Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 186 of 221
Found at i:55052017 original size:28 final size:27
Alignment explanation
Indices: 55051984--55052045 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
55051974 TTCATTTTTT
55051984 TATTTTTAG-TTT-TTCATTTTTTTGAAA
1 TATTTTTAGATTTATT--TTTTTTTGAAA
*
55052011 TATTTTTCGATTTGATTTTTTTTTGAAA
1 TATTTTTAGATTT-ATTTTTTTTTGAAA
55052039 TATTTTT
1 TATTTTT
55052046 TTGGATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 8 0.26
28 21 0.68
30 2 0.06
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (27 bp):
TATTTTTAGATTTATTTTTTTTTGAAA
Found at i:55053556 original size:25 final size:25
Alignment explanation
Indices: 55053522--55053569 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
55053512 CTCGCCCTCA
*
55053522 TACTCCAAGAAACAACGTCAATCAG
1 TACTCCAAGAAACAACATCAATCAG
55053547 TACTCCAAGAAACAACATCAATC
1 TACTCCAAGAAACAACATCAATC
55053570 TTTCCTTCAT
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:0.29, G:0.08, T:0.17
Consensus pattern (25 bp):
TACTCCAAGAAACAACATCAATCAG
Found at i:55055811 original size:19 final size:20
Alignment explanation
Indices: 55055787--55055824 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
55055777 CAGCATATCA
55055787 TAATAAAACA-AAATTTTAG
1 TAATAAAACATAAATTTTAG
*
55055806 TAATAATACATAAATTTTA
1 TAATAAAACATAAATTTTA
55055825 AAACAAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
TAATAAAACATAAATTTTAG
Found at i:55056025 original size:15 final size:14
Alignment explanation
Indices: 55056007--55056045 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
55055997 TAATAATAGC
55056007 AATAATAATATTAA
1 AATAATAATATTAA
55056021 AA-ATATATATATTAA
1 AATA-ATA-ATATTAA
55056036 AATAATAATA
1 AATAATAATA
55056046 AATATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.05
14 8 0.36
15 12 0.55
16 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATAATATTAA
Found at i:55056066 original size:22 final size:22
Alignment explanation
Indices: 55056025--55056066 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
55056015 TATTAAAAAT
*
55056025 ATATATATTAAAATAATAATAA
1 ATATATATTAAAAAAATAATAA
55056047 ATATA-ATTAAAAAAACTAAT
1 ATATATATTAAAAAAA-TAAT
55056067 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATATATTAAAAAAATAATAA
Found at i:55056623 original size:5 final size:5
Alignment explanation
Indices: 55056615--55056655 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
55056605 TTTTATTCGC
* *
55056615 AAATA AAATA AAATA AAAT- AAATC AAAGA AAA-A AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
55056656 ATCAGTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:55056630 original size:10 final size:10
Alignment explanation
Indices: 55056615--55056655 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
55056605 TTTTATTCGC
55056615 AAATAAAATA
1 AAATAAAATA
55056625 AAATAAAAT-
1 AAATAAAATA
* *
55056634 AAATCAAAGA
1 AAATAAAATA
55056644 AAA-AAAATA
1 AAATAAAATA
55056653 AAA
1 AAA
55056656 ATCAGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (10 bp):
AAATAAAATA
Found at i:55059976 original size:55 final size:55
Alignment explanation
Indices: 55059853--55059979 Score: 148
Period size: 55 Copynumber: 2.3 Consensus size: 55
55059843 TTAATGAAAG
* * * * *
55059853 CAAGTCAGTGATTTACATGGGCTAGTCACACGGACGTGTGGTTAGCCGCGTGACC
1 CAAGTCAGTGAGTTACATGGACTAGTCACACAGACATGTGGCTAGCCGCGTGACC
** * *
55059908 CAAGTCAACGAGTTACATGGACTAGTCACACA-AGCATGTGGCTGGCCGTGTGACC
1 CAAGTCAGTGAGTTACATGGACTAGTCACACAGA-CATGTGGCTAGCCGCGTGACC
*
55059963 CAAGTTAGTGAGTTACA
1 CAAGTCAGTGAGTTACA
55059980 CGGGTGGGGA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 1 0.02
55 58 0.98
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (55 bp):
CAAGTCAGTGAGTTACATGGACTAGTCACACAGACATGTGGCTAGCCGCGTGACC
Found at i:55066628 original size:55 final size:55
Alignment explanation
Indices: 55066544--55066667 Score: 176
Period size: 55 Copynumber: 2.3 Consensus size: 55
55066534 TTAATGAAAG
* * *
55066544 TAAGTCAGTAAGTTGCATGGGCTAGTCACATAGGCGTGTGGTTGGCCATGTGACC
1 TAAGTCAGTGAGTTCCACGGGCTAGTCACATAGGCGTGTGGTTGGCCATGTGACC
* * *
55066599 TAAGTCAGTGAGTTCCACGGGCTAGTCACATGGGTGTGTGGTTGGCCGTGTGACC
1 TAAGTCAGTGAGTTCCACGGGCTAGTCACATAGGCGTGTGGTTGGCCATGTGACC
* *
55066654 CAATTCAGTGAGTT
1 TAAGTCAGTGAGTT
55066668 ACATGGGGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (55 bp):
TAAGTCAGTGAGTTCCACGGGCTAGTCACATAGGCGTGTGGTTGGCCATGTGACC
Found at i:55066822 original size:43 final size:43
Alignment explanation
Indices: 55066735--55066823 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
55066725 ATGGACTGAG
* * ** *
55066735 ACACGGATGTGTCTCTTGGCCGTGTAAGACACACGGTTTGGCC
1 ACACAGATGCGTCTCTTGGCCGTGTAAGACACACGGCCTAGCC
*
55066778 ACACAGATGCGTCTCTTGGCCGTGTGAGACACACGGCCTAGCC
1 ACACAGATGCGTCTCTTGGCCGTGTAAGACACACGGCCTAGCC
55066821 ACA
1 ACA
55066824 TAGACGTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.21
Consensus pattern (43 bp):
ACACAGATGCGTCTCTTGGCCGTGTAAGACACACGGCCTAGCC
Found at i:55070720 original size:12 final size:12
Alignment explanation
Indices: 55070705--55070752 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
55070695 GAAATTTGAT
55070705 TTTTTTTCTCTC
1 TTTTTTTCTCTC
*
55070717 TTTTTTT-TCAC
1 TTTTTTTCTCTC
*
55070728 TTTCTTTTTTACTC
1 TTT-TTTTCT-CTC
55070742 TTTTTTTCTCT
1 TTTTTTTCTCT
55070753 TATAATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.20
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:55071479 original size:21 final size:21
Alignment explanation
Indices: 55071450--55071491 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55071440 TGTTAACAAA
* *
55071450 ACAATAATATTAGCGGTGTTG
1 ACAAAAATATTAGAGGTGTTG
55071471 ACAAAAATATTAGAGGTGTTG
1 ACAAAAATATTAGAGGTGTTG
55071492 TTAGGATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (21 bp):
ACAAAAATATTAGAGGTGTTG
Found at i:55077724 original size:18 final size:18
Alignment explanation
Indices: 55077701--55077739 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55077691 TAGATAGTAT
* *
55077701 ATTAATTTTTTTATATTC
1 ATTAATTGTGTTATATTC
*
55077719 ATTAATTGTGTTATTTTC
1 ATTAATTGTGTTATATTC
55077737 ATT
1 ATT
55077740 CTCAATTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (18 bp):
ATTAATTGTGTTATATTC
Found at i:55079115 original size:27 final size:26
Alignment explanation
Indices: 55079069--55079121 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
55079059 CACCAATGAT
*
55079069 TTGGGGAATCAGCATATAGCAACCCC
1 TTGGGGAATCAACATATAGCAACCCC
55079095 TTGGGAGAATCAACACT-TAGCAACCCC
1 TTGGG-GAATCAACA-TATAGCAACCCC
55079122 CTTCACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 18 0.75
28 1 0.04
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (26 bp):
TTGGGGAATCAACATATAGCAACCCC
Found at i:55079191 original size:102 final size:98
Alignment explanation
Indices: 55079003--55079196 Score: 275
Period size: 102 Copynumber: 1.9 Consensus size: 98
55078993 GTGATTCGGG
* *
55079003 GAATCAACACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACAACCACCAATGA
1 GAATCAACACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACAACCACCAATGA
*
55079068 TTTGGGGAATCAGCATATAGCAACCCCTTGGGA
66 ATTGGGGAATCAGCATATAGCAACCCCTTGGGA
* *
55079101 GAATCAACACTTAGCAACCCCCTTCACATTTAAA-ATACGGTGGGATCAGCACTTAGCAACCACC
1 GAATCAACACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAG--C--A-CAACCACC
55079165 AATGAATTGGGGAATCAGCACT-TAGCAACCCC
61 AATGAATTGGGGAATCAGCA-TATAGCAACCCC
55079197 CTTCACATTT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
97 13 0.15
98 32 0.38
99 1 0.01
101 1 0.01
102 37 0.44
103 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (98 bp):
GAATCAACACTTAGCAACCCCCTTCACATTCAAAGATACGGTGGAATCAGCACAACCACCAATGA
ATTGGGGAATCAGCATATAGCAACCCCTTGGGA
Found at i:55082083 original size:22 final size:20
Alignment explanation
Indices: 55082035--55082086 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
55082025 TATTGATATG
*
55082035 AGATAAATTGATTATGTTTT
1 AGATAAATTGATTAGGTTTT
55082055 AGATAAATTGATTAGGTTACTT
1 AGATAAATTGATTAGGTT--TT
*
55082077 AGTTAAATTG
1 AGATAAATTG
55082087 CATAATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (20 bp):
AGATAAATTGATTAGGTTTT
Found at i:55087521 original size:75 final size:74
Alignment explanation
Indices: 55087423--55088040 Score: 722
Period size: 75 Copynumber: 8.2 Consensus size: 74
55087413 ACCACTTCTT
* * *
55087423 TTTCTGTTTTTCAAAAATCAACTCATAATCTAATAGGTGAGTTGAGCATCGGGTCGCACGCTGAT
1 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA-
55087488 GTATTTTCAA
65 GTATTTTCAA
* * * * *
55087498 TTTCAGTTTTTCAAAAATGAACTCATAATCTGATAGGTGAGTTGAGCCTCAGGTCGCAAGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA-
*
55087563 GTGTTTTCAA
65 GTATTTTCAA
* * * *
55087573 TTTCTGTTTTTC-AAAATCAACTCATAATCCGAGAGGTGAATTGAGCCTCAGGTCGCACGTTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
55087637 ATATTTTCAA
66 -TATTTTCAA
** *
55087647 TTTCTAATTTTCAAAAATCAACTCATAAT-TCGAGAGGTGAGTTGAGCCTCGGGTCGTACGCTGA
1 TTTCTGTTTTTCAAAAATCAACTCATAATCT-GAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
*
55087711 GGTATTTTTAA
65 -GTATTTTCAA
* * *
55087722 TTTCTTTTTTTTCAAAAATCAACTTATAAT-TCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTG
1 TTTC-TGTTTTTCAAAAATCAACTCATAATCT-GAGAGGTGAGTTGAGCCTCGGGTCGCACGCTG
55087786 ATGTATTTTCAA
64 A-GTATTTTCAA
* * * * * **
55087798 TTTCTAG-TTTTCAAAAATCAACTCGTAATCCGAGAGGTGAGTTAAGCCTTGGGTCACACAATGA
1 TTTCT-GTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
55087862 GCTATTTTCAA
65 G-TATTTTCAA
* * * *
55087873 TTTTTGTTTTTCCAAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGA
