Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 15
Found at i:1516267 original size:27 final size:27
Alignment explanation
Indices: 1516237--1516291 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1516227 TCTTGACATC
** *
1516237 TTACAATATAAGGGTATTTTCGTAATT
1 TTACAATATAAGAATATTTTCATAATT
* *
1516264 TTACACTATCAGAATATTTTCATAATT
1 TTACAATATAAGAATATTTTCATAATT
1516291 T
1 T
1516292 CTCATCCAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (27 bp):
TTACAATATAAGAATATTTTCATAATT
Found at i:1518099 original size:14 final size:13
Alignment explanation
Indices: 1518080--1518109 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1518070 AAGATCACTT
1518080 GATGAACAATATTC
1 GATGAACAATA-TC
1518094 GATGAACAATATC
1 GATGAACAATATC
1518107 GAT
1 GAT
1518110 ACTTCAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (13 bp):
GATGAACAATATC
Found at i:1521786 original size:31 final size:30
Alignment explanation
Indices: 1521722--1521787 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
1521712 ACAGTGTTCC
*** *
1521722 ACTCGTATTCGTTAAAATTTTTTTTGCTCG
1 ACTCGTATTCGTTAAAAAACTTGTTGCTCG
*
1521752 ACTCGTATTCGTTAAAAAAACTTGTTGCTTG
1 ACTCGTATTCGTT-AAAAAACTTGTTGCTCG
1521783 ACTCG
1 ACTCG
1521788 ACTCGTTGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (30 bp):
ACTCGTATTCGTTAAAAAACTTGTTGCTCG
Found at i:1534312 original size:30 final size:30
Alignment explanation
Indices: 1534276--1534378 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
1534266 TCCGAAGGAC
1534276 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1534306 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1534336 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1534366 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1534379 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1534395 original size:30 final size:30
Alignment explanation
Indices: 1534352--1534445 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
1534342 AGAGGTCATA
* * *
1534352 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
1534382 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
1534413 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
1534444 AA
1 AA
1534446 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:1534395 original size:60 final size:61
Alignment explanation
Indices: 1534276--1534403 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 61
1534266 TCCGAAGGAC
* * *
1534276 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
1534336 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
1534397 CTATCCA
1 CTATCCA
1534404 TATGTTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 51 0.85
61 9 0.15
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:1534452 original size:31 final size:30
Alignment explanation
Indices: 1534361--1534456 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
1534351 AAAGATCCTC
* * *
1534361 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
1534391 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
1534422 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
1534453 GGTA
1 GGTA
1534457 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:1534639 original size:4 final size:4
Alignment explanation
Indices: 1534630--1534654 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1534620 ATATAACCAT
1534630 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
1534655 GTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1535483 original size:21 final size:21
Alignment explanation
Indices: 1535459--1535501 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1535449 TCATATTCGT
* *
1535459 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
1535480 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
1535501 T
1 T
1535502 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:1542277 original size:15 final size:16
Alignment explanation
Indices: 1542246--1542284 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1542236 TCTCTAAATC
*
1542246 TCCCTAAATCGTTAAA
1 TCCCAAAATCGTTAAA
1542262 TCCCAAAATC-TTAAA
1 TCCCAAAATCGTTAAA
1542277 TCCTCAAA
1 TCC-CAAA
1542285 CTCATAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (16 bp):
TCCCAAAATCGTTAAA
Found at i:1543820 original size:17 final size:17
Alignment explanation
Indices: 1543798--1543858 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
1543788 GACTTCAATT
1543798 TTTTAATATATGGGTTC
1 TTTTAATATATGGGTTC
* * *
1543815 TTTTAATATGT-AGTTA
1 TTTTAATATATGGGTTC
*
1543831 TTATAACTA-ATGGGTTC
1 TTTTAA-TATATGGGTTC
*
1543848 TTTTACTATAT
1 TTTTAATATAT
1543859 AAAATATTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTTAATATATGGGTTC
Found at i:1547289 original size:12 final size:12
Alignment explanation
Indices: 1547272--1547296 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1547262 AAACTTTTTC
1547272 GAATCGAGTCGA
1 GAATCGAGTCGA
1547284 GAATCGAGTCGA
1 GAATCGAGTCGA
1547296 G
1 G
1547297 TTTTGCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (12 bp):
GAATCGAGTCGA
Found at i:1563930 original size:3 final size:3
Alignment explanation
Indices: 1563924--1564035 Score: 152
Period size: 3 Copynumber: 36.7 Consensus size: 3
1563914 TCATTTAAAT
** *
1563924 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1563972 ATA TTA TAA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1564018 TTA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TT
1564036 TAATAAATAA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
3 89 0.94
4 6 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1564074 original size:25 final size:26
Alignment explanation
Indices: 1564046--1564096 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
1564036 TAATAAATAA
1564046 TTACAAACAAACT-GAACCGGCCCAG
1 TTACAAACAAACTAGAACCGGCCCAG
1564071 TTACAAACAAACTAGAACCGGCCCAG
1 TTACAAACAAACTAGAACCGGCCCAG
1564097 ACTAACCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.41, C:0.31, G:0.16, T:0.12
Consensus pattern (26 bp):
TTACAAACAAACTAGAACCGGCCCAG
