAATTTTATGAAACACG-GTCAATT
1 TTTTTTTGAAAACACGAAATTTT-TGAAACACGAG--AA-T
*
7534645 TTTTTTTGAAAACACGAAAATTTTTGAAAGACGAGAAT
1 TTTTTTTGAAAACACG-AAATTTTTGAAACACGAGAAT
* * * * *
7534683 TTTTTTTGAAAATACGGAAATTTATAAAATA-GGGAAAT
1 TTTTTTTGAAAACAC-GAAATTTTTGAAACACGAG-AAT
* * * *
7534721 TTTTTCTGAAAACAAGAAAGTTTTTGAAATACGCGAA-
1 TTTTTTTGAAAACACGAAA-TTTTTGAAACACGAGAAT
* *
7534758 --TTTTTGAAAACACGAGAATTATTGAAA-ACGTGAA-
1 TTTTTTTGAAAACACGA-AATTTTTGAAACACGAGAAT
** * *
7534792 AATTTTT-AAAACACGAAAATTTTTGAAATACGATAAT
1 TTTTTTTGAAAACACG-AAATTTTTGAAACACGAGAAT
7534829 TTTTTT
1 TTTTTT
7534835 GTTTTAAAAA
Statistics
Matches: 156, Mismatches: 21, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
34 6 0.04
35 39 0.25
36 13 0.08
37 10 0.06
38 52 0.33
39 13 0.08
40 15 0.10
41 8 0.05
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (37 bp):
TTTTTTTGAAAACACGAAATTTTTGAAACACGAGAAT
Found at i:7534670 original size:18 final size:18
Alignment explanation
Indices: 7534647--7534832 Score: 114
Period size: 17 Copynumber: 10.3 Consensus size: 18
7534637 GGTCAATTTT
7534647 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
**
7534665 TTTTTGAAAGACGA-GAATTT
1 TTTTTGAAA-AC-ACGAA-AA
* *
7534685 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACACGAAAA
* * * *
7534703 TTTAT-AAAATAGGGAAATT
1 TTTTTGAAAACA-CGAAA-A
* *
7534722 TTTTCTGAAAACAAGAAAG
1 TTTT-TGAAAACACGAAAA
*
7534741 TTTTTGAAATACGCG--AA
1 TTTTTGAAA-ACACGAAAA
*
7534758 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* **
7534776 TTATTGAAAACGTGAAAA
1 TTTTTGAAAACACGAAAA
7534794 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
7534811 TTTTTG-AAATACGATAA
1 TTTTTGAAAACACGAAAA
7534828 TTTTT
1 TTTTT
7534833 TTGTTTTAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
16 4 0.03
17 45 0.35
18 42 0.33
19 18 0.14
20 15 0.12
21 5 0.04
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.34
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:7535670 original size:16 final size:15
Alignment explanation
Indices: 7535645--7535679 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
7535635 GTTTGCAGCA
7535645 GGTCGATCCGGGTCG
1 GGTCGATCCGGGTCG
7535660 GGTCGGATCCGGGTCG
1 GGTC-GATCCGGGTCG
7535676 GGTC
1 GGTC
7535680 AACAGGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.06, C:0.26, G:0.49, T:0.20
Consensus pattern (15 bp):
GGTCGATCCGGGTCG
Found at i:7535738 original size:9 final size:10
Alignment explanation
Indices: 7535715--7535740 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
7535705 TCTCTTTCTA
7535715 TTTTTCATTC
1 TTTTTCATTC
7535725 TTTTTCATTC
1 TTTTTCATTC
7535735 TTTTTC
1 TTTTTC
7535741 TCTCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTCATTC
Found at i:7535866 original size:12 final size:12
Alignment explanation
Indices: 7535843--7535876 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7535833 CCCTTCCCTC
7535843 CTTTCTTCCTCTT
1 CTTTCTT-CTCTT
7535856 CTTTCTTCTCTT
1 CTTTCTTCTCTT
*
7535868 CCTTCTTCT
1 CTTTCTTCT
7535877 TTACTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
CTTTCTTCTCTT
Found at i:7536525 original size:5 final size:5
Alignment explanation
Indices: 7536515--7536542 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
7536505 ATAAAAACAT
7536515 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
7536543 ACAATGGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:7547342 original size:24 final size:25
Alignment explanation
Indices: 7547315--7547367 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
7547305 AGGAAGAAGC
7547315 AAAAGAT-AAAGAAAA-ATAAAGAAA
1 AAAAGATAAAAGAAAATA-AAAGAAA
* *
7547339 AAAAGTTAAAAGAACATAAAAGAAA
1 AAAAGATAAAAGAAAATAAAAGAAA
7547364 AAAA
1 AAAA
7547368 TTAAATTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.09
Consensus pattern (25 bp):
AAAAGATAAAAGAAAATAAAAGAAA
Found at i:7547350 original size:25 final size:24
Alignment explanation
Indices: 7547322--7547372 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
7547312 AGCAAAAGAT
7547322 AAAGAAAA-ATAAAGAAAAAAAGTTA
1 AAAGAAAATA-AAAGAAAAAAA-TTA
*
7547347 AAAGAACATAAAAGAAAAAAATTA
1 AAAGAAAATAAAAGAAAAAAATTA
7547371 AA
1 AA
7547373 TTACTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (24 bp):
AAAGAAAATAAAAGAAAAAAATTA
Found at i:7547918 original size:17 final size:16
Alignment explanation
Indices: 7547896--7547953 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
7547886 TATTTTTAAG
7547896 AAGTATTTTTAGAATAA
1 AAGTATTTTTA-AATAA
*
7547913 AAGTATTTTTAAAACAA
1 AAGTATTTTT-AAATAA
* *
7547930 AAATATTCTTAAAT--
1 AAGTATTTTTAAATAA
7547944 AAGTATTTTT
1 AAGTATTTTT
7547954 TTAGAGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.24
16 3 0.09
17 22 0.65
18 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (16 bp):
AAGTATTTTTAAATAA
Found at i:7549766 original size:41 final size:40
Alignment explanation
Indices: 7549692--7549828 Score: 123
Period size: 41 Copynumber: 3.4 Consensus size: 40
7549682 TGGCGCTAAC
* *
7549692 GAAAAACGCGCAATAGGTAAATCATTAGCGGCGTTTATGA
1 GAAAAACGCGCAAAAGGTAAAGCATTAGCGGCGTTTATGA
* * *
7549732 GAAAAACGTCGCAAAAGGTCAAGCATTGGTGGCGTTTATGA
1 GAAAAACG-CGCAAAAGGTAAAGCATTAGCGGCGTTTATGA
* * * * * * *
7549773 GAAAAAAAGCTACAAAAGGTCAAGCACTAACGGCG-CTAGGA
1 G-AAAAACGC-GCAAAAGGTAAAGCATTAGCGGCGTTTATGA
7549814 GAAAAACGCCGCAAA
1 GAAAAACG-CGCAAA
7549829 GTATAATTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
40 18 0.23
41 35 0.45
42 25 0.32
ACGTcount: A:0.41, C:0.18, G:0.26, T:0.16
Consensus pattern (40 bp):
GAAAAACGCGCAAAAGGTAAAGCATTAGCGGCGTTTATGA
Found at i:7551774 original size:10 final size:10