1 TTTCTGTTTTT-CAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
55087938 GGTATTTTCAA
65 -GTATTTTCAA
* * * * * * * * *
55087949 ATTCTATTTTTCAAAGATCAATTCATAATCTGAGATGTGAGTTGAACTTTGGATCGCACGCTGAG
1 TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
55088014 TTATTTTCGA
66 -TATTTTCAA
55088024 TTTCTGTTTTTCAAAAA
1 TTTCTGTTTTTCAAAAA
55088041 AAAATAGACA
Statistics
Matches: 468, Mismatches: 63, Indels: 24
0.84 0.11 0.04
Matches are distributed among these distances:
73 1 0.00
74 66 0.14
75 269 0.57
76 131 0.28
77 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (74 bp):
TTTCTGTTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
TATTTTCAA
Found at i:55087811 original size:151 final size:150
Alignment explanation
Indices: 55087423--55088040 Score: 785
Period size: 151 Copynumber: 4.1 Consensus size: 150
55087413 ACCACTTCTT
** * *
55087423 TTTCTGTTTTTCAAAAATCAACTCATAATCTAATAGGTGAGTTGAGCATCGGGTCGCACGCTGAT
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAT
* * *
55087488 GTATTTTCAATTTC-AGTTTTTCAAAAATGAACTCATAATCTGATAGGTGAGTTGAGCCTCAGGT
66 GTATTTTCAATTTCTAG-TTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGT
* *
55087552 CGCAAGCTGAGGTGTTTTCAA
130 CGCACGCTGAGGTATTTTCAA
* * *
55087573 TTTCTGTTTTTC-AAAATCAACTCATAATCCGAGAGGTGAATTGAGCCTCAGGTCGCACGTTGA-
1 TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAT
*
55087636 GATATTTTCAATTTCTAATTTTCAAAAATCAACTCATAAT-TCGAGAGGTGAGTTGAGCCTCGGG
66 G-TATTTTCAATTTCTAGTTTTCAAAAATCAACTCATAATCT-GAGAGGTGAGTTGAGCCTCGGG
* *
55087700 TCGTACGCTGAGGTATTTTTAA
129 TCGCACGCTGAGGTATTTTCAA
* * * *
55087722 TTTCTTTTTTTTCAAAAATCAACTTATAATTCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTGA
1 TTTC-TGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
* * * *
55087787 TGTATTTTCAATTTCTAGTTTTCAAAAATCAACTCGTAATCCGAGAGGTGAGTTAAGCCTTGGGT
65 TGTATTTTCAATTTCTAGTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGT
* ** *
55087852 CACACAATGAGCTATTTTCAA
130 CGCACGCTGAGGTATTTTCAA
* * *
55087873 TTTTTGTTTTTCCAAAAATCAATTCATAATCCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGA
1 TTTCTGTTTTT-CAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGA
* * * * * * * * * *
55087938 GGTATTTTCAAATTCTATTTTTCAAAGATCAATTCATAATCTGAGATGTGAGTTGAACTTTGGAT
65 TGTATTTTCAATTTCTAGTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGT
* *
55088003 CGCACGCTGAGTTATTTTCGA
130 CGCACGCTGAGGTATTTTCAA
55088024 TTTCTGTTTTTCAAAAA
1 TTTCTGTTTTTCAAAAA
55088041 AAAATAGACA
Statistics
Matches: 402, Mismatches: 58, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
148 2 0.00
149 120 0.30
150 32 0.08
151 247 0.61
152 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (150 bp):
TTTCTGTTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAT
GTATTTTCAATTTCTAGTTTTCAAAAATCAACTCATAATCTGAGAGGTGAGTTGAGCCTCGGGTC
GCACGCTGAGGTATTTTCAA
Found at i:55088439 original size:30 final size:30
Alignment explanation
Indices: 55088349--55088517 Score: 122
Period size: 30 Copynumber: 5.8 Consensus size: 30
55088339 TACAAAAATT
55088349 TAAAATTTACATTTTGACCCCTAAATATTTCC
1 TAAAA-TTACATTTTGACCCCTAAAT-TTTCC
* * * *
55088381 TAAAATTACATTTTG-GCTCTCAATTTTTCT
1 TAAAATTACATTTTGACCCCT-AAATTTTCC
* *
55088411 TAAAATTACATTTTGACCCCTTACTTTTCC
1 TAAAATTACATTTTGACCCCTAAATTTTCC
*
55088441 T--ACTTACATTTTGA--CCTAAA-TTTCAC
1 TAAAATTACATTTTGACCCCTAAATTTTC-C
* * * *
55088467 T--ATTTATATTTTGGCCCCTAACTTTTCC
1 TAAAATTACATTTTGACCCCTAAATTTTCC
* *
55088495 TAAAATTACACTTT-AACCCTAAA
1 TAAAATTACATTTTGACCCCTAAA
55088518 AGTTTTGCAT
Statistics
Matches: 107, Mismatches: 22, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
25 4 0.04
26 16 0.15
28 19 0.18
29 10 0.09
30 37 0.35
31 16 0.15
32 5 0.05
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (30 bp):
TAAAATTACATTTTGACCCCTAAATTTTCC
Found at i:55089185 original size:4 final size:4
Alignment explanation
Indices: 55089172--55089237 Score: 63
Period size: 4 Copynumber: 18.0 Consensus size: 4
55089162 TTGAGAAGAT
* *
55089172 GAAA -AAA GAAA GAAA GGAA G-AA GAAG GAAA -AAA GAAA G-AA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
55089215 GAAA GAAG GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA
55089238 AAGAATTAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
3 16 0.31
4 35 0.69
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:55089192 original size:8 final size:8
Alignment explanation
Indices: 55089172--55089237 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 8
55089162 TTGAGAAGAT
55089172 GAAA-AAA
1 GAAAGAAA
55089179 GAAAGAAA
1 GAAAGAAA
*
55089187 GGAAG-AA
1 GAAAGAAA
*
55089194 GAAGGAAA
1 GAAAGAAA
55089202 -AAAGAAA
1 GAAAGAAA
55089209 G-AA-AAA
1 GAAAGAAA
*
55089215 GAAAGAAG
1 GAAAGAAA
55089223 GAAA-AAA
1 GAAAGAAA
55089230 GAAAGAAA
1 GAAAGAAA
55089238 AAGAATTAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
6 4 0.09
7 25 0.53
8 18 0.38
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
GAAAGAAA
Found at i:55089194 original size:25 final size:24
Alignment explanation
Indices: 55089172--55089242 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 24
55089162 TTGAGAAGAT
55089172 GAAAAAAGAAAGAAAGGAAGAAGAAG
1 GAAAAAAGAAAGAAA--AAGAAGAAG
55089198 GAAAAAAGAAAGAAAAAGAAAGAAG
1 GAAAAAAGAAAGAAAAAG-AAGAAG
55089223 GAAAAAAGAAAGAAAAAGAA
1 GAAAAAAGAAAGAAAAAGAA
55089243 TTAGTTGGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.11
25 24 0.55
26 15 0.34
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAAGAAAAAGAAGAAG
Found at i:55089198 original size:10 final size:10
Alignment explanation
Indices: 55089165--55089242 Score: 50
Period size: 11 Copynumber: 7.4 Consensus size: 10
55089155 CTAAGGTTTG
*
55089165 AGAAGATGAA
1 AGAAGAAGAA
*
55089175 AAAAGAAAGAA
1 AGAAG-AAGAA
55089186 AGGAAGAAGAA
1 A-GAAGAAGAA
* *
55089197 GGAAAAAAGAA
1 AG-AAGAAGAA
*
55089208 AGAAAAAGAA
1 AGAAGAAGAA
*
55089218 AGAAGGAAAAA
1 AGAA-GAAGAA
55089229 AGAAAGAA-AA
1 AG-AAGAAGAA
55089239 AGAA
1 AGAA
55089243 TTAGTTGGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
9 2 0.04
10 21 0.38
11 27 0.49
12 5 0.09
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (10 bp):
AGAAGAAGAA
Found at i:55089210 original size:15 final size:15
Alignment explanation
Indices: 55089192--55089236 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
55089182 AGAAAGGAAG
55089192 AAGAAGGAAAAAAG-
1 AAGAAGGAAAAAAGA
55089206 -A-AA-G-AAAAAGA
1 AAGAAGGAAAAAAGA
55089217 AAGAAGGAAAAAAGA
1 AAGAAGGAAAAAAGA
55089232 AAGAA
1 AAGAA
55089237 AAAGAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 3 0.12
13 3 0.12
14 1 0.04
15 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAGAAGGAAAAAAGA
Found at i:55093157 original size:44 final size:43
Alignment explanation
Indices: 55093109--55093332 Score: 133
Period size: 45 Copynumber: 4.9 Consensus size: 43
55093099 TACCTTTGAT
* *
55093109 CTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGAC
1 CTACTTCACACCAGTACATGAAGACAAGATCTG-TTTCTTCGAC
* * * * * *
55093153 CTACTCCACCACCAGTATAGGGAGACAAGATCTGTTTCTTTGAT
1 CTACTTCA-CACCAGTACATGAAGACAAGATCTGTTTCTTCGAC
* ** * *
55093197 CTACTTCACTCGGGTACATGAAGACAAGATCTGCTTTCTTTGAT
1 CTACTTCACACCAGTACATGAAGACAAGATCTG-TTTCTTCGAC
* * *** * *
55093241 CTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGCTTTTTCCGATCTCTGAT
1 CTACTTC-ACACCAGTACATGAAGACAAGATCTG---TTT-C--T-TC-GAC
* *
55093293 CTACTTCACGCCAGTACATAAAGACAAGATCTGTTATCTT
1 CTACTTCACACCAGTACATGAAGACAAGATCTGTT-TCTT
55093333 TCAACCTGCT
Statistics
Matches: 135, Mismatches: 34, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
43 19 0.14
44 38 0.28
45 39 0.29
46 1 0.01
47 3 0.02
48 4 0.03
49 1 0.01
50 1 0.01
51 20 0.15
52 9 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
CTACTTCACACCAGTACATGAAGACAAGATCTGTTTCTTCGAC
Found at i:55093198 original size:88 final size:90
Alignment explanation
Indices: 55093101--55093347 Score: 275
Period size: 88 Copynumber: 2.7 Consensus size: 90
55093091 GGACCTACTA
* *
55093101 CCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACC
1 CCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
55093166 AGTATAGGG-AGACAAGATCTG-TTT
66 AGTAT-GGGAAGACAAGATCTGTTTT
* ** * * * * *
55093190 -CTTTGATCTACTTCACTCGGGTACATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACC
1 CCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
*
55093254 AGTATGGGAAGGCAAGATCTGCTTTTT
66 AGTATGGGAAGACAAGATCTG--TTTT
* * *
55093281 CCGATCTCTGATCTACTTCACGCCAGTACATAAAGACAAGATCTGTTATCTTTCAACCTGCTCCA
1 CC--T-T-TGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTC-TTCGACCTGCTCCA
55093346 CC
61 CC
55093348 GCTGCTTAGG
Statistics
Matches: 126, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
87 3 0.02
88 70 0.56
91 3 0.02
92 1 0.01
94 1 0.01
95 1 0.01
96 36 0.29
97 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (90 bp):
CCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTGCTCCACCACC
AGTATGGGAAGACAAGATCTGTTTT
Found at i:55115699 original size:88 final size:86
Alignment explanation
Indices: 55115606--55115775 Score: 236
Period size: 88 Copynumber: 2.0 Consensus size: 86
55115596 TCCTCCTCTC
* * *
55115606 TTTTTTTTGCACTCAATT-GAGCACTTGAACTTTTAAAATGCATTAAAAAGGCCCTC-AAATTTC
1 TTTTTTTTGCACTCAATTGGA-CACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTT-
55115669 TTCAAAAAAAAAGCAATTAAGTTCT
64 TTC-AAAAAAAA-CAATTAAGTTCT
* * *
55115694 TTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAATGCATCAACATGACCCTCAAAATTTTT
1 TTTTTTTTGCACTCAATTGGACACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTTTT
55115759 CAAAAAAAACAATTAAG
66 CAAAAAAAACAATTAAG
55115776 GCCCTGCTCT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