Found at i:1565418 original size:17 final size:15
Alignment explanation
Indices: 1565384--1565431 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
1565374 TAAATATTGT
*
1565384 ATAAATATATAATAA
1 ATAAATATTTAATAA
1565399 ATAAATATTTAATTTAA
1 ATAAATATTTAA--TAA
1565416 ATAAATTATTTTAATA
1 ATAAA-TA-TTTAATA
1565432 TTTAGTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.39
17 10 0.36
18 2 0.07
19 5 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATATTTAATAA
Found at i:1568645 original size:187 final size:186
Alignment explanation
Indices: 1568272--1568832 Score: 864
Period size: 187 Copynumber: 3.0 Consensus size: 186
1568262 AAGAATATAC
* * *
1568272 GCTTGGATTCACCACCCATCTCTCTATGATCTCCTTTTGAACCATCTTCTTCAAATTCAAAGAA-
1 GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGAACCATCTTCTTCAAATTCAAGGAAC
* * * *
1568336 CC--TTTTT--TTTATTCTATAATATTCGTTTCTCCCTCGTTTTTCTGGTAGAAAACTGCAAAGG
66 CCATTTTTTAGTTTATTCTATAATATTCGTTTCT--CTCTTTTTTCTGGCAGAAAACTGAAAAAG
* *
1568397 AATTGGATTTGATGCATGCATACCATGTTTTTGTGAATATTTCTGAATAAAACTTTGA
129 AATTGGATTTGATGCATGCACACCATGTGTTTGTGAATATTTCTGAATAAAACTTTGA
* *
1568455 GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGGACAAT-TCTCTTCAAATTCAAGGAA
1 GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGAACCATCT-TCTTCAAATTCAAGGAA
* * * *
1568519 CCCATTTTTTAGTTTCTTCTATAACATTCGTTTCTCTCTTTTTTGCTGGCAGAAATCTGAAAAAC
65 CCCATTTTTTAGTTTATTCTATAATATTCGTTTCTCTCTTTTTT-CTGGCAGAAAACTGAAAAAG
* * *
1568584 AATTGGATTTGATGCATGCACACCATGTGTTTATGAATGTTTCTGAATAAATCTTTGA
129 AATTGGATTTGATGCATGCACACCATGTGTTTGTGAATATTTCTGAATAAAACTTTGA
1568642 GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGAACCATCTTCTTCAAATTCAAGGAAC
1 GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGAACCATCTTCTTCAAATTCAAGGAAC
* *
1568707 CCATTTTTTAGTTTATTCTATAATATTCGTTTATCTCTTTTTTATGGCAGAAAACTGAAAAAGAA
66 CCATTTTTTAGTTTATTCTATAATATTCGTTTCTCTCTTTTTTCTGGCAGAAAACTGAAAAAGAA
1568772 TTGGATTTGATGCATGCACACCATGTGTTTGTGAATATTTCTGAATAAAACTTTGA
131 TTGGATTTGATGCATGCACACCATGTGTTTGTGAATATTTCTGAATAAAACTTTGA
1568828 GCTTG
1 GCTTG
1568833 TATTGTTTGA
Statistics
Matches: 341, Mismatches: 29, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
182 1 0.00
183 57 0.17
184 2 0.01
186 90 0.26
187 169 0.50
188 22 0.06
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (186 bp):
GCTTGAATTCACCACCCATCTCTCTATGATCTCCTCTTGAACCATCTTCTTCAAATTCAAGGAAC
CCATTTTTTAGTTTATTCTATAATATTCGTTTCTCTCTTTTTTCTGGCAGAAAACTGAAAAAGAA
TTGGATTTGATGCATGCACACCATGTGTTTGTGAATATTTCTGAATAAAACTTTGA
Found at i:1587434 original size:32 final size:31
Alignment explanation
Indices: 1587398--1587474 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1587388 CGGGGCCGTG
* *
1587398 GGGCCTACCTAAGAACACATCTTAGGGTCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1587430 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1587461 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1587475 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1588380 original size:17 final size:17
Alignment explanation
Indices: 1588358--1588426 Score: 111
Period size: 17 Copynumber: 4.1 Consensus size: 17
1588348 ACGGTCACAT
*
1588358 TCAACGGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
*
1588375 TCAACGGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
*
1588392 TCAACAGTCGGGTAGGG
1 TCAACAGTCGGGTCGGG
1588409 TCAACAGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
1588426 T
1 T
1588427 TAACCCGGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.16, C:0.22, G:0.43, T:0.19
Consensus pattern (17 bp):
TCAACAGTCGGGTCGGG
Found at i:1588452 original size:9 final size:9
Alignment explanation
Indices: 1588440--1588482 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
1588430 CCCGGTTCAG
1588440 ACCGGTCAA
1 ACCGGTCAA
1588449 ACCGGTCAA
1 ACCGGTCAA
1588458 ACCGGTTCAA
1 ACCGG-TCAA
**
1588468 AATGGTCAA
1 ACCGGTCAA
1588477 ACCGGT
1 ACCGGT
1588483 TTTTCCAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 22 0.76
10 7 0.24
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1588467 original size:19 final size:19
Alignment explanation
Indices: 1588440--1588483 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1588430 CCCGGTTCAG
*
1588440 ACCGG-TCAAACCGGTCAA
1 ACCGGTTCAAAACGGTCAA
*
1588458 ACCGGTTCAAAATGGTCAA
1 ACCGGTTCAAAACGGTCAA
1588477 ACCGGTT
1 ACCGGTT
1588484 TTTCCAGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (19 bp):
ACCGGTTCAAAACGGTCAA
Found at i:1594775 original size:32 final size:31
Alignment explanation
Indices: 1594739--1594815 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1594729 CGGGGCCGTG
*
1594739 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1594771 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
**
1594802 AAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1594816 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1595674 original size:21 final size:21
Alignment explanation
Indices: 1595648--1595692 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1595638 GATTTCTGGG
* *
1595648 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
* *
1595669 CAAGGGTAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1595690 CAA
1 CAA
1595693 ACGACAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1596297 original size:18 final size:18
Alignment explanation
Indices: 1596274--1596308 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1596264 CTAGGAGATT
1596274 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1596292 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1596309 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1596394 original size:21 final size:22
Alignment explanation
Indices: 1596365--1596408 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1596355 GTTGTATGAT
1596365 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
1596386 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
1596408 A
1 A