Alignment explanation
Indices: 7551761--7551792 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
7551751 ATTTTCTATT
7551761 TTCTTCTGAA
1 TTCTTCTGAA
7551771 TTCTTCTGAA
1 TTCTTCTGAA
*
7551781 TTCTTCTAAA
1 TTCTTCTGAA
7551791 TT
1 TT
7551793 TGTGTGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (10 bp):
TTCTTCTGAA
Found at i:7552220 original size:39 final size:39
Alignment explanation
Indices: 7552166--7552240 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
7552156 CCTAGAGGTA
7552166 TTTAATGTTGCTACTTGTTCTTGGTTGATTCTTTAAGTG
1 TTTAATGTTGCTACTTGTTCTTGGTTGATTCTTTAAGTG
7552205 TTTAATGTTGCTACTTGTTCTTGGTTGATTCTTTAA
1 TTTAATGTTGCTACTTGTTCTTGGTTGATTCTTTAA
7552241 CAATAGAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.55
Consensus pattern (39 bp):
TTTAATGTTGCTACTTGTTCTTGGTTGATTCTTTAAGTG
Found at i:7552506 original size:5 final size:5
Alignment explanation
Indices: 7552496--7552529 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
7552486 TTAAAAAAAT
*
7552496 GGGTC GGGTC GGGTC GGGTC GGGCC GGGCTC GGG
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGG-TC GGG
7552530 CTTAGAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.00, C:0.24, G:0.62, T:0.15
Consensus pattern (5 bp):
GGGTC
Found at i:7555264 original size:35 final size:35
Alignment explanation
Indices: 7555197--7555264 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
7555187 AATTGTATTA
*
7555197 TTAATTTATTATTTTAAATTCTAAATTTAAATTCG
1 TTAATTTATTATTTTAAATTCTAAATTAAAATTCG
*
7555232 TTAATTT-TTATATTT-AATTTTAAAGTTAAAATT
1 TTAATTTATTAT-TTTAAATTCTAAA-TTAAAATT
7555265 TTATAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (35 bp):
TTAATTTATTATTTTAAATTCTAAATTAAAATTCG
Found at i:7555618 original size:13 final size:14
Alignment explanation
Indices: 7555575--7555627 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
7555565 ACAAATTTAT
* *
7555575 AAATTAAAAGAGTA
1 AAATTTAAAGATTA
* *
7555589 TAATTAAAAGATTA
1 AAATTTAAAGATTA
7555603 AAATTTAAAG-TTA
1 AAATTTAAAGATTA
7555616 AAATTTAAAGAT
1 AAATTTAAAGAT
7555628 GATAATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (14 bp):
AAATTTAAAGATTA
Found at i:7555748 original size:52 final size:52
Alignment explanation
Indices: 7555676--7555847 Score: 272
Period size: 52 Copynumber: 3.3 Consensus size: 52
7555666 AAAACTTTGG
* * * *
7555676 ATCATAACGTACATAACTTACATAACGTACATGATACATAAATATATACCAT
1 ATCATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCAT
* * *
7555728 ATCATAACTTACTTCACTTACATAACTTACATAATTCATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCAT
*
7555780 ATCATAACTTACATAACTTACATAACTTACATTATACATAAATATATATCAT
1 ATCATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCAT
7555832 ATCATAACTTACATAA
1 ATCATAACTTACATAA
7555848 AACTTTGGAT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 109 1.00
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (52 bp):
ATCATAACTTACATAACTTACATAACTTACATAATACATAAATATATATCAT
Found at i:7555755 original size:9 final size:9
Alignment explanation
Indices: 7555678--7555811 Score: 91
Period size: 9 Copynumber: 15.3 Consensus size: 9
7555668 AACTTTGGAT
*
7555678 CATAACGTA
1 CATAACTTA
7555687 CATAACTTA
1 CATAACTTA
*
7555696 CATAACGTA
1 CATAACTTA
*
7555705 CATGA--TA
1 CATAACTTA
*
7555712 CATAA-ATA
1 CATAACTTA
* * *
7555720 TATACCATA
1 CATAACTTA
7555729 TCATAACTTA
1 -CATAACTTA
* *
7555739 CTTCACTTA
1 CATAACTTA
7555748 CATAACTTA
1 CATAACTTA
7555757 CATAA-TT-
1 CATAACTTA
*
7555764 CATAA-ATA
1 CATAACTTA
* * *
7555772 TATATCATA
1 CATAACTTA
7555781 TCATAACTTA
1 -CATAACTTA
7555791 CATAACTTA
1 CATAACTTA
7555800 CATAACTTA
1 CATAACTTA
7555809 CAT
1 CAT
7555812 TATACATAAA
Statistics
Matches: 100, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
7 12 0.12
8 10 0.10
9 66 0.66
10 12 0.12
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:7557702 original size:9 final size:9
Alignment explanation
Indices: 7557688--7557727 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
7557678 TTTGGTTAAC
7557688 AATTAACCG
1 AATTAACCG
7557697 AATTAACCG
1 AATTAACCG
*
7557706 AATTACCCG
1 AATTAACCG
*
7557715 AATTATCCG
1 AATTAACCG
7557724 AATT
1 AATT
7557728 GAATCACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:7557767 original size:37 final size:37
Alignment explanation
Indices: 7557726--7557800 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
7557716 ATTATCCGAA
*
7557726 TTGAATCACTACATAATTAAAAATATGACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATGACATAAGTCT
* *
7557763 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATGACATAAGTCT
7557800 T
1 T
7557801 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATGACATAAGTCT
Found at i:7558016 original size:39 final size:38
Alignment explanation
Indices: 7557931--7558035 Score: 176
Period size: 39 Copynumber: 2.8 Consensus size: 38
7557921 ACTTAAGAGT
*
7557931 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTGGG
*
7557968 TAGACTTTAGTTTTAGTTTTATTTGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT-ATTGGG
7558007 TAGACTTTAGTTTTAGTTTTATTGGGTTG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTG
7558036 TGTTGGATAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 26 0.41
38 3 0.05
39 34 0.54
ACGTcount: A:0.17, C:0.03, G:0.27, T:0.53
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTGGG
Found at i:7562142 original size:57 final size:57
Alignment explanation
Indices: 7562054--7562167 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
7562044 AAGGTATGGT
*
7562054 CGGGTTCGATTTCAAGGATCTTTTGTACATGCCTTCGGGGAATTAGGCTCAAGCTGA