86 8 0.11
87 8 0.11
88 50 0.68
89 8 0.11
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (86 bp):
TTTTTTTTGCACTCAATTGGACACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAATTTTT
CAAAAAAAACAATTAAGTTCT
Found at i:55115858 original size:26 final size:26
Alignment explanation
Indices: 55115829--55115889 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
55115819 TAAATTATAG
*
55115829 ATAAAATTTTAAATTTTAATAAAAAT
1 ATAAAATTTTAAAATTTAATAAAAAT
* *
55115855 ATAAAATTTGAAAATTTATTAAAAAT
1 ATAAAATTTTAAAATTTAATAAAAAT
*
55115881 -TAGAATTTT
1 ATAAAATTTT
55115890 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATAAAATTTTAAAATTTAATAAAAAT
Found at i:55115859 original size:18 final size:19
Alignment explanation
Indices: 55115818--55115859 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
55115808 TTAAAAATAA
*
55115818 ATAAATTATAGATAAAATT
1 ATAAATTATAGATAAAAAT
* *
55115837 TTAAATTTTA-ATAAAAAT
1 ATAAATTATAGATAAAAAT
55115855 ATAAA
1 ATAAA
55115860 ATTTGAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAATTATAGATAAAAAT
Found at i:55115934 original size:19 final size:18
Alignment explanation
Indices: 55115854--55115936 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
55115844 TTAATAAAAA
*
55115854 TATAAAATTTGAAAA-TT
1 TATAAAAATTGAAAATTT
**
55115871 TATTAAAAATTAGAATTTTT
1 TA-TAAAAATT-GAAAATTT
***
55115891 TATAAAAATTGTAAAAAGG
1 TATAAAAATTG-AAAATTT
55115910 TA-AAAAATTGTAAAATTT
1 TATAAAAATTG-AAAATTT
55115928 TATAAAAAT
1 TATAAAAAT
55115937 CATCAAAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 2 0.04
18 23 0.46
19 21 0.42
20 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (18 bp):
TATAAAAATTGAAAATTT
Found at i:55115944 original size:20 final size:20
Alignment explanation
Indices: 55115927--55115967 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
55115917 TTGTAAAATT
55115927 TTATAAAAAT-CATCAAAAAA
1 TTAT-AAAATGCATCAAAAAA
55115947 TTATAAAATGCATCAAAAAA
1 TTATAAAATGCATCAAAAAA
55115967 T
1 T
55115968 CTCTTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (20 bp):
TTATAAAATGCATCAAAAAA
Found at i:55116217 original size:48 final size:47
Alignment explanation
Indices: 55116165--55116279 Score: 126
Period size: 47 Copynumber: 2.4 Consensus size: 47
55116155 TTTTACGAAA
55116165 TTTATATTTCATTATATTTTGTATAATTTCCTTA-CAACTTTATAAAAT
1 TTTATATTTC-TTATATTTT-TATAATTTCCTTATCAACTTTATAAAAT
** * **
55116213 TTTATATTTC-TATATATTTTATAATTTTTTTATGATTTTTATAAAAT
1 TTTATATTTCTTATAT-TTTTATAATTTCCTTATCAACTTTATAAAAT
*
55116260 TTTATGATTTTTTATATTTT
1 TTTAT-ATTTCTTATATTTT
55116280 ATATTTTTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
46 16 0.28
47 19 0.33
48 17 0.30
49 5 0.09
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (47 bp):
TTTATATTTCTTATATTTTTATAATTTCCTTATCAACTTTATAAAAT
Found at i:55116242 original size:27 final size:26
Alignment explanation
Indices: 55116203--55116305 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 26
55116193 TCCTTACAAC
**
55116203 TTTATAAAATTTTATATTTCTATATAT
1 TTTATAATTTTTTATATTT-TATATAT
*
55116230 TTTATAATTTTTTTATGATTTTTATAAAAT
1 TTTATAA-TTTTTTAT-A-TTTTAT-ATAT
* *
55116260 TTTATGATTTTTTATATTTTATATTTT
1 TTTATAATTTTTTATATTTTATA-TAT
* *
55116287 TTTCTAATTTTTAATATTT
1 TTTATAATTTTTTATATTT
55116306 GAAAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.02
27 30 0.48
28 7 0.11
29 12 0.19
30 12 0.19
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTATAATTTTTTATATTTTATATAT
Found at i:55116254 original size:20 final size:19
Alignment explanation
Indices: 55116240--55116287 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
55116230 TTTATAATTT
55116240 TTTTATGATTTTTATAAAA
1 TTTTATGATTTTTATAAAA
*
55116259 TTTTATGATTTTT-T-ATA
1 TTTTATGATTTTTATAAAA
55116276 TTTTAT-ATTTTT
1 TTTTATGATTTTT
55116288 TTCTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 1 0.04
19 13 0.46
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTATGATTTTTATAAAA
Found at i:55116256 original size:47 final size:46
Alignment explanation
Indices: 55116203--55116299 Score: 142
Period size: 47 Copynumber: 2.1 Consensus size: 46
55116193 TCCTTACAAC
*
55116203 TTTATAAAATTTTAT-ATTTCTATATATTTTATAATTTTTTTATGATT
1 TTTATAAAATTTTATGATTT-TATATATTTTAT-ATTTTTTTATAATT
* *
55116250 TTTATAAAATTTTATGATTTTTTATATTTTATATTTTTTTCTAATT
1 TTTATAAAATTTTATGATTTTATATATTTTATATTTTTTTATAATT
55116296 TTTA
1 TTTA
55116300 ATATTTGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 16 0.35
47 26 0.57
48 4 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (46 bp):
TTTATAAAATTTTATGATTTTATATATTTTATATTTTTTTATAATT
Found at i:55116270 original size:29 final size:28
Alignment explanation
Indices: 55116212--55116279 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
55116202 CTTTATAAAA
* *
55116212 TTTTATATTTCTATATATTTTATAATTT
1 TTTTATATTTTTATAAATTTTATAATTT
*
55116240 TTTTATGATTTTTATAAAATTTTATGA-TT
1 TTTTAT-ATTTTTAT-AAATTTTATAATTT
55116269 TTTTATATTTT
1 TTTTATATTTT
55116280 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.31
29 15 0.43
30 9 0.26
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTATATTTTTATAAATTTTATAATTT
Found at i:55117395 original size:26 final size:26
Alignment explanation
Indices: 55117359--55117410 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55117349 ACTTGCTCTC
55117359 ACTGATATAGATCATATTTTCGAGGT
1 ACTGATATAGATCATATTTTCGAGGT
55117385 ACTGATATAGATCATATTTTCGAGGT
1 ACTGATATAGATCATATTTTCGAGGT
55117411 TATCCGATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
ACTGATATAGATCATATTTTCGAGGT
Found at i:55117786 original size:17 final size:17
Alignment explanation
Indices: 55117764--55117797 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55117754 ATACATTAAC
55117764 CCTTTAATATATTAAAT
1 CCTTTAATATATTAAAT
55117781 CCTTTAATATATTAAAT
1 CCTTTAATATATTAAAT
55117798 ATAGGAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
CCTTTAATATATTAAAT
Found at i:55121944 original size:3 final size:3
Alignment explanation
Indices: 55121936--55121981 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
55121926 TTCCAAAAGT
55121936 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
55121982 GATGATGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55122150 original size:30 final size:29
Alignment explanation
Indices: 55122080--55122151 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
55122070 TTTTAAGAAG
55122080 ATTAGAGTTTTTAAAAATTTTAGAAATTTA
1 ATTAGA-TTTTTAAAAATTTTAGAAATTTA
* * * *
55122110 CTTGAAATTTTTAGAACTTTTAGAAAATTTA
1 ATT-AGATTTTTAAAAATTTTAG-AAATTTA
55122141 ATTAGATTTTT
1 ATTAGATTTTT
55122152 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 23 0.68
31 11 0.32
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (29 bp):
ATTAGATTTTTAAAAATTTTAGAAATTTA
Found at i:55138582 original size:39 final size:41
Alignment explanation
Indices: 55138506--55138582 Score: 122
Period size: 39 Copynumber: 1.9 Consensus size: 41
55138496 GTTACTTGAC
**
55138506 AGCTTGTGTGAGTAGCACTGTGTAGCTACGTTCCGATCAAT
1 AGCTTGTGTGAGTAGCACTGTACAGCTACGTTCCGATCAAT
55138547 AGCTTGTGTGAGTAG-ACTG-ACAGCTACGTTCCGATC
1 AGCTTGTGTGAGTAGCACTGTACAGCTACGTTCCGATC
55138583 GACAGCTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 15 0.44
40 4 0.12
41 15 0.44
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
AGCTTGTGTGAGTAGCACTGTACAGCTACGTTCCGATCAAT
Found at i:55146104 original size:24 final size:24
Alignment explanation
Indices: 55146058--55146159 Score: 107
Period size: 24 Copynumber: 4.2 Consensus size: 24
55146048 TCCAGGCTTA
55146058 ATAACGGGAAGCTCACAAAGAGCCT
1 ATAACGGGAAGCT-ACAAAGAGCCT
* * *
55146083 ATATCGGGTAGCTTCAAAGAGCACT
1 ATAACGGGAAGCTACAAAGAGC-CT
* * *
55146108 -TAACGGGAAGCTCCGAGGAGCCT
1 ATAACGGGAAGCTACAAAGAGCCT
*
55146131 TTAACGGGAAGCTCACAAAGAGCCT
1 ATAACGGGAAGCT-ACAAAGAGCCT
55146156 ATAA
1 ATAA
55146160 GCAGAACGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
23 2 0.03
24 36 0.58
25 24 0.39
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
ATAACGGGAAGCTACAAAGAGCCT
Found at i:55146150 original size:49 final size:49
Alignment explanation
Indices: 55146059--55146153 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
55146049 CCAGGCTTAA
* * *
55146059 TAACGGGAAGCTCACAAAGAGCCTATATCGGGTAGCTTCAAAGAGCACT
1 TAACGGGAAGCTCACAAAGAGCCTATAACGGGAAGCTACAAAGAGCACT
* * *
55146108 TAACGGGAAGCTC-CGAGGAGCCTTTAACGGGAAGCTCACAAAGAGC
1 TAACGGGAAGCTCACAAAGAGCCTATAACGGGAAGCT-ACAAAGAGC
55146154 CTATAAGCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 18 0.46
49 21 0.54
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (49 bp):
TAACGGGAAGCTCACAAAGAGCCTATAACGGGAAGCTACAAAGAGCACT
Found at i:55164736 original size:10 final size:10
Alignment explanation
Indices: 55164723--55164777 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
55164713 TTGTAAAAAA
55164723 TATAAAATTT
1 TATAAAATTT
55164733 TATAAAATTT
1 TATAAAATTT
*
55164743 TATAAAA-AT
1 TATAAAATTT
* **
55164752 CATAAAAAAT
1 TATAAAATTT
55164762 TATAAAATTT
1 TATAAAATTT
55164772 TATAAA
1 TATAAA
55164778 GTCAAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
9 7 0.18
10 32 0.82
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TATAAAATTT
Found at i:55164758 original size:29 final size:28
Alignment explanation
Indices: 55164704--55164777 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
55164694 TCGTTTCGAC
* *
55164704 TTTATAAAATTGTA-AAAAATATAAAAT
1 TTTATAAAATTTTATAAAAATATAAAAA
55164731 TTTATAAAATTTTATAAAAATCATAAAAA
1 TTTATAAAATTTTATAAAAAT-ATAAAAA
*
55164760 ATTATAAAATTTTATAAA
1 TTTATAAAATTTTATAAA
55164778 GTCAAAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 13 0.31