1596409 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:1597358 original size:149 final size:149
Alignment explanation
Indices: 1597180--1597483 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1597170 GAGTCGAGGG
1597180 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1597245 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1597310 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1597329 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1597394 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1597459 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1597478 TCTACG
1 TCTACG
1597484 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1597506 original size:23 final size:23
Alignment explanation
Indices: 1597462--1597506 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1597452 ATCATTATAT
*
1597462 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1597485 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1597507 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1598956 original size:17 final size:17
Alignment explanation
Indices: 1598934--1598970 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1598924 GTCAACGGTA
1598934 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
1598951 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
1598968 AAC
1 AAC
1598971 CCGGTTCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.16
Consensus pattern (17 bp):
AACGGTCGGGTCGGGTC
Found at i:1598986 original size:19 final size:19
Alignment explanation
Indices: 1598964--1599016 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1598954 GGTCGGGTCG
1598964 GGTCAACCCGGTTCAGACC
1 GGTCAACCCGGTTCAGACC
1598983 GGTCAACCCGGTTCAGACC
1 GGTCAACCCGGTTCAGACC
*
1599002 GGTCAAACCGGTTCA
1 GGTCAACCCGGTTCA
1599017 AAACTGGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAACCCGGTTCAGACC
Found at i:1599017 original size:10 final size:10
Alignment explanation
Indices: 1598966--1599034 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
1598956 TCGGGTCGGG
*
1598966 TCAACCCGGT
1 TCAAACCGGT
*
1598976 TCAGACCGG-
1 TCAAACCGGT
*
1598985 TCAACCCGGT
1 TCAAACCGGT
*
1598995 TCAGACCGG-
1 TCAAACCGGT
1599004 TCAAACCGGT
1 TCAAACCGGT
*
1599014 TCAAAACTGG-
1 TC-AAACCGGT
1599024 TCAAACCGGT
1 TCAAACCGGT
1599034 T
1 T
1599035 TTTCCAGCAG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1602419 original size:21 final size:20
Alignment explanation
Indices: 1602392--1602442 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1602382 AAAAAATAAA
*
1602392 AATTTATATTATAATATATTT
1 AATTTATATGATAATA-ATTT
1602413 -ATATTATAATGATAATAATTT
1 AAT-TTAT-ATGATAATAATTT
1602434 AATTTATAT
1 AATTTATAT
1602443 AAATTAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 4 0.15
21 12 0.46
22 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AATTTATATGATAATAATTT
Found at i:1606845 original size:121 final size:120
Alignment explanation
Indices: 1606609--1606850 Score: 403
Period size: 121 Copynumber: 2.0 Consensus size: 120
1606599 GGCCGTCATT
* *
1606609 TGGACATCTAGACTTGAATTATTTTATGGAAGAATTTGCATAGTTGGAGGAAAAAAATATGACTG
1 TGGACATCTAGACTTGAATTATTTTATGGAAGAACTTGCATAGTTGGAGAAAAAAAATATGACTG
* *
1606674 CAAGAATCTATTCTAACTTCTCTGTTAGAAATATTGAGGAAGAATTGGAAATTAA
66 CAAGAATCTATTCTAACTTCACTGCTAGAAATATTGAGGAAGAATTGGAAATTAA
*
1606729 TGGACATCTAGACTTGTATTATTTTATGGAAGAACTTGCATAGTTGGAGAAAAAAAAATATGACT
1 TGGACATCTAGACTTGAATTATTTTATGGAAGAACTTGCATAGTTGGAG-AAAAAAAATATGACT
* * *
1606794 GCAAGAATCTATTCTCATTTCACTGCTAGAAATATTGTGGAAGAATTGGAAATTAA
65 GCAAGAATCTATTCTAACTTCACTGCTAGAAATATTGAGGAAGAATTGGAAATTAA
1606850 T
1 T
1606851 TTACAATGTT
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
120 47 0.42
121 66 0.58
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (120 bp):
TGGACATCTAGACTTGAATTATTTTATGGAAGAACTTGCATAGTTGGAGAAAAAAAATATGACTG
CAAGAATCTATTCTAACTTCACTGCTAGAAATATTGAGGAAGAATTGGAAATTAA
Found at i:1609978 original size:60 final size:59
Alignment explanation
Indices: 1609848--1609991 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 59
1609838 AGTTTGGAAA
* *
1609848 ATATTA-ATAGTCG-AGTGACCATTTTATAATTTTTAATAGTCAAGGGACTCAACAAAGC
1 ATATTACATAGTCGAAG-GACCATTTTATAACTTCTAATAGTCAAGGGACTCAACAAAGC
**** * *
1609906 ATCGCCCTATAGTCGAAGGACCATTTTATAACTTCTAATAGTCGAGGGACTCAACAAAGT
1 ATATTAC-ATAGTCGAAGGACCATTTTATAACTTCTAATAGTCAAGGGACTCAACAAAGC
*
1609966 AGTATTACATAGTCAAAGGACCATTT
1 A-TATTACATAGTCGAAGGACCATTT
1609992 ATGTACTTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
58 2 0.03
60 63 0.91
61 4 0.06
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (59 bp):
ATATTACATAGTCGAAGGACCATTTTATAACTTCTAATAGTCAAGGGACTCAACAAAGC
Found at i:1610050 original size:23 final size:23
Alignment explanation
Indices: 1610007--1610051 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1609997 CTTTACCCTT
* *
1610007 TTTTATATTAGTTTTAGGAAAAG
1 TTTTATATTACTTTTAAGAAAAG
1610030 TTTTATATT-CTTTTGAAGAAAA
1 TTTTATATTACTTTT-AAGAAAA
1610052 TCAATTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTTATATTACTTTTAAGAAAAG
Found at i:1610335 original size:7 final size:7
Alignment explanation
Indices: 1610323--1610353 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1610313 TTAAGAAATT
1610323 ATTTAAA
1 ATTTAAA
1610330 ATTTAAA
1 ATTTAAA
1610337 ATTTAAA
1 ATTTAAA
*
1610344 ATATAAA
1 ATTTAAA
1610351 ATT
1 ATT
1610354 ACAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:1610335 original size:19 final size:20
Alignment explanation
Indices: 1610283--1610335 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
1610273 GTTTGAGTAT
*
1610283 TTATTTAATATTTAAGAAAA
1 TTATTTAAAATTTAAGAAAA
* **
1610303 TAAAATAAAA-TTAAG-AAA
1 TTATTTAAAATTTAAGAAAA
1610321 TTATTTAAAATTTAA
1 TTATTTAAAATTTAA
1610336 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
18 10 0.40
19 9 0.36
20 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
TTATTTAAAATTTAAGAAAA
Found at i:1610391 original size:15 final size:15
Alignment explanation
Indices: 1610371--1610414 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1610361 TTAGAACACT