1 CGGGTTCGATTTCAAGGATCTTTTGTACATGCCTTCGGGGAATCAGGCTCAAGCTGA
7562111 CGGGTTCGATTTCAAGGATCTTTTGTACATGCCTTCGGGGAATCAGGCTCAAGCTGA
1 CGGGTTCGATTTCAAGGATCTTTTGTACATGCCTTCGGGGAATCAGGCTCAAGCTGA
7562168 AGTTCAGAGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (57 bp):
CGGGTTCGATTTCAAGGATCTTTTGTACATGCCTTCGGGGAATCAGGCTCAAGCTGA
Found at i:7562341 original size:66 final size:65
Alignment explanation
Indices: 7562229--7562362 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 65
7562219 GCAAATTGCT
* *
7562229 CAACTTAAAGCGAAGACAACATCGAGAGAAGTAGAGGCTCAAAGAAAATATGAAGAACTCCAGCT
1 CAACTTAAAACGAAGACAACAACGAGAGAAGTAGAGGC-CAAAGAAAATATGAAGAACTCCAGCT
7562294 A
65 A
* * * *
7562295 CAACTTAAAACGGAGGCAACAACGAGGGAAGTAGAGG-CAAGTAGAAAATATGACGAACTCCAGC
1 CAACTTAAAACGAAGACAACAACGAGAGAAGTAGAGGCCAA--AGAAAATATGAAGAACTCCAGC
7562359 TA
64 TA
7562361 CA
1 CA
7562363 GCTTCAGAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
64 3 0.05
66 57 0.95
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (65 bp):
CAACTTAAAACGAAGACAACAACGAGAGAAGTAGAGGCCAAAGAAAATATGAAGAACTCCAGCTA
Found at i:7562733 original size:43 final size:42
Alignment explanation
Indices: 7562686--7562895 Score: 169
Period size: 43 Copynumber: 4.9 Consensus size: 42
7562676 GACTTTTAGA
7562686 GGCGTTTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAC
1 GGCGTTTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAC
*
7562728 TGGCGTTTGTGGGG-AAAGCGTCGCTAAAGGTCATGTTCTTTA-
1 -GGCGTTT-TGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAC
** * **
7562770 -GCAGTGTTTGTGGGAAAATTGCCTCTAAAGGTCATGTTCCATAGC
1 GGC-GT-TTTG-GGGAAAAGCGCCGCTAAAGGTCATGTTCTTTA-C
* * *
7562815 GGCATTTGTGTGG-AAAGCGCCGCTAAGGGTCATGTTCTTTA-
1 GGCGTTT-TGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAC
* * * * **
7562856 GTTGCATTTTTGTGAGAAGCATCGCTAAAGGTCATGTTCT
1 G--GCGTTTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCT
7562896 ATAGCAAAAT
Statistics
Matches: 133, Mismatches: 22, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
40 2 0.02
41 5 0.04
42 7 0.05
43 105 0.79
44 9 0.07
45 3 0.02
46 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
GGCGTTTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAC
Found at i:7562830 original size:86 final size:85
Alignment explanation
Indices: 7562691--7562856 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 85
7562681 TTAGAGGCGT
** * *
7562691 TTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTACTGGCGTTTGTGGGGAAAGCGTCGCTAAA
1 TTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCCATACTGGCATTTGTGGGGAAAGCGCCGCTAAA
7562756 GGTCATGTTCTTTAGCAGTG
66 GGTCATGTTCTTTAGCAGTG
** * *
7562776 TTTGTGGGAAAATTGCCTCTAAAGGTCATGTTCCATAGC-GGCATTTGTGTGGAAAGCGCCGCTA
1 TTTG-GGGAAAAGCGCCGCTAAAGGTCATGTTCCATA-CTGGCATTTGTGGGGAAAGCGCCGCTA
*
7562840 AGGGTCATGTTCTTTAG
64 AAGGTCATGTTCTTTAG
7562857 TTGCATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 4 0.06
86 65 0.93
87 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (85 bp):
TTTGGGGAAAAGCGCCGCTAAAGGTCATGTTCCATACTGGCATTTGTGGGGAAAGCGCCGCTAAA
GGTCATGTTCTTTAGCAGTG
Found at i:7562884 original size:86 final size:86
Alignment explanation
Indices: 7562705--7562900 Score: 222
Period size: 86 Copynumber: 2.3 Consensus size: 86
7562695 GGGAAAAGCG
* * *
7562705 CCGCTAAAGGTCATGTTCTTTA-CTGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCATGTTCTTT
1 CCGCTAAAGGTCATGTTCTATAGCTGGCATTTGTGGGGAAAGCGCCGCTAAAGGTCATGTTCTTT
*
7562769 AGCAGTGTTTGTGGGAAAATT
66 AGCAGTGTTTGTGAGAAAATT
* * * *
7562790 GCCTCTAAAGGTCATGTTCCATAGC-GGCATTTGTGTGGAAAGCGCCGCTAAGGGTCATGTTCTT
1 -CCGCTAAAGGTCATGTTCTATAGCTGGCATTTGTGGGGAAAGCGCCGCTAAAGGTCATGTTCTT
* *
7562854 TAGTTGCA-TTTTTGTGAGAAGCA-T
65 TA---GCAGTGTTTGTGAGAA-AATT
7562878 -CGCTAAAGGTCATGTTCTATAGC
1 CCGCTAAAGGTCATGTTCTATAGC
7562901 AAAATTTTTG
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
86 77 0.83
87 1 0.01
88 11 0.12
89 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (86 bp):
CCGCTAAAGGTCATGTTCTATAGCTGGCATTTGTGGGGAAAGCGCCGCTAAAGGTCATGTTCTTT
AGCAGTGTTTGTGAGAAAATT
Found at i:7562908 original size:43 final size:43
Alignment explanation
Indices: 7562743--7562952 Score: 152
Period size: 43 Copynumber: 4.9 Consensus size: 43
7562733 TTTGTGGGGA
* *** * * *
7562743 AAGCGTCGCTAAAGGTCATGTTCTTTAGCAGTGTTTGTGGGAA
1 AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTTGTGAG
** * * * ** *
7562786 AATTGCCTCTAAAGGTCATGTTCCATAGCGGCATTTGTGTG-G
1 AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTTGTGAG
* * * ***
7562828 AAAGCGCCGCTAAGGGTCATGTTCTTTAGTTGCATTTTTGTGAG
1 -AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTTGTGAG
* * *
7562872 AAGCATCGCTAAAGGTCATGTTCTATAGCAAAATTTTTGTGAA
1 AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTTGTGAG
* * * *
7562915 AAACGTTGCTAAATGTCATGCTCTATAGCAACATTTTT
1 AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTT
7562953 TCACATAAAC
Statistics
Matches: 130, Mismatches: 35, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
43 129 0.99
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (43 bp):
AAGCGTCGCTAAAGGTCATGTTCTATAGCAACATTTTTGTGAG
Found at i:7562933 original size:129 final size:129
Alignment explanation
Indices: 7562699--7562943 Score: 287
Period size: 129 Copynumber: 1.9 Consensus size: 129
7562689 GTTTTGGGGA
* * *
7562699 AAAGCGCCGCTAAAGGTCATGTTCTTTACTGGCGTTTGTGGGGAAAGCGTCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTTCTTTACTGGCATTTGTGGAGAAAGCATCGCTAAAGGTCATGT
* *** ** *
7562764 TCTTTAGCAGTGTTTGTGGGAAAATTGCCTCTAAAGGTCATGTTCCATAGCGGCATTTGTGTGG
66 TCTATAGCAAAATTTGTGGGAAAAACGCCTCTAAAGGTCATGCTCCATAGCGGCATTTGTGTGG