28 6 0.14
29 23 0.55
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTATAAAATTTTATAAAAATATAAAAA
Found at i:55164789 original size:29 final size:29
Alignment explanation
Indices: 55164705--55164794 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
55164695 CGTTTCGACT
* * **
55164705 TTATAAAATTGTA-AAAAAT-ATAAAATT
1 TTATAAAATTTTATAAAAATCAAAAAAAA
*
55164732 TTATAAAATTTTATAAAAATCATAAAAAA
1 TTATAAAATTTTATAAAAATCAAAAAAAA
*
55164761 TTATAAAATTTTAT-AAAGTCAAAAGAAAA
1 TTATAAAATTTTATAAAAATCAAAA-AAAA
55164790 TTATA
1 TTATA
55164795 CAAAATGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 12 0.22
28 14 0.25
29 29 0.53
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (29 bp):
TTATAAAATTTTATAAAAATCAAAAAAAA
Found at i:55164790 original size:39 final size:39
Alignment explanation
Indices: 55164716--55164800 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
55164706 TATAAAATTG
* ** *
55164716 TAAAAAA-TATAAAATTTTATAAAATTTTATAAAAATCA
1 TAAAAAATTATAAAATTTTATAAAAGTCAAAAAAAATCA
*
55164754 TAAAAAATTATAAAATTTTAT-AAAGTCAAAAGAAAATTA
1 TAAAAAATTATAAAATTTTATAAAAGTCAAAA-AAAATCA
*
55164793 TACAAAAT
1 TAAAAAAT
55164801 GTAAAGAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 13 0.33
39 26 0.67
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (39 bp):
TAAAAAATTATAAAATTTTATAAAAGTCAAAAAAAATCA
Found at i:55165072 original size:11 final size:11
Alignment explanation
Indices: 55165058--55165089 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55165048 TTTTATAAAA
55165058 TTTTACAATTT
1 TTTTACAATTT
55165069 TTTTAC--TTT
1 TTTTACAATTT
55165078 TTTTACAATTT
1 TTTTACAATTT
55165089 T
1 T
55165090 ATAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTACAATTT
Found at i:55165141 original size:19 final size:18
Alignment explanation
Indices: 55165108--55165166 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
55165098 AATTCTAATT
*
55165108 TTTAATAAATT-TTAAAA
1 TTTAATAATTTATTAAAA
* *
55165125 TTTTATATTTTTATTAAAA
1 TTTAATA-ATTTATTAAAA
55165144 TTTAATAATTTATCTAAAA
1 TTTAATAATTTAT-TAAAA
55165163 TTTA
1 TTTA
55165167 TTTGTTTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 21 0.62
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAATAATTTATTAAAA
Found at i:55165156 original size:26 final size:26
Alignment explanation
Indices: 55165096--55165154 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
55165086 TTTTATAAAA
* *
55165096 AAAATTCTA-ATTTTTAATAAATTTT
1 AAAATTTTATATTTTTAATAAAATTT
*
55165121 AAAATTTTATATTTTTATTAAAATTT
1 AAAATTTTATATTTTTAATAAAATTT
55165147 AATAATTT
1 AA-AATTT
55165155 ATCTAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 8 0.28
26 16 0.55
27 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
AAAATTTTATATTTTTAATAAAATTT
Found at i:55166585 original size:29 final size:32
Alignment explanation
Indices: 55166553--55166612 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
55166543 TTTTTGCTTC
55166553 TTTCTTCAATCTAG-CCC-AATTGT-TTCCTT
1 TTTCTTCAATCTAGCCCCAAATTGTATTCCTT
* *
55166582 TTTCTTCTATTTAGCCCCAAATTGTATTCCT
1 TTTCTTCAATCTAGCCCCAAATTGTATTCCT
55166613 GCACAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 12 0.46
30 3 0.12
31 6 0.23
32 5 0.19
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (32 bp):
TTTCTTCAATCTAGCCCCAAATTGTATTCCTT
Found at i:55167462 original size:18 final size:20
Alignment explanation
Indices: 55167422--55167464 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
55167412 CAAAAATTAA
*
55167422 AAAAATTAAAAGTAATTTTT
1 AAAAATTAAAAGTAATTTAT
*
55167442 AAAATTTAAAA-T-ATTTAT
1 AAAAATTAAAAGTAATTTAT
55167460 AAAAA
1 AAAAA
55167465 ATTCAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATTAAAAGTAATTTAT
Found at i:55168478 original size:58 final size:58
Alignment explanation
Indices: 55168412--55168533 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 58
55168402 AAGAACAATT
55168412 AAAC-ATTCATAATTAAAAACAAAGAAACTAATGTTTTATTGCATAAAAATATAAACC
1 AAACAATTCATAATTAAAAACAAAGAAACTAATGTTTTATTGCATAAAAATATAAACC
* * *
55168469 AAACAATTCATAATTGAAAACAAAGAAACTAATGTTTTATTGCATAAAAGTATAAATC
1 AAACAATTCATAATTAAAAACAAAGAAACTAATGTTTTATTGCATAAAAATATAAACC
55168527 AAACAAT
1 AAACAAT
55168534 AGAATACATC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (58 bp):
AAACAATTCATAATTAAAAACAAAGAAACTAATGTTTTATTGCATAAAAATATAAACC
Found at i:55169043 original size:27 final size:27
Alignment explanation
Indices: 55169005--55169059 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55168995 ATAAAGAATT
55169005 AAGAGTATATAATTCACAATTAATACC
1 AAGAGTATATAATTCACAATTAATACC
55169032 AAGAGTATATAATTCACAATTAATACC
1 AAGAGTATATAATTCACAATTAATACC
55169059 A
1 A
55169060 CATAATCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (27 bp):
AAGAGTATATAATTCACAATTAATACC
Found at i:55170847 original size:41 final size:40
Alignment explanation
Indices: 55170781--55171098 Score: 193
Period size: 41 Copynumber: 7.8 Consensus size: 40
55170771 ATTTTTAAAC
* *
55170781 CTTTAGCGGCGTTTTTA-CTTTAGCGCTGCTAATTCTCCGAT
1 CTTTAGCGGCGTTTTTATC-TGAGCGCCGCTAATTCT-CGAT
* **
55170822 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGT-TCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAAT-TCTC-GAT
* * *
55170863 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGTAT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCG-AT
* * * * * *
55170904 C-ATAGTGGCGTTATTGTCTGAGCGCCACTAATTCTCTATT
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCGA-T
* * *
55170944 CTTTAGCGACGTTTTTTTTCTAAGCGCCGCTAAAGTTCAT-G-T
1 CTTTAGCGGCG-TTTTTATCTGAGCGCCGCT-AA-TTC-TCGAT
* * * * **
55170986 TTTTAGTGGCGTTTTTATCTGAGCGCCACTAATACTCTGGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTC-GAT
* * * * *
55171027 CTTTGGCGGCGTTTTATATGTAAGCGCCGCTAATGCT--AC
1 CTTTAGCGGCGTTTT-TATCTGAGCGCCGCTAATTCTCGAT
* *
55171066 CTTTAGCGGCATTTTT-TCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTG-AGCGCCGCTAAT
55171099 AGTAACAAAA
Statistics
Matches: 214, Mismatches: 47, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
37 1 0.00
38 14 0.07
39 17 0.08
40 36 0.17
41 97 0.45
42 43 0.20
43 2 0.01
44 3 0.01
45 1 0.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCGCTAATTCTCGAT
Found at i:55171016 original size:83 final size:82
Alignment explanation
Indices: 55170780--55171059 Score: 275
Period size: 83 Copynumber: 3.4 Consensus size: 82
55170770 GATTTTTAAA
* * ** *
55170780 CCTTTAGCGGCG-TTTTTA-CTTTAGCGCTGCTAATTCTCCG-ATCTTTAGCGGCGTTTTTATCT
1 CCTTTAGCGGCGTTTTTTATC-TAAGCGCCGCTAAAGCT-CGTAT-TTTAGTGGCGTTTTTATCT
55170842 GAGCGCCACTAATGT-TCTGG
63 GAGCGCCACTAAT-TCTCTGG
* * ** * *
55170862 CCTTTAGCGGCG-TTTTTGTCTAAGCGCCGCTAATGCTCGTATCATAGTGGCGTTATTGTCTGAG
1 CCTTTAGCGGCGTTTTTTATCTAAGCGCCGCTAAAGCTCGTATTTTAGTGGCGTTTTTATCTGAG
**
55170926 CGCCACTAATTCTCTAT
66 CGCCACTAATTCTCTGG
* * * *
55170943 TCTTTAGCGACGTTTTTTTTCTAAGCGCCGCTAAAGTTCATGT-TTTTAGTGGCGTTTTTATCTG
1 CCTTTAGCGGCGTTTTTTATCTAAGCGCCGCTAAAGCTC--GTATTTTAGTGGCGTTTTTATCTG
*
55171007 AGCGCCACTAATACTCTGG
64 AGCGCCACTAATTCTCTGG
* * *
55171026 CCTTTGGCGGCGTTTTATATGTAAGCGCCGCTAA
1 CCTTTAGCGGCGTTTTTTATCTAAGCGCCGCTAA
55171060 TGCTACCTTT
Statistics
Matches: 163, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
80 1 0.01
81 42 0.26
82 56 0.34
83 62 0.38
84 2 0.01
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (82 bp):
CCTTTAGCGGCGTTTTTTATCTAAGCGCCGCTAAAGCTCGTATTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATTCTCTGG
Found at i:55171632 original size:15 final size:15
Alignment explanation
Indices: 55171611--55171648 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
55171601 TTTAAGGTTA
55171611 ATTTAGGGGTTGGAG
1 ATTTAGGGGTTGGAG
* *
55171626 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTGGAG
55171641 ATTTAGGG
1 ATTTAGGG
55171649 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTGGAG
Found at i:55171651 original size:14 final size:14
Alignment explanation
Indices: 55171584--55171651 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
55171574 GACTGGGTAT
*
55171584 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
55171598 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
55171610 A-ATTTAGGGGTTGG
1 AGATTTA-GGGTTTG
*
55171624 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
55171639 AGATTTAGGGTTT
1 AGATTTAGGGTTT
55171652 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:55173391 original size:10 final size:10
Alignment explanation
Indices: 55173376--55173413 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
55173366 TATTTTTACT
55173376 TATATATAGA
1 TATATATAGA
55173386 TATATAT-GAA
1 TATATATAG-A
*
55173396 TATATATGGA
1 TATATATAGA
55173406 TATATATA
1 TATATATA
55173414 TAGTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (10 bp):
TATATATAGA
Found at i:55176007 original size:16 final size:16
Alignment explanation
Indices: 55175946--55176024 Score: 65
Period size: 16 Copynumber: 5.0 Consensus size: 16
55175936 ACACATAGCC
* *
55175946 TACATGACTTATATAA
1 TACATAACTTACATAA
** *
55175962 TACACGACTTAAATAA
1 TACATAACTTACATAA
*
55175978 TTTAAATAACTTACATAA
1 --TACATAACTTACATAA
55175996 TACATAACTTACAT--
1 TACATAACTTACATAA
55176010 T-CATAACTTACATAA
1 TACATAACTTACATAA
55176025 ACTTATATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 27 0.52
18 12 0.23
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:55176016 original size:13 final size:15
Alignment explanation
Indices: 55175983--55176023 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
55175973 AATAATTTAA
55175983 ATAACTTACATAATAC
1 ATAACTTACAT-ATAC
55175999 ATAACTTACAT-T-C
1 ATAACTTACATATAC
55176012 ATAACTTACATA
1 ATAACTTACATA