1610371 ATTAAATATATAAAA
1 ATTAAATATATAAAA
*
1610386 ATTAAATA-ATAAAT
1 ATTAAATATATAAAA
1610400 A-TAAA-AT-TAAAA
1 ATTAAATATATAAAA
1610412 ATT
1 ATT
1610415 TTAAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 6 0.24
13 5 0.20
14 6 0.24
15 8 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAATATATAAAA
Found at i:1610458 original size:8 final size:8
Alignment explanation
Indices: 1610307--1610459 Score: 68
Period size: 8 Copynumber: 18.8 Consensus size: 8
1610297 AGAAAATAAA
1610307 ATAAAATT
1 ATAAAATT
1610315 A-AGAAATT
1 ATA-AAATT
1610323 ATTTAAAATT
1 A--TAAAATT
1610333 -TAAAATT
1 ATAAAATT
1610340 -TAAAA-T
1 ATAAAATT
1610346 ATAAAATT
1 ATAAAATT
*
1610354 ACAAAAATT
1 A-TAAAATT
* * *
1610363 AGAACACT
1 ATAAAATT
*
1610371 ATTAAATAT
1 ATAAAAT-T
1610380 ATAAAAATT
1 AT-AAAATT
*
1610389 AAATAATAAAT
1 --ATAA-AATT
1610400 ATAAAATT
1 ATAAAATT
1610408 A-AAAATT
1 ATAAAATT
* **
1610415 TTAAAAAA
1 ATAAAATT
*
1610423 ACAAAATCT
1 ATAAAAT-T
*
1610432 ATAAAATG
1 ATAAAATT
1610440 AT-AAATT
1 ATAAAATT
1610447 -TAAAATT
1 ATAAAATT
1610454 ATAAAA
1 ATAAAA
1610460 AAAATCAAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
6 2 0.02
7 33 0.31
8 35 0.32
9 21 0.19
10 11 0.10
11 6 0.06
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (8 bp):
ATAAAATT
Found at i:1610488 original size:25 final size:26
Alignment explanation
Indices: 1610431--1610489 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1610421 AAACAAAATC
*
1610431 TATAAAATGATAAATTTAAAATTATA
1 TATAAAATCATAAATTTAAAATTATA
* * * *
1610457 AAAAAAATCA-AAATTTAAATTTATT
1 TATAAAATCATAAATTTAAAATTATA
1610482 TATAAAAT
1 TATAAAAT
1610490 ATTAATAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
TATAAAATCATAAATTTAAAATTATA
Found at i:1610775 original size:17 final size:17
Alignment explanation
Indices: 1610748--1610830 Score: 82
Period size: 17 Copynumber: 4.9 Consensus size: 17
1610738 TATTCTATTT
1610748 TTTTA-ATATTTTAATA
1 TTTTATATATTTTAATA
* *
1610764 TTTTATAGATTTTAATT
1 TTTTATATATTTTAATA
*
1610781 TTTTAATAATTTTTTAAT-
1 TTTT-AT-ATATTTTAATA
*
1610799 TTTTAGTATTTTTTAATA
1 TTTTA-TATATTTTAATA
1610817 TTTTA-ATATTTTAA
1 TTTTATATATTTTAA
1610831 ATTATTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.23
17 24 0.42
18 12 0.21
19 8 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATATATTTTAATA
Found at i:1610779 original size:25 final size:24
Alignment explanation
Indices: 1610748--1610847 Score: 78
Period size: 26 Copynumber: 3.9 Consensus size: 24
1610738 TATTCTATTT
1610748 TTTTAATATTTTAATATTTTATAGA
1 TTTTAATATTTTAATATTTTATA-A
* *
1610773 TTTTAATTTTTTAATAATTTTTTAA
1 TTTTAATATTTTAAT-ATTTTATAA
*
1610798 TTTTTAGTATTTTTTAATATTTTA-ATA
1 -TTTTA--ATATTTTAATATTTTATA-A
*
1610825 TTTTAAATTATTTTTAT-TTTTAT
1 TTTT-AA-TATTTTAATATTTTAT
1610848 TTTTTAAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
25 21 0.34
26 24 0.39
27 7 0.11
28 10 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAATATTTTAATATTTTATAA
Found at i:1610801 original size:18 final size:17
Alignment explanation
Indices: 1610747--1610828 Score: 80
Period size: 18 Copynumber: 4.8 Consensus size: 17
1610737 GTATTCTATT
1610747 TTTTTAATA--TTTTAA
1 TTTTTAATATTTTTTAA
**
1610762 TATTTT-ATAGATTTTAA
1 T-TTTTAATATTTTTTAA
1610779 TTTTTTAATAATTTTTTAA
1 -TTTTTAAT-ATTTTTTAA
*
1610798 TTTTTAGTATTTTTTAA
1 TTTTTAATATTTTTTAA
1610815 TATTTTAATATTTT
1 T-TTTTAATATTTT
1610829 AAATTATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.07
16 4 0.07
17 20 0.36
18 21 0.38
19 7 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTTAATATTTTTTAA
Found at i:1610813 original size:36 final size:36
Alignment explanation
Indices: 1610744--1610828 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
1610734 AAGGTATTCT
*
1610744 ATTTTTT--TAATATTTTAATATTTTATAGATTTTA
1 ATTTTTTAATAATTTTTTAATATTTTATAGATTTTA
**
1610778 ATTTTTTAATAATTTTTTAAT-TTTTAGTATTTTTTA
1 ATTTTTTAATAATTTTTTAATATTTTA-TAGATTTTA
*
1610814 ATATTTTAAT-ATTTT
1 ATTTTTTAATAATTTT
1610829 AAATTATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
34 7 0.16
35 10 0.23
36 27 0.61
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (36 bp):
ATTTTTTAATAATTTTTTAATATTTTATAGATTTTA
Found at i:1610838 original size:10 final size:8
Alignment explanation
Indices: 1610748--1610830 Score: 78
Period size: 8 Copynumber: 9.8 Consensus size: 8
1610738 TATTCTATTT
1610748 TTTTAATA
1 TTTTAATA
1610756 TTTTAATA
1 TTTTAATA
*
1610764 TTTTATAGA
1 TTTTA-ATA
*
1610773 TTTTAATT
1 TTTTAATA
1610781 TTTTAATAA
1 TTTTAAT-A
1610790 TTTTTTAAT-
1 --TTTTAATA
*
1610799 TTTTAGTATT
1 TTTTA--ATA
1610809 TTTTAATA
1 TTTTAATA
1610817 TTTTAATA
1 TTTTAATA
1610825 TTTTAA
1 TTTTAA
1610831 ATTATTTTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
7 5 0.08
8 37 0.59
9 9 0.14
10 5 0.08
11 7 0.11
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTTAATA
Found at i:1612450 original size:73 final size:72
Alignment explanation
Indices: 1612319--1612536 Score: 233
Period size: 73 Copynumber: 2.9 Consensus size: 72
1612309 TTTACAAATG
* * *
1612319 ATTTTTGAAAATACGTATATGATATATAGTTTTTAAAACATTTTTTTGAAACTATATATATTATA
1 ATTTTCGAAAATA--TATATAATATATAGTTTTTAAAACA--TTTTTGAAAAT-TATATATTATA
*
1612384 TAGTTTTTAAAAC
61 TAATTTTT-AAAC
1612397 ATTTTCGAAAAT-TATATAATATATAGTTTTTAAAACATTTTTGGAAAATTATATATTATATAAT
1 ATTTTCGAAAATATATATAATATATAGTTTTTAAAACATTTTT-GAAAATTATATATTATATAAT
* *
1612461 TTTTGAAT
65 TTTTAAAC
* ** * * *
1612469 TTTTTTTAAAATATATATAATATATAGTTTTTTAAATCA-TTTTGAAAACTTATATAATATATTA
1 ATTTTCGAAAATATATATAATATATAG-TTTTTAAAACATTTTTGAAAA-TTATATATTATATAA
1612533 TTTT
64 TTTT
1612537 GGAAAAAATA
Statistics
Matches: 124, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
72 16 0.13
73 58 0.47
74 15 0.12
75 24 0.19
78 11 0.09
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (72 bp):
ATTTTCGAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAATTATATATTATATAATT
TTTAAAC
Found at i:1612523 original size:37 final size:36
Alignment explanation