* * * *
7562828 AAAGCGCCGCTAAGGGTCATGTTCTTTAGTTGCATTTTTGTGAG-AAGCATCGCTAAAGGTCATG
1 AAAGCGCCGCTAAAGGTCATGTTCTTTACTGGCATTTGTG-GAGAAAGCATCGCTAAAGGTCATG
* * * * *
7562892 TTCTATAGCAAAATTTTTGTGAAAAACG-TTGCTAAATGTCATGCTCTATAGC
65 TTCTATAGCAAAATTTGTGGGAAAAACGCCT-CTAAAGGTCATGCTCCATAGC
7562944 AACATTTTTT
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
128 1 0.01
129 92 0.97
130 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (129 bp):
AAAGCGCCGCTAAAGGTCATGTTCTTTACTGGCATTTGTGGAGAAAGCATCGCTAAAGGTCATGT
TCTATAGCAAAATTTGTGGGAAAAACGCCTCTAAAGGTCATGCTCCATAGCGGCATTTGTGTGG
Found at i:7562970 original size:44 final size:43
Alignment explanation
Indices: 7562878--7562971 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
7562868 TGAGAAGCAT
* * *
7562878 CGCTAAAGGTCATGTTCTATAGCAAAATTTTTGTGAAAAACGT
1 CGCTAAAGGTCATGCTCTATAGCAAAATTTTTGTCAAAAACGC
* * *
7562921 TGCTAAATGTCATGCTCTATAGCAACATTTTT-TCACATAAACGC
1 CGCTAAAGGTCATGCTCTATAGCAAAATTTTTGTCA-A-AAACGC
7562965 CGCTAAA
1 CGCTAAA
7562972 AACCTGTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.05
43 29 0.69
44 11 0.26
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (43 bp):
CGCTAAAGGTCATGCTCTATAGCAAAATTTTTGTCAAAAACGC
Found at i:7566434 original size:25 final size:25
Alignment explanation
Indices: 7566397--7566489 Score: 104
Period size: 25 Copynumber: 3.9 Consensus size: 25
7566387 AAAGAAAATA
** *
7566397 TTTTAATTTTATATTATCATTCAAG
1 TTTTAATGATATATTATCATACAAG
7566422 TTTTAATGATATA--ATCATACAAG
1 TTTTAATGATATATTATCATACAAG
** *
7566445 TTTTAATTTTATATTATCATGCAAG
1 TTTTAATGATATATTATCATACAAG
7566470 TTTTAATGATATA--ATCATAC
1 TTTTAATGATATATTATCATAC
7566490 CAATTAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
23 26 0.46
25 31 0.54
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (25 bp):
TTTTAATGATATATTATCATACAAG
Found at i:7566438 original size:23 final size:23
Alignment explanation
Indices: 7566407--7566489 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
7566397 TTTTAATTTT
* *
7566407 ATATTATCATTCAAGTTTTAATG
1 ATATAATCATACAAGTTTTAATG
*
7566430 ATATAATCATACAAGTTTTAATTTT
1 ATATAATCATACAAGTTTTAA--TG
* *
7566455 ATATTATCATGCAAGTTTTAATG
1 ATATAATCATACAAGTTTTAATG
7566478 ATATAATCATAC
1 ATATAATCATAC
7566490 CAATTAGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 30 0.60
25 20 0.40
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (23 bp):
ATATAATCATACAAGTTTTAATG
Found at i:7566453 original size:48 final size:48
Alignment explanation
Indices: 7566397--7566489 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
7566387 AAAGAAAATA
*
7566397 TTTTAATTTTATATTATCATTCAAGTTTTAATGATATAATCATACAAG
1 TTTTAATTTTATATTATCATGCAAGTTTTAATGATATAATCATACAAG
7566445 TTTTAATTTTATATTATCATGCAAGTTTTAATGATATAATCATAC
1 TTTTAATTTTATATTATCATGCAAGTTTTAATGATATAATCATAC
7566490 CAATTAGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (48 bp):
TTTTAATTTTATATTATCATGCAAGTTTTAATGATATAATCATACAAG
Found at i:7577462 original size:14 final size:15
Alignment explanation
Indices: 7577428--7577461 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
7577418 CAAAAGGTAT
7577428 AAAAATTCTTAGCAA
1 AAAAATTCTTAGCAA
*
7577443 AAAAATTCTTAGTAA
1 AAAAATTCTTAGCAA
7577458 AAAA
1 AAAA
7577462 TGGAAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAAATTCTTAGCAA
Found at i:7577860 original size:11 final size:11
Alignment explanation
Indices: 7577844--7577906 Score: 71
Period size: 10 Copynumber: 6.1 Consensus size: 11
7577834 TTAAATATTA
7577844 TAAAAAATATG
1 TAAAAAATATG
7577855 T-AAAAATATG
1 TAAAAAATATG
7577865 TAAAAAATAT-
1 TAAAAAATATG
*
7577875 TAAAAATTAT-
1 TAAAAAATATG
* *
7577885 TTAAAAA-ATC
1 TAAAAAATATG
7577895 TAAAAAATATG
1 TAAAAAATATG
7577906 T
1 T
7577907 CGAATAAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 2 0.05
10 30 0.68
11 12 0.27
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (11 bp):
TAAAAAATATG
Found at i:7577870 original size:21 final size:20
Alignment explanation
Indices: 7577844--7577906 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
7577834 TTAAATATTA
7577844 TAAAAAATATGTAAAAATATG
1 TAAAAAATAT-TAAAAATATG
*
7577865 TAAAAAATATTAAAAATTATT
1 TAAAAAATATTAAAAA-TATG
* *
7577886 TAAAAAATCTAAAAAATATG
1 TAAAAAATATTAAAAATATG
7577906 T
1 T
7577907 CGAATAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 10 0.27
21 27 0.73
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAAATATTAAAAATATG
Found at i:7580308 original size:9 final size:9
Alignment explanation
Indices: 7580294--7580370 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
7580284 CATAATAAAA
7580294 TTTTAATAT
1 TTTTAATAT
7580303 TTTTAATAT
1 TTTTAATAT
7580312 TTTTAATA-
1 TTTTAATAT
*
7580320 -ATTAATA-
1 TTTTAATAT
*
7580327 ATTTATATAT
1 TTTTA-ATAT
* **
7580337 TATTACCAT
1 TTTTAATAT
7580346 TTTTAATAAT
1 TTTTAAT-AT
7580356 TTTTAGA-AT
1 TTTTA-ATAT
7580365 TTTTAA
1 TTTTAA
7580371 CAACTATTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
7 6 0.11
8 4 0.07
9 33 0.61
10 10 0.19
11 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTAATAT
Found at i:7590747 original size:220 final size:219
Alignment explanation
Indices: 7590365--7590801 Score: 775
Period size: 220 Copynumber: 2.0 Consensus size: 219
7590355 TGGATGTGAC
* *
7590365 ATCTTATTACTTCGGAACAAGAAGGTCTTAACATCAAATTCGATTTATTCAGGTTTTTAAAGAGG
1 ATCTTATTACTTCGGAACAAGAAGGTCTTAACATCAAATTCAATTTATTCAGGTTTTTAAAAAGG
7590430 ATCGTATTTTAAAATCTTTTCAAATTTTCGACATTAGGACGTTAATTAATCAATTAGGTACCAAT
66 ATCGTATTTTAAAATCTTTTCAAATTTTCGACATTAGGACGTTAATTAATCAATTAGGTACCAAT
* * *