55176024 AACTTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAACTTACATATAC
Found at i:55176129 original size:25 final size:22
Alignment explanation
Indices: 55176101--55176154 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
55176091 ATACATAAAT
55176101 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
55176126 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
55176148 TACATAA
1 TACATAA
55176155 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:55176144 original size:22 final size:22
Alignment explanation
Indices: 55176111--55176161 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
55176101 TACATAACTT
55176111 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
55176132 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
55176154 AATTACAT
1 AATTACAT
55176162 AACTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:55176149 original size:56 final size:56
Alignment explanation
Indices: 55176086--55176251 Score: 323
Period size: 56 Copynumber: 3.0 Consensus size: 56
55176076 GGGTGATGTG
55176086 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
55176142 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
*
55176198 ATATTATACATAAATTACATAACTTAGTTAATTAATATTATACATAACTTACAT
1 ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACAT
55176252 AACTTAGTTA
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 109 1.00
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.41
Consensus pattern (56 bp):
ATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAACTTACATTA
Found at i:55176181 original size:34 final size:34
Alignment explanation
Indices: 55176138--55176287 Score: 132
Period size: 34 Copynumber: 4.8 Consensus size: 34
55176128 CATAACTTAC
*
55176138 ATTAATATTATACATAAATTACATAACTTAATTA
1 ATTAATATTATACATAACTTACATAACTTAATTA
55176172 ATTAATATTATACATAACTTACATTAA--T-ATT-
1 ATTAATATTATACATAACTTACA-TAACTTAATTA
* *
55176203 A-TACATA-AATTACATAAC-T---T-A----GTTA
1 ATTA-ATATTA-TACATAACTTACATAACTTAATTA
*
55176228 ATTAATATTATACATAACTTACATAACTTAGTTA
1 ATTAATATTATACATAACTTACATAACTTAATTA
55176262 ATTAATATTATACATAACTTACATAA
1 ATTAATATTATACATAACTTACATAA
55176288 GATTTTAACA
Statistics
Matches: 97, Mismatches: 4, Indels: 30
0.74 0.03 0.23
Matches are distributed among these distances:
24 2 0.02
25 13 0.13
26 5 0.05
29 1 0.01
30 5 0.05
31 12 0.12
32 3 0.03
33 1 0.01
34 52 0.54
35 3 0.03
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.41
Consensus pattern (34 bp):
ATTAATATTATACATAACTTACATAACTTAATTA
Found at i:55176186 original size:25 final size:22
Alignment explanation
Indices: 55176157--55176210 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
55176147 ATACATAAAT
55176157 TACATAACTTAATTAATTAATATTA
1 TACATAACTT-A--AATTAATATTA
*
55176182 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
55176204 TACATAA
1 TACATAA
55176211 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
24 1 0.04
25 10 0.36
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:55176194 original size:90 final size:87
Alignment explanation
Indices: 55176126--55176287 Score: 263
Period size: 90 Copynumber: 1.8 Consensus size: 87
55176116 ATTAATATTA
*
55176126 TACATAACTTA-CATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
1 TACATAACTTATAATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
55176190 TTACATTAATATTATACATAAAT
66 TTACA-TAATATTATACATAAAT
* *
55176213 TACATAACTTAGTTAATTAATATTATACATAACTTACATAACTTAGTTAATTAATATTATACATA
1 TACATAACTTA--TAATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATA
55176278 ACTTACATAA
64 ACTTACATAA
55176288 GATTTTAACA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
87 11 0.16
89 3 0.04
90 55 0.80
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (87 bp):
TACATAACTTATAATTAATATTATACATAAATTACATAACTTAATTAATTAATATTATACATAAC
TTACATAATATTATACATAAAT
Found at i:55176200 original size:22 final size:22
Alignment explanation
Indices: 55176167--55176217 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
55176157 TACATAACTT
55176167 AATTA-ATTAATATTATACATA
1 AATTACATTAATATTATACATA
*
55176188 ACTTACATTAATATTATACATA
1 AATTACATTAATATTATACATA
55176210 AATTACAT
1 AATTACAT
55176218 AACTTAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTACATTAATATTATACATA
Found at i:55176252 original size:9 final size:9
Alignment explanation
Indices: 55176092--55176365 Score: 73
Period size: 9 Copynumber: 30.7 Consensus size: 9
55176082 TGTGATATTA
*
55176092 TACATAAAT
1 TACATAACT
55176101 TACATAACT
1 TACATAACT
55176110 TA-ATTAA-T
1 TACA-TAACT
*
55176118 TA-AT-ATT
1 TACATAACT
55176125 ATACATAACT
1 -TACATAACT
*
55176135 TACATTAATATT
1 TACA-T-A-ACT
*
55176147 ATACATAAAT
1 -TACATAACT
55176157 TACATAACT
1 TACATAACT
55176166 TA-ATTAA-T
1 TACA-TAACT
*
55176174 TA-AT-ATT
1 TACATAACT
55176181 ATACATAACT
1 -TACATAACT
*
55176191 TACATTAATATT
1 TACA-T-A-ACT
*
55176203 ATACATAAAT
1 -TACATAACT
55176213 TACATAACT
1 TACATAACT
**
55176222 TAGTTAA-T
1 TACATAACT
*
55176230 TA-AT-ATT
1 TACATAACT
55176237 ATACATAACT
1 -TACATAACT
55176247 TACATAACT
1 TACATAACT
**
55176256 TAGTTAA-T
1 TACATAACT
*
55176264 TA-AT-ATT
1 TACATAACT
55176271 ATACATAACT
1 -TACATAACT
*
55176281 TACATAAGATTT
1 TACAT-A-A-CT
* *
55176293 TA-ACAATT
1 TACATAACT
*
55176301 TGCATAA--
1 TACATAACT
*
55176308 TAAATAACT
1 TACATAACT
55176317 TACATAACT
1 TACATAACT
55176326 TACATAA--
1 TACATAACT
55176333 TACATAACT
1 TACATAACT
* *
55176342 TATATGACT
1 TACATAACT
*
55176351 TATATAACT
1 TACATAACT
55176360 TACATA
1 TACATA
55176366 GCATAATTTT
Statistics
Matches: 203, Mismatches: 28, Indels: 68
0.68 0.09 0.23
Matches are distributed among these distances:
6 4 0.02
7 20 0.10
8 27 0.13
9 113 0.56
10 16 0.08
11 6 0.03
12 9 0.04
13 8 0.04
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (9 bp):
TACATAACT
Found at i:55176331 original size:25 final size:25
Alignment explanation
Indices: 55176303--55176428 Score: 82
Period size: 25 Copynumber: 5.2 Consensus size: 25
55176293 TAACAATTTG
55176303 CATAATAAATAACTTACATAACTTA
1 CATAATAAATAACTTACATAACTTA
* * *
55176328 CATAATACATAACTTATATGACTT-
1 CATAATAAATAACTTACATAACTTA
* * * * *
55176352 -AT-ATAACTTACATAGCATAATTTT
1 CATAATAAATAACTTA-CATAACTTA
* * * ** *
55176376 CATAATACACAACTCACATAGTTTT
1 CATAATAAATAACTTACATAACTTA
55176401 CATAATAAATAACTTACATAA--TA
1 CATAATAAATAACTTACATAACTTA
55176424 CATAA
1 CATAA
55176429 CTTACATAGC
Statistics
Matches: 75, Mismatches: 22, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
22 8 0.11
23 13 0.17
25 48 0.64
26 6 0.08
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (25 bp):
CATAATAAATAACTTACATAACTTA
Found at i:55176336 original size:16 final size:16
Alignment explanation
Indices: 55176317--55176436 Score: 69
Period size: 16 Copynumber: 7.9 Consensus size: 16
55176307 ATAAATAACT
55176317 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
55176333 TACATAACTTATATGACT
1 TACATAACTTACAT-A-A
*
55176351 TATATAACTTACAT-A
1 TACATAACTTACATAA
* * *
55176366 -GCATAATTTTCATAA
1 TACATAACTTACATAA
* * *
55176381 TACACAACTCACATAG
1 TACATAACTTACATAA
55176397 T---T---TT-CATAA
1 TACATAACTTACATAA
*
55176406 TAAATAACTTACATAA
1 TACATAACTTACATAA
55176422 TACATAACTTACATA
1 TACATAACTTACATA
55176437 GCTTAATTAT
Statistics
Matches: 74, Mismatches: 19, Indels: 22
0.64 0.17 0.19
Matches are distributed among these distances:
9 5 0.07
10 1 0.01
12 1 0.01
14 9 0.12
15 3 0.04
16 42 0.57
17 1 0.01
18 12 0.16
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:55181420 original size:21 final size:21
Alignment explanation
Indices: 55181394--55181439 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55181384 CAGCAGCTTA
*
55181394 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
55181415 AAGCAGAGGCGGCAGCTAGAG
1 AAGCAGAGGCGGCAGCAAGAG
55181436 AAGC
1 AAGC
55181440 TGCAGCGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.39, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:55181467 original size:21 final size:21
Alignment explanation
Indices: 55181443--55181500 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
55181433 GAGAAGCTGC
55181443 AGCGAGGGAAGCAGAGGCTAA
1 AGCGAGGGAAGCAGAGGCTAA
* **
55181464 AGCGAGGGAAACAGAGGCTGC
1 AGCGAGGGAAGCAGAGGCTAA
55181485 AGCGAGGGAAGCAGAG
1 AGCGAGGGAAGCAGAG
55181501 CAGCGTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.45, T:0.03
Consensus pattern (21 bp):
AGCGAGGGAAGCAGAGGCTAA
Found at i:55181863 original size:43 final size:43
Alignment explanation
Indices: 55181797--55182151 Score: 252
Period size: 43 Copynumber: 8.2 Consensus size: 43
55181787 ATCTGCCAAA
* * ** *
55181797 TTTAGTGGCGTTTTTGGTTAAAGCGCCGCTAAAGATAAGGGTC
1 TTTAGCGGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
* * *
55181840 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
* * ** * *
55181883 TTTAGCTGCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTC
1 TTTAGCGGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
** * * * * * *
55181926 TTTAGTAGTGTTTTGTGGTCGAAGTGCCACTATAGATCAGGGTC
1 TTTAGCGGCG-TTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
** * *
55181970 TATT-GCGGCGTTT-TAGGGGAAAGCGCCGCTAAAGATTAGGTTC
1 T-TTAGCGGCGTTTGT-GGACAAAGCGCCGCTAAAGATCAGGGTC
* *
55182013 TTTA-CTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTC
1 TTTAGC-GGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
* * * * * * ** *
55182056 TATT-GTGGCGTTTGAGAAAAAAACGCCGCTAAAGACCCTGATC
1 T-TTAGCGGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
* * * *
55182099 TATAGCGGCGCTTCTAGCACAAA-CGCCGCTAAAGATCAGGGTC
1 TTTAGCGGCGTTTGT-GGACAAAGCGCCGCTAAAGATCAGGGTC
55182142 TTTAGCGGCG
1 TTTAGCGGCG
55182152 CTTCCACTAA