Indices: 1612294--1612602 Score: 239
Period size: 37 Copynumber: 8.2 Consensus size: 36
1612284 TATATATACA
** **
1612294 TATATATATATATAGTTTACAAATGATTTTTGAAAAT
1 TATATA-ATATATAGTTTTTAAAACATTTTTGAAAAT
* *
1612331 ACGTATATGATATATAGTTTTTAAAACATTTTTTTGAAACT
1 ---TATATAATATATAGTTTTTAAAACA--TTTTTGAAAAT
* *
1612372 ATATATATTATATAGTTTTTAAAACATTTTCGAAAAT
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
1612409 TATATAATATATAGTTTTTAAAACATTTTTGGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAAAT
* * * ** *
1612446 TATATATTATATAATTTTT-GAATTTTTTTTAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
*
1612481 ATATATAATATATAGTTTTTTAAATCA-TTTTGAAAACT
1 -TATATAATATATAG-TTTTTAAAACATTTTTGAAAA-T
* * *
1612519 TATATAATATATTA-TTTTGGAAAAAATATTTATGAAAAC
1 TATATAATATA-TAGTTTT-TAAAACAT-TTT-TGAAAAT
* * *
1612558 AATTATATTATATAGTTTTTCAAAAACATGTTTGAAAA-
1 TA-TATAATATATAGTTTTT--AAAACATTTTTGAAAAT
1612596 TATATAA
1 TATATAA
1612603 ATTTAAAATA
Statistics
Matches: 216, Mismatches: 37, Indels: 35
0.75 0.13 0.12
Matches are distributed among these distances:
35 5 0.02
36 51 0.24
37 64 0.30
38 5 0.02
39 50 0.23
40 25 0.12
41 16 0.07
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:1613936 original size:12 final size:13
Alignment explanation
Indices: 1613919--1613950 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1613909 TCAAATCGAA
1613919 TAATTTTAA-TTT
1 TAATTTTAATTTT
1613931 TAATTTTAATTTT
1 TAATTTTAATTTT
1613944 TAATTTT
1 TAATTTT
1613951 TGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:1613951 original size:7 final size:6
Alignment explanation
Indices: 1613919--1613950 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1613909 TCAAATCGAA
1613919 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
1613951 TGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:1615119 original size:42 final size:42
Alignment explanation
Indices: 1615060--1615179 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
1615050 TTTCTCCGAA
*
1615060 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1615102 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1615144 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1615180 TGTAATTCAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:1615436 original size:24 final size:22
Alignment explanation
Indices: 1615387--1615436 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
1615377 TATTAATATT
* *
1615387 TATAATAATAATATAATATTTA
1 TATAATAATAATATAATAATAA
1615409 -ATAATAATAAATATATATAATAA
1 TATAATAAT-AATATA-ATAATAA
1615432 TATAA
1 TATAA
1615437 GATTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 8 0.35
22 6 0.26
23 5 0.22
24 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATAATAATAATATAATAATAA
Found at i:1615483 original size:29 final size:30
Alignment explanation
Indices: 1615423--1615514 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 30
1615413 TAATAAATAT
* * *
1615423 ATATAATAATATAAGATTATATTTTAT-TTTA
1 ATATAATGA-ATAATATTAT-TTATATATTTA
* *
1615454 ATATAAT-AATAATTTTTTTTATATATTT-
1 ATATAATGAATAATATTATTTATATATTTA
1615482 A-ATAATGAATAATATTATTTATATATTTCA
1 ATATAATGAATAATATTATTTATATATTT-A
1615512 ATA
1 ATA
1615515 ATATTTTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
27 5 0.10
28 25 0.50
29 10 0.20
30 2 0.04
31 8 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (30 bp):
ATATAATGAATAATATTATTTATATATTTA
Found at i:1615484 original size:21 final size:22
Alignment explanation
Indices: 1615429--1615487 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1615419 ATATATATAA
* *
1615429 TAATATAAGATTATATTTTATTT
1 TAATATAATAATA-ATTTTATTT
1615452 TAATATAATAATAATTTT-TTT
1 TAATATAATAATAATTTTATTT
*
1615473 T-ATATATTTAATAAT
1 TAATATA-ATAATAAT
1615488 GAATAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 5 0.16
23 11 0.34
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TAATATAATAATAATTTTATTT
Found at i:1615502 original size:28 final size:28
Alignment explanation
Indices: 1615456--1615517 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1615446 TTATTTTAAT
* *
1615456 ATAATAATAATTTTTTTTATATATTT-A
1 ATAATAATAATATTATTTATATATTTCA
1615483 ATAATGAATAATATTATTTATATATTTCA
1 ATAAT-AATAATATTATTTATATATTTCA
1615512 ATAATA
1 ATAATA
1615518 TTTTAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 5 0.16
28 20 0.65
29 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
ATAATAATAATATTATTTATATATTTCA
Found at i:1615751 original size:14 final size:14
Alignment explanation
Indices: 1615730--1615812 Score: 89
Period size: 14 Copynumber: 5.8 Consensus size: 14
1615720 TTACAGAAAT
1615730 GTAATTCATTTTCCA
1 GTAATTCA-TTTCCA
*
1615745 G-AATTCAAATTCCA
1 GTAATTC-ATTTCCA
1615759 GTAATTCATTTCCA
1 GTAATTCATTTCCA
1615773 GTAATTCAAATTT-CA
1 GTAATTC--ATTTCCA
* *
1615788 GTAATTAAATTCCA
1 GTAATTCATTTCCA
1615802 GTAATTCATTT
1 GTAATTCATTT
1615813 TCTGGAAAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.05
14 35 0.61
15 15 0.26
16 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (14 bp):
GTAATTCATTTCCA
Found at i:1615756 original size:20 final size:20
Alignment explanation
Indices: 1615678--1615747 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1615668 TTTCCAGATG
1615678 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1615698 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1615718 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1615738 TTTTCCAGAA
1 TTTTCCAGAA
1615748 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1615756 original size:40 final size:40
Alignment explanation
Indices: 1615678--1615756 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1615668 TTTCCAGATG
* **
1615678 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
1615718 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1615757 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1615778 original size:29 final size:29
Alignment explanation
Indices: 1615730--1615809 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