7590495 TTTTGGGCGTACGAGGGTGCTAATCCTTCCTCGTGCATAACCGACCCCCTGAGCCCGTTTTCTCG
131 TTTTGGGCGTACGAGGGTGCTAATCCTTCCTCGTGCATAACCGACCCCC-AAACCCATTTTCTCG
*
7590560 GATTTTGTAGACCAAAATCATTAAA
195 AATTTTGTAGACCAAAATCATTAAA
*
7590585 ATCTTATTACTTCGGGACAAGAAGGTCTTAACATCAAATTCAATTTATTCAGGTTTTTAAAAAGG
1 ATCTTATTACTTCGGAACAAGAAGGTCTTAACATCAAATTCAATTTATTCAGGTTTTTAAAAAGG
* *
7590650 GTCGTATTTTAAAATCTTTTCAAATTTTTGACATTAGGACGTTAATTAATCAATTAGGTACCAAT
66 ATCGTATTTTAAAATCTTTTCAAATTTTCGACATTAGGACGTTAATTAATCAATTAGGTACCAAT
*
7590715 TTTTGGGCGTTCGAGGGTGCTAATCCTTCCTCGTGCATAACCGACCCCCAAACCCATTTTCTCGA
131 TTTTGGGCGTACGAGGGTGCTAATCCTTCCTCGTGCATAACCGACCCCCAAACCCATTTTCTCGA
7590780 ATTTTGTAGACCAAAATCATTA
196 ATTTTGTAGACCAAAATCATTA
7590802 TTTTAATAAA
Statistics
Matches: 207, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
219 34 0.16
220 173 0.84
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (219 bp):
ATCTTATTACTTCGGAACAAGAAGGTCTTAACATCAAATTCAATTTATTCAGGTTTTTAAAAAGG
ATCGTATTTTAAAATCTTTTCAAATTTTCGACATTAGGACGTTAATTAATCAATTAGGTACCAAT
TTTTGGGCGTACGAGGGTGCTAATCCTTCCTCGTGCATAACCGACCCCCAAACCCATTTTCTCGA
ATTTTGTAGACCAAAATCATTAAA
Found at i:7594076 original size:7 final size:7
Alignment explanation
Indices: 7594066--7594142 Score: 67
Period size: 6 Copynumber: 11.7 Consensus size: 7
7594056 AAAAAGAGAA
7594066 AAAAATC
1 AAAAATC
7594073 AAAAATC
1 AAAAATC
7594080 AAAAAT-
1 AAAAATC
*
7594086 TAAAAT-
1 AAAAATC
*
7594092 TAAAAT-
1 AAAAATC
*
7594098 AAAAATA
1 AAAAATC
7594105 AAATAATC
1 AAA-AATC
7594113 -AAAATC
1 AAAAATC
*
7594119 -AAAATA
1 AAAAATC
7594125 AAAAATC
1 AAAAATC
7594132 -AAAATC
1 AAAAATC
7594138 AAAAA
1 AAAAA
7594143 ATGAAAATGA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
6 31 0.51
7 27 0.44
8 3 0.05
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATC
Found at i:7594096 original size:19 final size:19
Alignment explanation
Indices: 7594074--7594142 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
7594064 AAAAAAATCA
7594074 AAAATCAAAAATTAAAATT
1 AAAATCAAAAATTAAAATT
7594093 AAAAT-AAAAA-TAAAATAAT
1 AAAATCAAAAATTAAAAT--T
* *
7594112 CAAAATC-AAAATAAAAAATC
1 -AAAATCAAAAAT-TAAAATT
7594132 AAAATCAAAAA
1 AAAATCAAAAA
7594143 ATGAAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
17 6 0.15
18 5 0.12
19 12 0.29
20 13 0.32
22 5 0.12
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATCAAAAATTAAAATT
Found at i:7594096 original size:26 final size:25
Alignment explanation
Indices: 7594067--7594141 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 25
7594057 AAAAGAGAAA
* *
7594067 AAAATCAAAAATCAAAAATTAAAATT
1 AAAAT-AAAAATCAAAAATCAAAATC
*
7594093 AAAATAAAAATAAAATAATCAAAATC
1 AAAATAAAAATCAAA-AATCAAAATC
7594119 AAAATAAAAAATC-AAAATCAAAA
1 AAAAT-AAAAATCAAAAATCAAAA
7594142 AATGAAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 17 0.40
26 20 0.47
27 6 0.14
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (25 bp):
AAAATAAAAATCAAAAATCAAAATC
Found at i:7594130 original size:33 final size:31
Alignment explanation
Indices: 7594066--7594150 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
7594056 AAAAAGAGAA
* * *
7594066 AAAAATCAAAAATCAAAAATTAAAATTAAAAT
1 AAAAATAAAAAATC-AAAATCAAAATAAAAAT
7594098 AAAAATAAAATAATCAAAATCAAAATAAAAAAT
1 AAAAATAAAA-AATCAAAATCAAAAT-AAAAAT
* *
7594131 CAAAATCAAAAAATGAAAAT
1 AAAAAT-AAAAAATCAAAAT
7594151 GATAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 19 0.42
33 22 0.49
34 4 0.09
ACGTcount: A:0.73, C:0.07, G:0.01, T:0.19
Consensus pattern (31 bp):
AAAAATAAAAAATCAAAATCAAAATAAAAAT
Found at i:7594143 original size:14 final size:13
Alignment explanation
Indices: 7594067--7594150 Score: 75
Period size: 13 Copynumber: 6.4 Consensus size: 13
7594057 AAAAGAGAAA
*
7594067 AAAATCAAAAATC
1 AAAATAAAAAATC
* *
7594080 AAAA-ATTAAAATT
1 AAAATA-AAAAATC
7594093 AAAAT-AAAAAT-
1 AAAATAAAAAATC
7594104 AAAATAATCAAAATC
1 AAAATAA--AAAATC
7594119 AAAATAAAAAATC
1 AAAATAAAAAATC
*
7594132 AAAATCAAAAAATG
1 AAAAT-AAAAAATC
7594146 AAAAT
1 AAAAT
7594151 GATAAAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 5 0.08
12 6 0.10
13 24 0.41
14 17 0.29
15 7 0.12
ACGTcount: A:0.73, C:0.07, G:0.01, T:0.19
Consensus pattern (13 bp):
AAAATAAAAAATC
Found at i:7594150 original size:20 final size:18
Alignment explanation
Indices: 7594067--7594142 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 18
7594057 AAAAGAGAAA
7594067 AAAATCAAAAATCAAAAATT
1 AAAATC-AAAATCAAAAA-T
*
7594087 AAAATTAAAAT-AAAAAT
1 AAAATCAAAATCAAAAAT
*
7594104 AAAATAATCAAAATCAAAATAA
1 --AA-AATCAAAATCAAAA-AT
7594126 AAAATCAAAATCAAAAA
1 AAAATCAAAATCAAAAA
7594143 ATGAAAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.02
18 6 0.12
19 21 0.44
20 15 0.31
21 4 0.08
22 1 0.02
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAATCAAAATCAAAAAT
Found at i:7594157 original size:14 final size:13
Alignment explanation
Indices: 7594074--7594157 Score: 66
Period size: 14 Copynumber: 6.3 Consensus size: 13
7594064 AAAAAAATCA
7594074 AAAATCAAAA-ATT
1 AAAATCAAAATA-T
*
7594087 AAAATTAAAATA-
1 AAAATCAAAATAT
7594099 AAAAT-AAAATAAT
1 AAAATCAAAAT-AT
*
7594112 CAAAATCAAAATAA
1 -AAAATCAAAATAT
*
7594126 AAAATCAAAATCAA
1 AAAATCAAAAT-AT
*
7594140 AAAATGAAAATGAT
1 AAAATCAAAAT-AT
7594154 AAAA
1 AAAA
7594158 AAAGGAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
11 5 0.08
12 6 0.10
13 20 0.33
14 24 0.40
15 5 0.08
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAATCAAAATAT
Found at i:7596729 original size:169 final size:168
Alignment explanation
Indices: 7596530--7596989 Score: 672
Period size: 169 Copynumber: 2.7 Consensus size: 168