Statistics
Matches: 236, Mismatches: 66, Indels: 20
0.73 0.20 0.06
Matches are distributed among these distances:
42 5 0.02
43 193 0.82
44 36 0.15
45 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGACAAAGCGCCGCTAAAGATCAGGGTC
Found at i:55182090 original size:86 final size:86
Alignment explanation
Indices: 55181801--55182068 Score: 326
Period size: 86 Copynumber: 3.1 Consensus size: 86
55181791 GCCAAATTTA
* ** * * **
55181801 GTGGCGTTTTTGGTTAAAGCGCCGCTAAAGATAAGGGTCTTTAGC-GGCGTTTGTGGAAAAAGCG
1 GTGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTA-CTGGCGTTTGTGGTCAAAGCG
* *
55181865 CCACTAAAGATCATGGTCT-TT
65 CCACTATAGATCAGGGTCTATT
* * * * *
55181886 AGCT-GCGTTTTTGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTAGTAGTGTTTTGTGGTCGAAG
1 -G-TGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTACTGGCG-TTTGTGGTCAAAG
*
55181950 TGCCACTATAGATCAGGGTCTATT
63 CGCCACTATAGATCAGGGTCTATT
*
55181974 GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTACTGGCGTTTGTGGTCAAAGCGC
1 GTGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTACTGGCGTTTGTGGTCAAAGCGC
*
55182039 CGCTATAGATCAGGGTCTATT
66 CACTATAGATCAGGGTCTATT
55182060 GTGGCGTTT
1 GTGGCGTTT
55182069 GAGAAAAAAA
Statistics
Matches: 155, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
86 81 0.52
87 72 0.46
88 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (86 bp):
GTGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTTCTTTACTGGCGTTTGTGGTCAAAGCGC
CACTATAGATCAGGGTCTATT
Found at i:55182328 original size:22 final size:22
Alignment explanation
Indices: 55182300--55182342 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55182290 TTGTGACGCT
* *
55182300 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
55182322 AAAAAGCACCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
55182343 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:55187007 original size:15 final size:14
Alignment explanation
Indices: 55186986--55187021 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
55186976 ATAATCCTTA
*
55186986 ATAATTATCTTAAT
1 ATAATTATCCTAAT
55187000 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
55187015 ATAATTA
1 ATAATTA
55187022 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:55187346 original size:3 final size:3
Alignment explanation
Indices: 55187340--55187389 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
55187330 TTTTTTAATT
55187340 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
55187388 AT
1 AT
55187390 TATTATTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:55192687 original size:10 final size:10
Alignment explanation
Indices: 55192674--55192703 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
55192664 AAAATGTTTC
55192674 AAAAAAAAG-
1 AAAAAAAAGA
55192683 AAAAAAAAGA
1 AAAAAAAAGA
55192693 AAAAAAAAGA
1 AAAAAAAAGA
55192703 A
1 A
55192704 GAGGTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:55192688 original size:9 final size:9
Alignment explanation
Indices: 55192674--55192699 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55192664 AAAATGTTTC
55192674 AAAAAAAAG
1 AAAAAAAAG
55192683 AAAAAAAAG
1 AAAAAAAAG
55192692 AAAAAAAA
1 AAAAAAAA
55192700 AGAAGAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:55195824 original size:44 final size:44
Alignment explanation
Indices: 55195730--55196080 Score: 174
Period size: 44 Copynumber: 7.9 Consensus size: 44
55195720 CATTATGGTG
*
55195730 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCACT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACT
* **
55195774 AATCTTATC-CCCTTAAAGTTGCAGTGGGGCAGA-TAGAAGTTAC-
1 AATCTTATCTCCC-TAAAGTTGCAGTGGAGCAGATTA-AAGCCACT
* * * * * ** *
55195817 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGTAGACTGAAGATAGCG
1 AA-TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-CT
* * ** * * *
55195863 AATCTTATTTCCCTGAAGTTGCAGTGGAATAGATTGAAGCTATAAATTGT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGC----CA--CT
* * * * * * * *
55195913 AGATCTTATCTCTCTGAATTTGCAGTAGAGAAGATCATA-TCA--
1 A-ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACT
* * * * * * *** *
55195955 AACCTTATCTCCCTGAAGTTGTAGTAGAGCAGGTTGAATATACG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACT
* * ** *
55195999 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTGCA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACT
*
55196043 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAA
55196081 ACGATGAGTC
Statistics
Matches: 239, Mismatches: 52, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
41 28 0.12
42 2 0.01
43 7 0.03
44 131 0.55
45 38 0.16
46 3 0.01
49 1 0.00
50 1 0.00
51 28 0.12
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACT
Found at i:55197715 original size:40 final size:42
Alignment explanation
Indices: 55197659--55197741 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 42
55197649 AAATTTTTAC
*
55197659 ATATATATATATTTTAAAACTG-TTTTATATGTTATTTTTTTT
1 ATATATATATATTTTAAAACTGTTTTTAT-TGTTATTTATTTT
*
55197701 ATAT-TATATA-TTTAAAATTGTTTTTATTGTTATTTATTTT
1 ATATATATATATTTTAAAACTGTTTTTATTGTTATTTATTTT
55197741 A
1 A
55197742 GTTTTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 22 0.58
41 12 0.32
42 4 0.11
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (42 bp):
ATATATATATATTTTAAAACTGTTTTTATTGTTATTTATTTT
Found at i:55201127 original size:238 final size:238
Alignment explanation
Indices: 55200709--55201148 Score: 837
Period size: 238 Copynumber: 1.8 Consensus size: 238
55200699 AGAAACCATT
*
55200709 ATAATATACAGCAGCATAAATTAAACAAAAAAAAATATGTTAAACTACATTTATAAAAAATTGTT
1 ATAATATACAGCAGCATAAATTAAACAAAAAAAAATATGTTAAACTACATTTATAAAAAATGGTT
*
55200774 GAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAATAACTAAATTAGAAAGAA
66 GAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAACAACTAAATTAGAAAGAA
55200839 CAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAAT
131 CAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAAT
55200904 AATTGACATTCTTTTCTCCTCAATTGATTAAATTAAAAATTAA
196 AATTGACATTCTTTTCTCCTCAATTGATTAAATTAAAAATTAA
*
55200947 ATAATATATAGCAGCATAAATTAAACAAAAAAAAAGTATGTTAAACTACATTTATAAAAAATGGT
1 ATAATATACAGCAGCATAAATTAAACAAAAAAAAA-TATGTTAAACTACATTTATAAAAAATGGT
55201012 TGAATTGTTTTA-TTTTATAATTATAAGTTTTTGAATATATAAAATAACAACTAAATTAGAAAGA
65 TGAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAACAACTAAATTAGAAAGA
55201076 ACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAA
130 ACAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAA
55201141 TAATTGAC
195 TAATTGAC
55201149 TGCATATTCC
Statistics
Matches: 198, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
238 158 0.80
239 40 0.20
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (238 bp):
ATAATATACAGCAGCATAAATTAAACAAAAAAAAATATGTTAAACTACATTTATAAAAAATGGTT
GAATTGTTTTATTTTTATAATTATAAGTTTTTGAATATATAAAATAACAACTAAATTAGAAAGAA
CAACAATAAATCTGCAGCTTCAAAATGATGGCTATAGTTTGATGATGATTGGTGCATACAAAAAT
AATTGACATTCTTTTCTCCTCAATTGATTAAATTAAAAATTAA
Found at i:55202837 original size:27 final size:29
Alignment explanation
Indices: 55202780--55202838 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
55202770 TTTGTTTTAA
*
55202780 ATGTAGTGTATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
55202809 ATGTAGTATATTTTAAAAATAAAAAATAT
1 ATGTAGTATATTTTAAAAATAAAAAATAT
55202838 A
1 A
55202839 GTTTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (29 bp):
ATGTAGTATATTTTAAAAATAAAAAATAT
Found at i:55202857 original size:9 final size:9
Alignment explanation
Indices: 55202843--55202880 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
55202833 AATATAGTTT
55202843 TTATTCGAA
1 TTATTCGAA
55202852 TTATTCGAA
1 TTATTCGAA
*
55202861 TTATTCGAG
1 TTATTCGAA
*
55202870 TTATTCAAA
1 TTATTCGAA
55202879 TT
1 TT
55202881 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:55205178 original size:3 final size:3
Alignment explanation
Indices: 55205170--55205212 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
55205160 ATATGTAGGT
*
55205170 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55205213 CAAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55205212 original size:12 final size:12
Alignment explanation
Indices: 55205170--55205226 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
55205160 ATATGTAGGT
*
55205170 ATAATAATAATA
1 ATAATAAAAATA
*
55205182 AT-ATATAATATA
1 ATAATA-AAAATA
55205194 ATAATAAAAATA
1 ATAATAAAAATA
55205206 ATAATAACAAA-A
1 ATAATAA-AAATA
*
55205218 TTAATAAAA
1 ATAATAAAA
55205227 TAGACTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.13
12 27 0.71
13 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:55205212 original size:15 final size:15
Alignment explanation
Indices: 55205172--55205228 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
55205162 ATGTAGGTAT
*
55205172 AATAATAATAATATAT
1 AATAATAATAATA-AA
55205188 AAT-ATAATAATAAA
1 AATAATAATAATAAA
*
55205202 AATAATAATAACAAA
1 AATAATAATAATAAA
*
55205217 ATTAATAA-AATA
1 AATAATAATAATA
55205229 GACTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.19
15 26 0.72
16 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:55205467 original size:19 final size:21
Alignment explanation
Indices: 55205429--55205467 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
55205419 CTTTTTTTAA
*
55205429 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
55205450 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
55205468 GAAAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:55205693 original size:21 final size:21
Alignment explanation
Indices: 55205667--55205721 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