1615720 TTACAGAAAT
1615730 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCA-TTTCCAGTAATTCAAATTCCA
*
1615759 GTAATTCATTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTCCAGTAATTCAAATTCCA
* *
1615788 GTAATTAAATTCCAGTAATTCA
1 GTAATTCATTTCCAGTAATTCA
1615810 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 40 0.85
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (29 bp):
GTAATTCATTTCCAGTAATTCAAATTCCA
Found at i:1615798 original size:43 final size:43
Alignment explanation
Indices: 1615730--1615812 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
1615720 TTACAGAAAT
*
1615730 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTCCA
1 GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTCCA
1615773 GTAATTCAAATTT-CAGTAATT-AAATTCCAGTAATTCATTT
1 GTAATTC-AATTTCCAG-AATTCAAATTCCAGTAATTCATTT
1615813 TCTGGAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
43 29 0.78
44 8 0.22
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (43 bp):
GTAATTCAATTTCCAGAATTCAAATTCCAGTAATTCATTTCCA
Found at i:1615907 original size:42 final size:42
Alignment explanation
Indices: 1615848--1615948 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
1615838 AAACAGACCC
* *
1615848 TACGTGAAACAAACACGGGAAAACGTTTTACAGAAAACGAAT
1 TACGTGAAACAAACACGGGAAAACATTTTACAGAAAACCAAT
* *
1615890 TACGTGAAACAAACACGGGAAAACATTTTTCGGAAAACCAAT
1 TACGTGAAACAAACACGGGAAAACATTTTACAGAAAACCAAT
1615932 TACGTGAAACAAACACG
1 TACGTGAAACAAACACG
1615949 AAAATTCGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TACGTGAAACAAACACGGGAAAACATTTTACAGAAAACCAAT
Found at i:1623884 original size:23 final size:23
Alignment explanation
Indices: 1623854--1623897 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1623844 GAAAACACTT
1623854 AACAAAGTAACAATAACTTGGAG
1 AACAAAGTAACAATAACTTGGAG
1623877 AACAAAGTAACAATAACTTGG
1 AACAAAGTAACAATAACTTGG
1623898 GTCAGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.16, T:0.18
Consensus pattern (23 bp):
AACAAAGTAACAATAACTTGGAG
Found at i:1632283 original size:31 final size:31
Alignment explanation
Indices: 1632245--1632493 Score: 455
Period size: 31 Copynumber: 8.0 Consensus size: 31
1632235 CCCGAAGGAC
* * *
1632245 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1632276 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632307 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632338 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632369 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632400 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632431 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632462 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1632493 C
1 C
1632494 CCTCGACCCT
Statistics
Matches: 214, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
31 213 1.00
32 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1636341 original size:31 final size:31
Alignment explanation
Indices: 1636303--1636551 Score: 455
Period size: 31 Copynumber: 8.0 Consensus size: 31
1636293 CCCGAAGGAC
* * *
1636303 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1636334 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636365 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636396 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636427 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636458 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636489 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636520 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1636551 C
1 C
1636552 CCTCGACCCT
Statistics
Matches: 214, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
31 213 1.00
32 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1637391 original size:21 final size:21
Alignment explanation
Indices: 1637361--1637405 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1637351 ATTCTGTCGT
* *
1637361 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1637382 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1637403 TTG
1 TTG
1637406 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1640654 original size:149 final size:149
Alignment explanation
Indices: 1640404--1640718 Score: 558
Period size: 149 Copynumber: 2.1 Consensus size: 149
1640394 TATAATTGCA
* *
1640404 CCGAAGTACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCATATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTAT
1640469 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* * *
1640534 CACATAATATATATATATC
131 CAAAGAATATACATATATC
* *
1640553 CCGAAGGACCGCGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTAT
1640618 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
1640683 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
1640702 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1640719 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 158 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:1640838 original size:14 final size:14
Alignment explanation
Indices: 1640819--1640846 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1640809 AACTTGTAAT
1640819 TCACGTATCACATA
1 TCACGTATCACATA
1640833 TCACGTATCACATA
1 TCACGTATCACATA
1640847 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:1643435 original size:2 final size:2
Alignment explanation
Indices: 1643430--1643465 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1643420 AATAAAAAAG
1643430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1643466 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1645317 original size:38 final size:38
Alignment explanation
Indices: 1645275--1645350 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
1645265 CTTTCCATAA
* *
1645275 ATATATATATACAATTTAGAATTAAGGTGATAAGAAAC
1 ATATATACATACAATATAGAATTAAGGTGATAAGAAAC
*
1645313 ATATATACGTACAATATAGAATTAAGGTGATAAGAAAC
1 ATATATACATACAATATAGAATTAAGGTGATAAGAAAC
1645351 CAGAGGTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (38 bp):
ATATATACATACAATATAGAATTAAGGTGATAAGAAAC