7596520 CCTGGCGTGA
* *
7596530 CAGCGAATCCTATCTCTTTGGCATTACAGTGGAACAAATTAAAGCTAAATGTAGCGAATCTTGTT
1 CAGCGAATCCTATCTCTTTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTT
*
7596595 TCCCTATCGTTGTAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTAATCTCCCTGACGTTAAG
66 TCCCTAGCGTTGTAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTAATCTCCCTGA-GTTAAG
*
7596660 ACTT-GAAATGGCTGAAGTGGAGCGGATTAAAGCTGTGGG
130 ACTTAG-AATAGCTGAAGTGGAGCGGATTAAAGCTGTGGG
* * * *
7596699 CAGCGAATCCTATCTCTTTGGCGTTACAGTGAAACAGATTAAAGCTAAAGGTAGCGAATTTTATT
1 CAGCGAATCCTATCTCTTTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTT
** * * *
7596764 TCCCGGGCGTTGAAGCGGAGCAGATTAAAGCTGAGGGCAACGAATC-ATTTCTCCCTAGAGTTAA
66 TCCCTAGCGTTGTAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTA-ATCTCCCT-GAGTTAA
7596828 GACTTAGAATAGCTGAAGTGGAGCGGATTAAAGCTGTGGG
129 GACTTAGAATAGCTGAAGTGGAGCGGATTAAAGCTGTGGG
* * * * *
7596868 CAGTGAATCCTATCTCTTTGGCCTTACAGTAGAACAGATTAAAGCTAAAGGTAGCGAGTCTGGTT
1 CAGCGAATCCTATCTCTTTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTT
* * * *
7596933 TCCCTAGCGTTGTAGCGGAGTAGATTAAAGTTGAAGGCAGCGAATCTCATCTCCCTG
66 TCCCTAGCGTTGTAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTAATCTCCCTG
7596990 GTGTTAAAAT
Statistics
Matches: 257, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
168 2 0.01
169 252 0.98
170 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (168 bp):
CAGCGAATCCTATCTCTTTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTGTT
TCCCTAGCGTTGTAGCGGAGCAGATTAAAGCTGAGGGCAGCGAATCTAATCTCCCTGAGTTAAGA
CTTAGAATAGCTGAAGTGGAGCGGATTAAAGCTGTGGG
Found at i:7597277 original size:89 final size:89
Alignment explanation
Indices: 7597153--7597326 Score: 206
Period size: 89 Copynumber: 2.0 Consensus size: 89
7597143 TCTTATCTCC
* * * * * *
7597153 CTGAGTTTACAGCGAAACAGACTGAAGATAACAAATCTTATCTTCTTGTA-TTGACAGCGAAGCA
1 CTGAGTTTACAGCGAAACAAACTGAAAACAACAAATCTTATCTTCCTGTACTAG-CAACGAAGCA
* *
7597217 AATTGAAGACACCAGCCTTGCCTCT
65 AATCGAAAACACCAGCCTTGCCTCT
* * * * * *
7597242 CTGAGTTTACAGCGGAGCAAACTGAAAACAGCAAATCTTGTCTTCCTGTACTAGCAATGAAGCAG
1 CTGAGTTTACAGCGAAACAAACTGAAAACAACAAATCTTATCTTCCTGTACTAGCAACGAAGCAA
7597307 ATCGAAAACACCAGCCTTGC
66 ATCGAAAACACCAGCCTTGC
7597327 TTCCTTGAGC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
89 68 0.97
90 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (89 bp):
CTGAGTTTACAGCGAAACAAACTGAAAACAACAAATCTTATCTTCCTGTACTAGCAACGAAGCAA
ATCGAAAACACCAGCCTTGCCTCT
Found at i:7599581 original size:5 final size:5
Alignment explanation
Indices: 7599571--7599595 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
7599561 TTTTTTACAA
7599571 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
7599596 GCGGATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:7605614 original size:18 final size:20
Alignment explanation
Indices: 7605591--7605632 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
7605581 CTCATTATTG
*
7605591 TAATTATTTT-T-ATATTAA
1 TAATTATTTTATAATAGTAA
7605609 TAATTATTTTATAATAGTAA
1 TAATTATTTTATAATAGTAA
7605629 TAAT
1 TAAT
7605633 AAGCTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TAATTATTTTATAATAGTAA
Found at i:7605629 original size:17 final size:18
Alignment explanation
Indices: 7605590--7605629 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
7605580 TCTCATTATT
*
7605590 GTAATTATTTTTATATTA
1 GTAATTATTTTTATAATA
*
7605608 ATAATTA-TTTTATAATA
1 GTAATTATTTTTATAATA
7605625 GTAAT
1 GTAAT
7605630 AATAAGCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
GTAATTATTTTTATAATA
Found at i:7608597 original size:43 final size:44
Alignment explanation
Indices: 7608547--7608644 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
7608537 TCCCAGATGT
*
7608547 GGTCTTACATGT-AATC-AAATATCAAAGCCA-CAGTCCCAGACAG
1 GGTCTTACACGTAAATCTAAAT-TCAAAGCCATCA-TCCCAGACAG
* * * *
7608590 GGTCTTACACGTAAATCTCAATTCGATGCCATCATCCCAGACAT
1 GGTCTTACACGTAAATCTAAATTCAAAGCCATCATCCCAGACAG
7608634 GGTCTTACACG
1 GGTCTTACACG
7608645 ATAACTCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 11 0.23
44 31 0.66
45 5 0.11
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (44 bp):
GGTCTTACACGTAAATCTAAATTCAAAGCCATCATCCCAGACAG
Found at i:7629577 original size:12 final size:13
Alignment explanation
Indices: 7629554--7629579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7629544 TCAATGAACC
7629554 CTTAATTTTTTTG
1 CTTAATTTTTTTG
7629567 CTTAATTTTTTTG
1 CTTAATTTTTTTG
7629580 GTACTCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
CTTAATTTTTTTG
Found at i:7631035 original size:12 final size:12
Alignment explanation
Indices: 7631005--7631037 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7630995 ATGCAACAGG
7631005 AAACCAGCA-GC
1 AAACCAGCATGC
7631016 AAACCAGCATGC
1 AAACCAGCATGC
*
7631028 AGACCAGCAT
1 AAACCAGCAT
7631038 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:7631963 original size:21 final size:21
Alignment explanation
Indices: 7631937--7631989 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
7631927 CGCTGTTTCT
*
7631937 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
* * *
7631958 AATCTCACCGCTGCAGTAACT
1 AATCTCACCGCTACAATAACC
7631979 AATCTCACCGC
1 AATCTCACCGC
7631990 CACCGCTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:7639084 original size:28 final size:29
Alignment explanation
Indices: 7639025--7639082 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
7639015 AAATATTTTT
* * *
7639025 AATTAATAATTTTGTTATTTATATAAATA
1 AATTAATAATTATGATAGTTATATAAATA
7639054 AATTAATAATTAT-ATAGTTATAT-AATA
1 AATTAATAATTATGATAGTTATATAAATA
7639081 AA