55205657 AATCATATCT
55205667 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
55205688 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
55205707 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
55205722 CCTCGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:55205707 original size:24 final size:22
Alignment explanation
Indices: 55205644--55205709 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
55205634 AAATTAAATC
* *
55205644 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
55205667 TCTAAGATTG--TAT-ATATCAT
1 TCTAAGATTGCATATCATATC-T
55205687 ATCTAAGATTGCATATCATATCT
1 -TCTAAGATTGCATATCATATCT
55205710 AAGATTGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.14
20 3 0.08
21 10 0.28
23 13 0.36
24 5 0.14
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:55212292 original size:21 final size:21
Alignment explanation
Indices: 55212253--55212293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55212243 GCTTGAACCA
*
55212253 TGAACTTTAAACCTTAAATCT
1 TGAACTTTAAACCTCAAATCT
55212274 TGAACTTTAAA-CTCCAAATC
1 TGAACTTTAAACCT-CAAATC
55212294 CTAAACCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (21 bp):
TGAACTTTAAACCTCAAATCT
Found at i:55212318 original size:7 final size:7
Alignment explanation
Indices: 55212306--55212330 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55212296 AAACCTTGGA
55212306 GTTTAAG
1 GTTTAAG
55212313 GTTTAAG
1 GTTTAAG
55212320 GTTTAAG
1 GTTTAAG
55212327 GTTT
1 GTTT
55212331 GAGTTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
GTTTAAG
Found at i:55216563 original size:43 final size:43
Alignment explanation
Indices: 55216540--55216657 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 43
55216530 TTCTCTTAAG
* *
55216540 TGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTCCCACAAA
1 TGCCGCTAAAGAACAAGACCTTTAGCGACACTTTTCCCACAAA
* * *
55216583 TGCCGCTAAAGAACATGACCTTTAGCGACACTTCTT-TCATAAA
1 TGCCGCTAAAGAACAAGACCTTTAGCGACACTT-TTCCCACAAA
* *
55216626 CGCCGC-AAACGAACAA-ACCTTTAACGACACTT
1 TGCCGCTAAA-GAACAAGACCTTTAGCGACACTT
55216658 GTAGCAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
42 18 0.28
43 45 0.69
44 2 0.03
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (43 bp):
TGCCGCTAAAGAACAAGACCTTTAGCGACACTTTTCCCACAAA
Found at i:55220678 original size:121 final size:118
Alignment explanation
Indices: 55220430--55220763 Score: 311
Period size: 121 Copynumber: 2.7 Consensus size: 118
55220420 AAAAACGTCG
* * * *
55220430 TAAAAAATTTTTATTTTAAACAAAATTACGCCGTTTTGCTATACTATGCTGAAAGGGGTCTA-TT
1 TAAAAAATTTTTATTTTAAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTT
55220494 TTTTAAAGTAAAATTATTTTGTGGCGTTTTAAAAAACGCCACTATTGAAAAACGCTGCA
66 TTTTAAAGTAAAATTATTTTGTGGCGTTTTAAAAAACGCCACTATT-----A-GCTGCA
* *
55220553 -AAAAAA-TTTCATTTTAAACAAAACGACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTT
1 TAAAAAATTTTTATTTTAAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTT
* * *
55220616 TTTTAAAGTAAAATTATTTTGTGGTGTTTTTTTTTATAAAAACGCCGCTATT-GCT-TA
66 TTTTAAAGTAAAATTATTTTGTGGCG-----TTTTA-AAAAACGCCACTATTAGCTGCA
* *
55220673 TAAAAACGCCGCAAAAATTTTTTATTTTGAACAAAACTACGCCGTTTTACTATGCTATGCTAAAA
1 T----A------AAAAA-TTTTTATTTTAAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAA
*
55220738 -TGGGCTATTTTTTTAAAGTAAAATTA
55 GGGGGCTATTTTTTTAAAGTAAAATTA
55220764 ACCCCTAACA
Statistics
Matches: 177, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
120 1 0.01
121 51 0.29
122 33 0.19
125 1 0.01
127 5 0.03
128 14 0.08
131 5 0.03
132 25 0.14
133 42 0.24
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (118 bp):
TAAAAAATTTTTATTTTAAACAAAACTACGCCGTTTTGCTATGCTATGCTAAAAGGGGGCTATTT
TTTTAAAGTAAAATTATTTTGTGGCGTTTTAAAAAACGCCACTATTAGCTGCA
Found at i:55220807 original size:14 final size:14
Alignment explanation
Indices: 55220761--55220807 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
55220751 TAAAGTAAAA
*
55220761 TTAACCCCT-AACA
1 TTAACCCCTAAACC
55220774 TCTAACCCCTAAACCC
1 T-TAACCCCTAAA-CC
55220790 TTAACCCCTAAACC
1 TTAACCCCTAAACC
55220804 TTAA
1 TTAA
55220808 ATCCCAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 14 0.47
15 13 0.43
16 2 0.07
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.23
Consensus pattern (14 bp):
TTAACCCCTAAACC
Found at i:55221082 original size:15 final size:15
Alignment explanation
Indices: 55221064--55221094 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55221054 CCCCAGCACG
55221064 TCTAACCCCTAAACC
1 TCTAACCCCTAAACC
*
55221079 TCTAACTCCTAAACC
1 TCTAACCCCTAAACC
55221094 T
1 T
55221095 TAAATCCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (15 bp):
TCTAACCCCTAAACC
Found at i:55221125 original size:14 final size:14
Alignment explanation
Indices: 55221106--55221132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55221096 AAATCCCAAC
55221106 CCCTAATCCATAAT
1 CCCTAATCCATAAT
55221120 CCCTAATCCATAA
1 CCCTAATCCATAA
55221133 ACTCTAAACC
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:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCCTAATCCATAAT
Found at i:55221139 original size:14 final size:14
Alignment explanation
Indices: 55221106--55221139 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55221096 AAATCCCAAC
*
55221106 CCCTAATCCATAAT
1 CCCTAATCCATAAA
55221120 CCCTAATCCATAAA
1 CCCTAATCCATAAA
*
55221134 CTCTAA
1 CCCTAA
55221140 ACCCATACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (14 bp):
CCCTAATCCATAAA
Found at i:55221397 original size:72 final size:73
Alignment explanation
Indices: 55221307--55221460 Score: 220
Period size: 72 Copynumber: 2.1 Consensus size: 73
55221297 TATTTTTTTG
* * * * * *
55221307 GCCGCTAAATCCCCGAAAGCTCACAAAATGGCGTCGTTTGGCTTA-TTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCGGCGCTTAC
*
55221371 TTAAAAAC
66 TCAAAAAC
55221379 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCGGCGCTTAC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCGGCGCTTAC
*
55221444 TCAAAAAT
66 TCAAAAAC
*
55221452 GCCGATAAA
1 GCCGCTAAA
55221461 GCCCTAAGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 41 0.57
73 31 0.43
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (73 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCGGCGCTTAC
TCAAAAAC
Found at i:55221564 original size:114 final size:114
Alignment explanation
Indices: 55221360--55221574 Score: 349
Period size: 114 Copynumber: 1.9 Consensus size: 114
55221350 TATTTTTTTT
*
55221360 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAG
1 GCGGCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAG
*
55221425 GTTTTTTTGCGGCGCTTACTCAAAAATGCCGATAAAGCCCTAAGCATTA
66 GTTTTTTTGCGGCGCTTACTCAAAAACGCCGATAAAGCCCTAAGCATTA
* * * *
55221474 GCGGCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTAT
1 GCGGCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAG
* * *
55221539 GTTTTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAA
66 GTTTTTTTGCGGCGCTTACTCAAAAACGCCGATAAA
55221575 TCCCCAAAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 92 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (114 bp):
GCGGCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAG
GTTTTTTTGCGGCGCTTACTCAAAAACGCCGATAAAGCCCTAAGCATTA
Found at i:55221593 original size:73 final size:73
Alignment explanation
Indices: 55221474--55221647 Score: 267
Period size: 73 Copynumber: 2.4 Consensus size: 73
55221464 CTAAGCATTA
* * * * *
55221474 GCGGCGCCTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
55221539 GTTTTTTT
66 GTTTTTTT
55221547 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
*
55221612 TTTTTTTT
66 GTTTTTTT
* * *
55221620 GCGGCACTTTCTCAAAAACGCTGCTAAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAA
55221648 GCACTAAGCA
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 92 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (73 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTAT
GTTTTTTT
Found at i:55221621 original size:187 final size:187
Alignment explanation
Indices: 55221307--55221761 Score: 716
Period size: 187 Copynumber: 2.4 Consensus size: 187
55221297 TATTTTTTTG
*
55221307 GCCGCTAAATCCCCGAAAGCTCACAAAATGGCGTCGTTTGGCTTAT-TTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
* *
55221371 TTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCG
66 TTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCG
* * *
55221436 GCGCTTACTCAAAAATGCCGATAAAGCCCTAAGCATTAGCGGCGCCTTCTTAAAAAC
131 GCACTTACTCAAAAACGCCGATAAAGCACTAAGCATTAGCGGCGCCTTCTTAAAAAC
55221493 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
* **
55221558 TTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAAC-AGCGTCGTTGGGCTTATTTTTTTTTGC
66 TTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGA-CGTCGTTGGGATTAGGTTTTTTTGC
* * * * * *
55221622 GGCACTTTCTCAAAAACGCTGCTAAAGCACTAAGCATTAGTGGCGCTTTCTTTAAAAC
130 GGCACTTACTCAAAAACGCCGATAAAGCACTAAGCATTAGCGGCGCCTTCTTAAAAAC
* * *
55221680 GCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGTTTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
*
55221745 TCAAAAACGCCGCTAAA
66 TTAAAAACGCCGCTAAA
55221762 GCCCTGAGCA
Statistics
Matches: 248, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
186 46 0.19
187 202 0.81
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (187 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTGGCTTATGTTTTTTTGCGGCGCTTTC
TTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGACGTCGTTGGGATTAGGTTTTTTTGCG
GCACTTACTCAAAAACGCCGATAAAGCACTAAGCATTAGCGGCGCCTTCTTAAAAAC
Found at i:55221749 original size:114 final size:114
Alignment explanation
Indices: 55221549--55221847 Score: 517