Found at i:1654265 original size:2 final size:2
Alignment explanation
Indices: 1654260--1654286 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1654250 GTGTGTGTGT
1654260 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1654287 TACTTGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1661573 original size:88 final size:87
Alignment explanation
Indices: 1661458--1661632 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 87
1661448 CACTCCTTAG
*
1661458 CATGGTTGGTAATTACTTCTTATATCAGATTCAGAGAACATATATAATTGGAAA-TAACTGAATT
1 CATGGTTGGTAATTACTTCTTATATCAGATTCAGAGAACATATATAATAGGAAACT-ACTGAA-T
1661522 TGTTTCTTAAACATGGAAACCAAT
64 TGTTTCTTAAACATGGAAACCAAT
1661546 CATGGTTGGTAATTACTTCTTATATCAGATTCAGAGAACATATATAATAGGAAACTACTGAATTG
1 CATGGTTGGTAATTACTTCTTATATCAGATTCAGAGAACATATATAATAGGAAACTACTGAATTG
1661611 TTTCTTAAACATGGAAACCAAT
66 TTTCTTAAACATGGAAACCAAT
1661633 ATGATGTAAC
Statistics
Matches: 85, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
87 25 0.29
88 59 0.69
89 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (87 bp):
CATGGTTGGTAATTACTTCTTATATCAGATTCAGAGAACATATATAATAGGAAACTACTGAATTG
TTTCTTAAACATGGAAACCAAT
Found at i:1677376 original size:31 final size:31
Alignment explanation
Indices: 1677341--1677435 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
1677331 AAAAATTTTG
* *
1677341 AAAATAATTATTAATTTTATTAAATTATTAT
1 AAAATAATCATTAATTTTATAAAATTATTAT
* ** *
1677372 AAAATAATCATTAACTTTAATAAAACCAATAT
1 AAAATAATCATTAA-TTTTATAAAATTATTAT
* * *
1677404 AAAATAATCATCAAATTTATCAAATTATTAT
1 AAAATAATCATTAATTTTATAAAATTATTAT
1677435 A
1 A
1677436 GAATTTCTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 25 0.50
32 25 0.50
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAATAATCATTAATTTTATAAAATTATTAT
Found at i:1683323 original size:13 final size:13
Alignment explanation
Indices: 1683305--1683329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1683295 ATAGTTAGGA
1683305 TATTTCTTTTTGG
1 TATTTCTTTTTGG
1683318 TATTTCTTTTTG
1 TATTTCTTTTTG
1683330 ATTTTGGTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.72
Consensus pattern (13 bp):
TATTTCTTTTTGG
Found at i:1684610 original size:95 final size:95
Alignment explanation
Indices: 1684379--1684665 Score: 436
Period size: 95 Copynumber: 3.0 Consensus size: 95
1684369 TTGCATGTTT
* * * *
1684379 TATTGTTGAATCTCGCTGCACGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTACATTTATG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTATG
*
1684444 TGCTGCTTCCC-TTT-T-CTTATTCAGACTA
66 TGCTGCTGCCCTTTTCTGCTTA-TCAGACTA
* *
1684472 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATATAGTTCCTTGCATTTAAG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTATG
1684537 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
66 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
*
1684567 TATTGTTAAATCTTGCTGCATGTCGTTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTATG
1 TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTATG
** * *
1684632 TAATGCTGCCGTTTTCTGCTTATCAGAATA
66 TGCTGCTGCCCTTTTCTGCTTATCAGACTA
1684662 TATT
1 TATT
1684666 CTTTTATTTG
Statistics
Matches: 177, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
93 69 0.39
94 3 0.02
95 101 0.57
96 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (95 bp):
TATTGTTAAATCTTGCTGCATGTCGCTTGAAGTATAAAATGAAGATTTAGTTCCTTGCATTTATG
TGCTGCTGCCCTTTTCTGCTTATCAGACTA
Found at i:1686511 original size:2 final size:2
Alignment explanation
Indices: 1686504--1686532 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1686494 AGGTACCTGT
1686504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1686533 GAACTCAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1688838 original size:63 final size:63
Alignment explanation
Indices: 1688755--1688920 Score: 271
Period size: 63 Copynumber: 2.7 Consensus size: 63
1688745 CCGAAGAACC
* * * *
1688755 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATATTGTCTATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
1688817 TAGGTAATTCTGTCCATATGTTCCGTAGAACATATGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
1688880 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGCATAC
1 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1688921 CCTCGACTCT
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
62 7 0.07
63 89 0.93
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:1688850 original size:32 final size:32
Alignment explanation
Indices: 1688742--1688915 Score: 166
Period size: 31 Copynumber: 5.5 Consensus size: 32
1688732 CTATCTATAG
* * *
1688742 GTTCCGAAGAACCTAGGTAA-ACTGTCCATAT
1 GTTCCGTAGAACATAGGTAATTCTGTCCATAT
* *
1688773 GTTCCTTAGAACATAGGT-ATAT-TGTCTATAT
1 GTTCCGTAGAACATAGGTAAT-TCTGTCCATAT
*
1688804 G-TCTCG-AAAGACATAGGTAATTCTGTCCATAT
1 GTTC-CGTAGA-ACATAGGTAATTCTGTCCATAT
* *
1688836 GTTCCGTAGAACATATGT-ATACTGTCCATAT
1 GTTCCGTAGAACATAGGTAATTCTGTCCATAT
*
1688867 G-TCTCG-AAAGACATAGGTAATTCTGTCCATAT
1 GTTC-CGTAGA-ACATAGGTAATTCTGTCCATAT
1688899 GTTCCGTAGAACATAGG
1 GTTCCGTAGAACATAGG
1688916 CATACCCTCG
Statistics
Matches: 115, Mismatches: 15, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
30 9 0.08
31 56 0.49
32 42 0.37
33 8 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
GTTCCGTAGAACATAGGTAATTCTGTCCATAT
Found at i:1693443 original size:31 final size:31
Alignment explanation
Indices: 1693408--1693525 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 31
1693398 ATTCCTTAGA
*
1693408 ACATAGGTATACTGTCTATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
** * *
1693439 ACATAGGTAATTTTGTCCATATCT-TCCGTATA-
1 ACATAGGT-ATACTGTCCATATGTCT-CG-AAAG
1693471 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
**
1693502 ACATAGGTAATTTTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
1693526 TTCGTAGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.03
31 31 0.44
32 35 0.50
33 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:1693474 original size:63 final size:63
Alignment explanation