1 AA
7639083 ATATATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 8 0.31
29 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
AATTAATAATTATGATAGTTATATAAATA
Found at i:7639137 original size:17 final size:18
Alignment explanation
Indices: 7639112--7639149 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
7639102 ATCATTGTGT
*
7639112 TAAATATATTTATTT-TA
1 TAAAAATATTTATTTATA
7639129 TAAAAATATTTATTTATA
1 TAAAAATATTTATTTATA
7639147 TAA
1 TAA
7639150 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAAATATTTATTTATA
Found at i:7640234 original size:21 final size:21
Alignment explanation
Indices: 7640189--7640236 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7640179 AACCCTGCTA
* *
7640189 TTTTGCTGTGGTTTTTTCATG
1 TTTTGCTATGGTTTTTCCATG
7640210 TTTTGCTATGGTTTTTCCACT-
1 TTTTGCTATGGTTTTTCCA-TG
7640231 TTTTGC
1 TTTTGC
7640237 CATTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.06, C:0.15, G:0.19, T:0.60
Consensus pattern (21 bp):
TTTTGCTATGGTTTTTCCATG
Found at i:7640281 original size:19 final size:20
Alignment explanation
Indices: 7640238--7640281 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
7640228 ACTTTTTGCC
*
7640238 ATTATTTTGCTACTATTTCAGT
1 ATTATGTTGCTACTATTT-A-T
7640260 ATTATGTTGCTACTATTT-T
1 ATTATGTTGCTACTATTTAT
7640279 ATT
1 ATT
7640282 GTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
22 17 0.81
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTATGTTGCTACTATTTAT
Found at i:7641476 original size:10 final size:10
Alignment explanation
Indices: 7641453--7641490 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
7641443 AATTTAAAAT
7641453 TAAAAA-ATA
1 TAAAAATATA
*
7641462 CAAAAATATA
1 TAAAAATATA
*
7641472 TAAAAACATA
1 TAAAAATATA
7641482 TAAAAATAT
1 TAAAAATAT
7641491 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAAAATATA
Found at i:7641497 original size:20 final size:20
Alignment explanation
Indices: 7641451--7641498 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
7641441 AAAATTTAAA
7641451 ATTAAAAAATACAAAAATAT
1 ATTAAAAAATACAAAAATAT
*
7641471 A-TAAAAACATATAAAAATAT
1 ATTAAAAA-ATACAAAAATAT
*
7641491 TTTAAAAA
1 ATTAAAAA
7641499 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 12 0.50
21 6 0.25
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
ATTAAAAAATACAAAAATAT
Found at i:7646818 original size:11 final size:11
Alignment explanation
Indices: 7646802--7646839 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7646792 AAAAAAAAAG
7646802 TTTTTTT-TTA
1 TTTTTTTGTTA
7646812 TTTTTTTGTTA
1 TTTTTTTGTTA
* *
7646823 TTTTCTTGTTG
1 TTTTTTTGTTA
7646834 TTTTTT
1 TTTTTT
7646840 CACTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTGTTA
Found at i:7647465 original size:31 final size:31
Alignment explanation
Indices: 7647407--7647465 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
7647397 AAACCCTAAA
* * *
7647407 GCCTTAATGTAAGAATAATTGCAAAGTTTAG
1 GCCTCAATGTAAGAACAACTGCAAAGTTTAG
* *
7647438 GCCTCAATGTGAGAACAACTGCCAAGTT
1 GCCTCAATGTAAGAACAACTGCAAAGTT
7647466 CAGGGACTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (31 bp):
GCCTCAATGTAAGAACAACTGCAAAGTTTAG
Found at i:7648519 original size:16 final size:17
Alignment explanation
Indices: 7648492--7648532 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
7648482 TGGTAAAGTA
7648492 AATAAA-AAAGT-AAAT
1 AATAAATAAAGTAAAAT
7648507 AATAAATAAAGTAAAAT
1 AATAAATAAAGTAAAAT
7648524 ATATAAATA
1 A-ATAAATA
7648533 TATAATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 5 0.22
17 5 0.22
18 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
AATAAATAAAGTAAAAT
Found at i:7649219 original size:122 final size:122
Alignment explanation
Indices: 7649002--7649248 Score: 494
Period size: 122 Copynumber: 2.0 Consensus size: 122
7648992 CGTAGCATTG
7649002 GAACTGCTATGTAGACTCTTGTTTACCAAGGGTTCGAATCCCTCTCTTTCCACATTACCTTCACC
1 GAACTGCTATGTAGACTCTTGTTTACCAAGGGTTCGAATCCCTCTCTTTCCACATTACCTTCACC
7649067 TAATTCGTCAATGTAACTGACTACAATGTATCAAATCAAATAAGAACATACACTAAA
66 TAATTCGTCAATGTAACTGACTACAATGTATCAAATCAAATAAGAACATACACTAAA
7649124 GAACTGCTATGTAGACTCTTGTTTACCAAGGGTTCGAATCCCTCTCTTTCCACATTACCTTCACC
1 GAACTGCTATGTAGACTCTTGTTTACCAAGGGTTCGAATCCCTCTCTTTCCACATTACCTTCACC
7649189 TAATTCGTCAATGTAACTGACTACAATGTATCAAATCAAATAAGAACATACACTAAA
66 TAATTCGTCAATGTAACTGACTACAATGTATCAAATCAAATAAGAACATACACTAAA
7649246 GAA
1 GAA
7649249 TTAGACCCTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (122 bp):
GAACTGCTATGTAGACTCTTGTTTACCAAGGGTTCGAATCCCTCTCTTTCCACATTACCTTCACC
TAATTCGTCAATGTAACTGACTACAATGTATCAAATCAAATAAGAACATACACTAAA
Found at i:7666159 original size:63 final size:61
Alignment explanation
Indices: 7666074--7666235 Score: 216
Period size: 63 Copynumber: 2.6 Consensus size: 61
7666064 TGCACCAGGT
* * * *
7666074 GAATCAAATGCCTGCTTTGCAACATCCTTCTGCTCTAAGTTCTGTTTGTTGGGAGGAGGAGGA
1 GAATCAAATGCC-GCTTTGCAACATCCTTCTGCTC-AAGTTATGTTCGTTGGAAGCAGGAGGA
* *
7666137 GAATCAAATGCTCGCTTCGCAACATCCTTCTGTTGCAAGTTATGTTCGTTGGAAGCAGGAGGA
1 GAATCAAATGC-CGCTTTGCAACATCCTTCTGCT-CAAGTTATGTTCGTTGGAAGCAGGAGGA
*
7666200 GAATCAAATGCCCGCTTTGCAACATCCTTCCGCTCA
1 GAATCAAATG-CCGCTTTGCAACATCCTTCTGCTCA
7666236 TAGCTGTGAC
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 2 0.02
63 82 0.94
64 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (61 bp):
GAATCAAATGCCGCTTTGCAACATCCTTCTGCTCAAGTTATGTTCGTTGGAAGCAGGAGGA
Found at i:7666413 original size:6 final size:6
Alignment explanation
Indices: 7666404--7666431 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7666394 ACTCCCACTG
7666404 CGGCTA CGGCTA CGGCTA CGGCTA CGGC