Period size: 114 Copynumber: 2.6 Consensus size: 114
55221539 GTTTTTTTGC
* *
55221549 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACAGCGTCGTTGGGCTTATTT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
*
55221614 TTTTTTGCGGCACTTTCTCAAAAACGCTGCTAAAGCACTAAGCATTAGT
66 TTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGT
*
55221663 GGCGCTTTCTTTAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
* * *
55221728 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGT
66 TTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGT
* *
55221777 GGTGCTTTCTTAAAAACGCCGTTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
55221842 TTTTTT
66 TTTTTT
55221848 TACGCCGTTA
Statistics
Matches: 175, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 175 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (114 bp):
GGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCCACAAAACGGCGTCGTTGGGCTTATGT
TTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCACTAAGCATTAGT
Found at i:55221920 original size:98 final size:98
Alignment explanation
Indices: 55221751--55221945 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 98
55221741 TTTCTCAAAA
* * * *
55221751 ACGCCGCTAAAGCCCTGAGCATTAGTGGTGCTTTCTTAAAAACGCCGTTAAATCCCCAAAAGCCC
1 ACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCC
*
55221816 ACAAAACGGCGTCGTTGGGCTTATGTTTTTTTT
66 ACAAAACGGCATCGTTGGGCTTATGTTTTTTTT
* * *
55221849 ACGCCGTTAAATCCCTGACCATTAGCGGCGCTTTCTTAAAAATGCCGCTAAATCCCCAAAAGCCC
1 ACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCC
55221914 ACAAAACGGCATCGTTGGGCTTATGTTTTTTT
66 ACAAAACGGCATCGTTGGGCTTATGTTTTTTT
55221946 GCGGCGCTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (98 bp):
ACGCCGCTAAAGCCCTGACCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCAAAAGCCC
ACAAAACGGCATCGTTGGGCTTATGTTTTTTTT
Found at i:55221993 original size:73 final size:72
Alignment explanation
Indices: 55221873--55222027 Score: 211
Period size: 73 Copynumber: 2.1 Consensus size: 72
55221863 CTGACCATTA
* * * **
55221873 GCGGCGCTTTCTTAAAAATGCCGCTAAATCCCCAAAAGCCCACAAAACGGCATCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCAGCTAAATCCCCAAAAGCCCACAAAACAACATCGTTGGGCTTA-
*
55221938 GTTTTTTT
65 GGTTTTTT
* ** *
55221946 GCGGCGCTTTCTCAAAAACGCAGCTAAATCCCCAAAAGCTCTGAAAACAACGTCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCAGCTAAATCCCCAAAAGCCCACAAAACAACATCGTTGGGCTTAG
55222011 GTTTTTT
66 GTTTTTT
55222018 GCGGCGCTTT
1 GCGGCGCTTT
55222028 TTGGAAAACG
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 17 0.24
73 55 0.76
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCAGCTAAATCCCCAAAAGCCCACAAAACAACATCGTTGGGCTTAG
GTTTTTT
Found at i:55222130 original size:12 final size:12
Alignment explanation
Indices: 55222113--55222138 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55222103 TTTTTTATCT
55222113 AAACGCCGCTAA
1 AAACGCCGCTAA
55222125 AAACGCCGCTAA
1 AAACGCCGCTAA
55222137 AA
1 AA
55222139 GCTTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:55222516 original size:15 final size:16
Alignment explanation
Indices: 55222498--55222527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55222488 TCACATTACA
55222498 AAAATTA-TTTACATG
1 AAAATTATTTTACATG
55222513 AAAATTATTTTACAT
1 AAAATTATTTTACAT
55222528 TGCCAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (16 bp):
AAAATTATTTTACATG
Found at i:55224170 original size:22 final size:21
Alignment explanation
Indices: 55224140--55224208 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
55224130 ATGCTAGAAT
*
55224140 TCATGATTAGGTTGACTGAAA
1 TCATAATTAGGTTGACTGAAA
*
55224161 TCATAAATTA---TG-CTAGAAT
1 TCAT-AATTAGGTTGACT-GAAA
*
55224180 TCATGATTAGGTTGACTGAAA
1 TCATAATTAGGTTGACTGAAA
55224201 TCA-AATTA
1 TCATAATTA
55224209 TATTTATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
18 6 0.16
19 9 0.24
20 4 0.11
21 12 0.32
22 6 0.16
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
TCATAATTAGGTTGACTGAAA
Found at i:55224178 original size:40 final size:40
Alignment explanation
Indices: 55224123--55224203 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
55224113 CAATGGTAGA
55224123 ATAAATTATGCTAGAATTCATGATTAGGTTGACTGAAATC
1 ATAAATTATGCTAGAATTCATGATTAGGTTGACTGAAATC
55224163 ATAAATTATGCTAGAATTCATGATTAGGTTGACTGAAATC
1 ATAAATTATGCTAGAATTCATGATTAGGTTGACTGAAATC
55224203 A
1 A
55224204 AATTATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (40 bp):
ATAAATTATGCTAGAATTCATGATTAGGTTGACTGAAATC
Found at i:55227207 original size:15 final size:15
Alignment explanation
Indices: 55227187--55227218 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55227177 AGCTAAATTG
55227187 AAATTAAAAGTAGAA
1 AAATTAAAAGTAGAA
55227202 AAATTAAAAGTAGAA
1 AAATTAAAAGTAGAA
55227217 AA
1 AA
55227219 CTAAGTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (15 bp):
AAATTAAAAGTAGAA
Found at i:55232859 original size:15 final size:16
Alignment explanation
Indices: 55232839--55232868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55232829 TGGTGCCTTG
55232839 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
55232854 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
55232869 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:55252911 original size:25 final size:26
Alignment explanation
Indices: 55252883--55252931 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
55252873 TAAATGAAGT
55252883 TATAAATGTAATG-TTG-GTTTGAATA
1 TATAAATGT-ATGTTTGTGTTTGAATA
55252908 TATAAATGTATGTTTGTGTTTGAA
1 TATAAATGTATGTTTGTGTTTGAA
55252932 GCCATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.14
25 12 0.55
26 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (26 bp):
TATAAATGTATGTTTGTGTTTGAATA
Found at i:55252938 original size:26 final size:25
Alignment explanation
Indices: 55252884--55252938 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
55252874 AAATGAAGTT
* *
55252884 ATAAATGTAATGTTGGTTTGAATAT
1 ATAAATGTAATGTTGGTTTGAAGAC
*
55252909 ATAAATGT-ATGTTTGTGTTTGAAGCC
1 ATAAATGTAATG-TTG-GTTTGAAGAC
55252935 ATAA
1 ATAA
55252939 TTTGACATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 3 0.12
25 11 0.44
26 11 0.44
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.42
Consensus pattern (25 bp):
ATAAATGTAATGTTGGTTTGAAGAC
Found at i:55253816 original size:18 final size:18
Alignment explanation
Indices: 55253793--55253828 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55253783 AATAGAGATA
55253793 GAGTCATTAGCTATGTTG
1 GAGTCATTAGCTATGTTG
55253811 GAGTCATTAGCTATGTTG
1 GAGTCATTAGCTATGTTG
55253829 ATGCTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (18 bp):
GAGTCATTAGCTATGTTG
Found at i:55261951 original size:35 final size:35
Alignment explanation
Indices: 55261912--55261982 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
55261902 AGAAAGAATC
55261912 TACCTTTGTTTTCTTGTTTTTTTGTTGTTAGCATA
1 TACCTTTGTTTTCTTGTTTTTTTGTTGTTAGCATA
55261947 TACCTTTGTTTTCTTGTTTTTTTGTTGTTAGCATA
1 TACCTTTGTTTTCTTGTTTTTTTGTTGTTAGCATA
55261982 T
1 T
55261983 CTTCAACAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.11, C:0.11, G:0.14, T:0.63
Consensus pattern (35 bp):
TACCTTTGTTTTCTTGTTTTTTTGTTGTTAGCATA
Found at i:55267196 original size:20 final size:20
Alignment explanation
Indices: 55267171--55267215 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
55267161 TGTTAAAACA
*
55267171 TTATTAACACGAAAATAACT
1 TTATTAACACAAAAATAACT
55267191 TTATTAACACAAAAATAACT
1 TTATTAACACAAAAATAACT
55267211 TTATT
1 TTATT
55267216 TTTGAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (20 bp):
TTATTAACACAAAAATAACT
Found at i:55267738 original size:3 final size:3
Alignment explanation
Indices: 55267730--55267758 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55267720 ATACTATCGC
55267730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55267759 AATCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55268086 original size:73 final size:75
Alignment explanation
Indices: 55267982--55268132 Score: 180
Period size: 73 Copynumber: 2.0 Consensus size: 75
55267972 GAAGTAAAAG
* *
55267982 AATAAATAAGTGAATAATAGATAAAACAAATGTAAACAATTTTAAATTTAAGCATTTGAAAAGTA
1 AATAAATAAGT-AATAATAGATAAAACAAATGTAAACAATATTAAATTTAAACATTTGAAAAGTA
55268047 AAAGAATAATA
65 AAAGAATAATA
** ** * * * *
55268058 AATAAATAAGT-A-AATAGATAAAGTAAATGTTCATAATATTAGATTTAAATATTTTAAAAGTAA
1 AATAAATAAGTAATAATAGATAAAACAAATGTAAACAATATTAAATTTAAACATTTGAAAAGTAA
*
55268121 AAGAATGATA
66 AAGAATAATA
55268131 AA
1 AA
55268133 AGGATGAGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
73 52 0.81
74 1 0.02
76 11 0.17
ACGTcount: A:0.57, C:0.03, G:0.11, T:0.30
Consensus pattern (75 bp):
AATAAATAAGTAATAATAGATAAAACAAATGTAAACAATATTAAATTTAAACATTTGAAAAGTAA
AAGAATAATA
Found at i:55268158 original size:73 final size:71
Alignment explanation
Indices: 55268035--55268201 Score: 167
Period size: 73 Copynumber: 2.3 Consensus size: 71
55268025 AAATTTAAGC
* * * * *
55268035 ATTTGAAAAGTAAAAGAATAATAAATAAATAAGTAAATAGATAAAGTAAATGTTCATAATATTAG
1 ATTTTAAAAGTAAAAGAATGATAAATAAATAAGTAAATAAATAAAGTAAAT-AT-ATAATATTAA
**
55268100 ATTTAAAT
64 ACATAAAT
* * *
55268108 ATTTTAAAAGTAAAAGAATGATAAA-AGGATGAGTAAATAAATGAAA-TAAATATATAGTATTAA
1 ATTTTAAAAGTAAAAGAATGATAAATA-AATAAGTAAATAAAT-AAAGTAAATATATAATATTAA
*
55268171 ACATAGAT
64 ACATAAAT
*
55268179 ATTTTAAACGGTAAAAGAATGAT
1 ATTTTAAA-AGTAAAAGAATGAT
55268202 GAACAAAAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
71 21 0.27
72 15 0.19
73 40 0.51
74 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.13, T:0.30
Consensus pattern (71 bp):
ATTTTAAAAGTAAAAGAATGATAAATAAATAAGTAAATAAATAAAGTAAATATATAATATTAAAC
ATAAAT
Done.