1 CGGCTA CGGCTA CGGCTA CGGCTA CGGC
7666432 GCCAAGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (6 bp):
CGGCTA
Found at i:7666808 original size:33 final size:33
Alignment explanation
Indices: 7666680--7666810 Score: 160
Period size: 33 Copynumber: 4.1 Consensus size: 33
7666670 CCCTCCAGGA
* * *
7666680 CCACCAAAGCCACTATCCCTCATACCACCACGA
1 CCACCAAAGCCACCATCCCTCATTCCACCACGG
* * * *
7666713 CCGCCAAA---ACCATCTCTCATGCCACCACGC
1 CCACCAAAGCCACCATCCCTCATTCCACCACGG
*
7666743 CCACCAAAGCCCCCATCCCTCATTCCACCACGG
1 CCACCAAAGCCACCATCCCTCATTCCACCACGG
*
7666776 CCACCAAAGCCTCCATCCCTCATTCCACCACGG
1 CCACCAAAGCCACCATCCCTCATTCCACCACGG
7666809 CC
1 CC
7666811 TCCAGAATCC
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.30
33 59 0.70
ACGTcount: A:0.27, C:0.52, G:0.08, T:0.13
Consensus pattern (33 bp):
CCACCAAAGCCACCATCCCTCATTCCACCACGG
Found at i:7672458 original size:392 final size:392
Alignment explanation
Indices: 7671734--7672516 Score: 1485
Period size: 392 Copynumber: 2.0 Consensus size: 392
7671724 ATTTTCCAAT
*
7671734 CAGTAGCAATTCAGACTACTAGTCATATATCAATTAATAAGACCCTAAAACAAGAATTACATAAA
1 CAGTAGCAATTCAGACTACCAGTCATATATCAATTAATAAGACCCTAAAACAAGAATTACATAAA
7671799 CAAAGAAACAAGATAATTGAATCTGACATCCAATACACCAAATAGCATTGGTAATACAATTATAC
66 CAAAGAAACAAGATAATTGAATCTGACATCCAATACACCAAATAGCATTGGTAATACAATTATAC
* *
7671864 ATACAAGAGAAAGTGAAAATGGACAAGCCTATTATTGAACAACAAATCTCAAGTAAAACGTTTTT
131 ATACAAAAGAAAGTGAAAATGGACAAGCCTATTATTGAACAACAAATCTCAAGTAAAACCTTTTT
*
7671929 TTCCCTTCCCATACTTACATGGGAGGGGAGAAAGCAACAGAACAGCAATTCCTTAATTAAAAGAG
196 TTCCCTTCCCATACTTACATGGGAGGGGAGAAAACAACAGAACAGCAATTCCTTAATTAAAAGAG
7671994 TCAATCAAAAGAGATGATAAGATAATCCAAAAAGGGAATCCTATAAGCAAACCACATGGTCAAGA
261 TCAATCAAAAGAGATGATAAGATAATCCAAAAAGGGAATCCTATAAGCAAACCACATGGTCAAGA
7672059 AAGAGGCTTCTATCTTTGTTGCTCAAAACCAAAACCCCCATGAAATAAACAAAAAGGAACAAGAA
326 AAGAGGCTTCTATCTTTGTTGCTCAAAACCAAAACCCCCATGAAATAAACAAAAAGGAACAAGAA
7672124 AG
391 AG
7672126 CAGTAGCAATTCAGACTACCAGTCATATATCAATTAATAAGACCCTAAAACAAGAATTACATAAA
1 CAGTAGCAATTCAGACTACCAGTCATATATCAATTAATAAGACCCTAAAACAAGAATTACATAAA
* * *
7672191 CAAAGAAACAAGATAATTGAATCTGGCATCCAATACACCAAATGGCATTGGTAATGCAATTATAC
66 CAAAGAAACAAGATAATTGAATCTGACATCCAATACACCAAATAGCATTGGTAATACAATTATAC
7672256 ATACAAAAGAAAGTGAAAATGGACAAGCCTATTATTGAACAACAAATCTCAAGTAAAACCTTTTT
131 ATACAAAAGAAAGTGAAAATGGACAAGCCTATTATTGAACAACAAATCTCAAGTAAAACCTTTTT
*
7672321 TTCCCTTCCCATACTTACATGGGAGGGGAGAAAACAACAGAACAGCAATTCCTTAATTAAAAGGG
196 TTCCCTTCCCATACTTACATGGGAGGGGAGAAAACAACAGAACAGCAATTCCTTAATTAAAAGAG
*
7672386 TCAATCAAAAGAGATGATAAGATAATCCAAAAAGGGAATCCTATAAGCAATCCACATGGTCAAGA
261 TCAATCAAAAGAGATGATAAGATAATCCAAAAAGGGAATCCTATAAGCAAACCACATGGTCAAGA
7672451 AAGAGGCTTCTATCTTTGTTGCTCAAAACCAAAACCCCCATGAAATAAACAAAAAGGAACAAGAA
326 AAGAGGCTTCTATCTTTGTTGCTCAAAACCAAAACCCCCATGAAATAAACAAAAAGGAACAAGAA
7672516 A
391 A
7672517 ACAATAGAGA
Statistics
Matches: 382, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
392 382 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (392 bp):
CAGTAGCAATTCAGACTACCAGTCATATATCAATTAATAAGACCCTAAAACAAGAATTACATAAA
CAAAGAAACAAGATAATTGAATCTGACATCCAATACACCAAATAGCATTGGTAATACAATTATAC
ATACAAAAGAAAGTGAAAATGGACAAGCCTATTATTGAACAACAAATCTCAAGTAAAACCTTTTT
TTCCCTTCCCATACTTACATGGGAGGGGAGAAAACAACAGAACAGCAATTCCTTAATTAAAAGAG
TCAATCAAAAGAGATGATAAGATAATCCAAAAAGGGAATCCTATAAGCAAACCACATGGTCAAGA
AAGAGGCTTCTATCTTTGTTGCTCAAAACCAAAACCCCCATGAAATAAACAAAAAGGAACAAGAA
AG
Found at i:7674619 original size:17 final size:18
Alignment explanation
Indices: 7674570--7674610 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
7674560 AGCTTTTACT
* *
7674570 CAAAAGTACTTTTTGGCC
1 CAAAAATACTTTCTGGCC
7674588 CAAAAATACTTTCTGGCC
1 CAAAAATACTTTCTGGCC
7674606 CAAAA
1 CAAAA
7674611 GTGCTTCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (18 bp):
CAAAAATACTTTCTGGCC
Found at i:7682253 original size:30 final size:30
Alignment explanation
Indices: 7682181--7682318 Score: 111
Period size: 30 Copynumber: 4.7 Consensus size: 30
7682171 TGTGCATAAC
* *
7682181 CCTATGGCGAACTCCCTTATGATGAACTCT
1 CCTATGGCGAACTCCCTTATGGTGAACTCA
** * **
7682211 CCTACAGTGAACTCCCTTATGGCAAACTCA
1 CCTATGGCGAACTCCCTTATGGTGAACTCA
*
7682241 CGTATGGCGAACT-CCTTATGGTGAACTCA
1 CCTATGGCGAACTCCCTTATGGTGAACTCA
* * ** * *
7682270 CATGTGGAAAACT-ACTCTATGGAGAACTC-
1 CCTATGGCGAACTCCCT-TATGGTGAACTCA
*
7682299 CCTATGGCGAACTCACTTAT
1 CCTATGGCGAACTCCCTTAT
7682319 CGTTGATCTG
Statistics
Matches: 83, Mismatches: 23, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
29 37 0.45
30 46 0.55
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (30 bp):
CCTATGGCGAACTCCCTTATGGTGAACTCA
Found at i:7697399 original size:5 final size:5
Alignment explanation
Indices: 7697377--7697414 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
7697367 GGAAAGAAAG
*
7697377 AAGGA AA-GA AAGGG AAGGA AAGGA AAGGA AAGGA AAGG
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGG
7697415 GAGGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:7727415 original size:44 final size:43
Alignment explanation
Indices: 7727305--7727417 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 43
7727295 AGCTCGTACA
* * *
7727305 ATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAACATAG
** * * *
7727348 ATGCCATTGTACTAGACAG-GGTCTTACACGTAAATCTCAA-ATAG
1 ATGCCAACGTCCCAGAC-GTGGTCTTACACGT-AATC-AAACATAG
7727392 ATGCCAACGTCCCAGACGTGGTCTTA
1 ATGCCAACGTCCCAGACGTGGTCTTA
7727418 TACGATAACT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
43 24 0.44
44 28 0.52
45 2 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAACATAG
Done.