Indices: 1693389--1693545 Score: 251
Period size: 63 Copynumber: 2.5 Consensus size: 63
1693379 CAAGGTAAAC
* *
1693389 TGTCCATATATTCCTTAGAACATAGGTATACTGTCTATATGTCTCGAAAGACATAGGTAATTT
1 TGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTT
* *
1693452 TGTCCATATCTTCCGTATAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTT
1 TGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTT
* * *
1693515 TGTCCATATGTTTCGTAGAATATAGGTATAC
1 TGTCCATATATTCCGTAGAACATAGGTATAC
1693546 CCTCGACTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 86 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (63 bp):
TGTCCATATATTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTT
Found at i:1693524 original size:32 final size:32
Alignment explanation
Indices: 1693420--1693525 Score: 128
Period size: 32 Copynumber: 3.3 Consensus size: 32
1693410 ATAGGTATAC
*
1693420 TGTCTATATGTCTCGAAAGACATAGGTAATTT
1 TGTCCATATGTCTCGAAAGACATAGGTAATTT
* * **
1693452 TGTCCATATCT-TCCGTATA-ACATAGGT-ATAC
1 TGTCCATATGTCT-CG-AAAGACATAGGTAATTT
1693483 TGTCCATATGTCTCGAAAGACATAGGTAATTT
1 TGTCCATATGTCTCGAAAGACATAGGTAATTT
1693515 TGTCCATATGT
1 TGTCCATATGT
1693526 TTCGTAGAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
30 2 0.03
31 23 0.38
32 33 0.55
33 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTCCATATGTCTCGAAAGACATAGGTAATTT
Found at i:1693540 original size:32 final size:32
Alignment explanation
Indices: 1693389--1693542 Score: 118
Period size: 32 Copynumber: 4.9 Consensus size: 32
1693379 CAAGGTAAAC
* * * * **
1693389 TGTCCATATATTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTTTCGTAAAACATAGGTAATTT
* *
1693420 TGTCTATATGTCTCG-AAAGACATAGGTAATTT
1 TGTCCATATGTTTCGTAAA-ACATAGGTAATTT
* * * **
1693452 TGTCCATATCTTCCGTATAACATAGGT-ATAC
1 TGTCCATATGTTTCGTAAAACATAGGTAATTT
*
1693483 TGTCCATATGTCTCG-AAAGACATAGGTAATTT
1 TGTCCATATGTTTCGTAAA-ACATAGGTAATTT
* *
1693515 TGTCCATATGTTTCGTAGAATATAGGTA
1 TGTCCATATGTTTCGTAAAACATAGGTA
1693543 TACCCTCGAC
Statistics
Matches: 93, Mismatches: 24, Indels: 11
0.73 0.19 0.09
Matches are distributed among these distances:
30 4 0.04
31 40 0.43
32 45 0.48
33 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTCCATATGTTTCGTAAAACATAGGTAATTT
Found at i:1694830 original size:64 final size:64
Alignment explanation
Indices: 1694678--1694834 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
1694668 CAATGAAAGT
* * * * **
1694678 ATGCATCGATGCACTA-CTGATGCATCGGTGTATAAAATGCATTCGATGTTGTATTATCACTGAG
1 ATGCATCGATGCACTACCTG-TGCATCGATGAATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * *
1694742 ATGCATCGATGCA-TGCCTTATGCATCGATGAACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGAA-TAAAATGCATTCGATG-TTCTATTATAAAAG
1694805 AG
63 AG
1694807 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
1694835 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 1 0.01
64 59 0.78
65 16 0.21
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGAATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:1703244 original size:23 final size:23
Alignment explanation
Indices: 1703189--1703363 Score: 159
Period size: 23 Copynumber: 7.7 Consensus size: 23
1703179 TCTTAACATG
*
1703189 TTTCTTCTTCTTTCATAAA-CAT
1 TTTCTTCTTCTTCCATAAATCAT
1703211 TTTCTTCTTCTTCCATACAATCA-
1 TTTCTTCTTCTTCCATA-AATCAT
*
1703234 TTACTTCTTCTTCCATAAACTCA-
1 TTTCTTCTTCTTCCATAAA-TCAT
*
1703257 TTTCTT-TTCTTCCATAAACCAT
1 TTTCTTCTTCTTCCATAAATCAT
*
1703279 TTTCTTCTTCTTCCATAAAT-TT
1 TTTCTTCTTCTTCCATAAATCAT
* * **
1703301 GTTTTTTCTACTTCCATTAACCCA-
1 -TTTCTTCTTCTTCCA-TAAATCAT
*
1703325 TTTCTTATT-TTCCCATAAACTCA-
1 TTTCTTCTTCTT-CCATAAA-TCAT
1703348 TTTCTTCTTCTTCCAT
1 TTTCTTCTTCTTCCAT
1703364 TCTTCTGAGA
Statistics
Matches: 125, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.02
22 42 0.34
23 74 0.59
24 7 0.06
ACGTcount: A:0.21, C:0.27, G:0.01, T:0.51
Consensus pattern (23 bp):
TTTCTTCTTCTTCCATAAATCAT
Found at i:1703280 original size:68 final size:69
Alignment explanation
Indices: 1703189--1703363 Score: 207
Period size: 68 Copynumber: 2.6 Consensus size: 69
1703179 TCTTAACATG
* * *
1703189 TTTCTTCTTCTTTCATAAA-CATTTTCTTCTTCTTCCATACAA-TCATTACTTCTTCTTCCATAA
1 TTTCTTATTCTTCCATAAACCATTTTCTTCTTCTTCCATA-AATTCATTACTTCTACTTCCATAA
*
1703252 ACTCA
65 ACCCA
** ** *
1703257 TTTCTT-TTCTTCCATAAACCATTTTCTTCTTCTTCCATAAATTTGTTTTTTCTACTTCCATTAA
1 TTTCTTATTCTTCCATAAACCATTTTCTTCTTCTTCCATAAATTCATTACTTCTACTTCCATAAA
1703321 CCCA
66 CCCA
1703325 TTTCTTATT-TTCCCATAAACTCA-TTTCTTCTTCTTCCAT
1 TTTCTTATTCTT-CCATAAAC-CATTTTCTTCTTCTTCCAT
1703364 TCTTCTGAGA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
67 13 0.14
68 53 0.56
69 26 0.28
70 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.01, T:0.51
Consensus pattern (69 bp):
TTTCTTATTCTTCCATAAACCATTTTCTTCTTCTTCCATAAATTCATTACTTCTACTTCCATAAA
CCCA
Found at i:1703364 original size:46 final size:45
Alignment explanation
Indices: 1703189--1703363 Score: 187
Period size: 45 Copynumber: 3.9 Consensus size: 45
1703179 TCTTAACATG
* *
1703189 TTTCTTCTTCTTTCATAAA--CATTTTCTTCTTCTTCCATACAATCA
1 TTTCTTCTTCTTCCATAAACTCA-TTTCTTCTTCTTCCATA-AACCA
*
1703234 TTACTTCTTCTTCCATAAACTCATTTCTT-TTCTTCCATAAACCA
1 TTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACCA
* ** * * *
1703278 TTTTCTTCTTCTTCCATAAATTTGTTTTTTCTACTTCCATTAACCCA
1 -TTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCA-TAAACCA
*
1703325 TTTCTTATT-TTCCCATAAACTCATTTCTTCTTCTTCCAT
1 TTTCTTCTTCTT-CCATAAACTCATTTCTTCTTCTTCCAT
1703364 TCTTCTGAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
44 4 0.04
45 54 0.50
46 42 0.39
47 8 0.07
ACGTcount: A:0.21, C:0.27, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTCTTCTTCTTCCATAAACTCATTTCTTCTTCTTCCATAAACCA
Found at i:1719698 original size:18 final size:18
Alignment explanation
Indices: 1719661--1719698 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1719651 AAGTATAAGG
*
1719661 ATTTATTTAAAATTATTT
1 ATTTATTTAAAATTAATT
1719679 ATTTA-TTAAAATTTAATT
1 ATTTATTTAAAA-TTAATT
1719697 AT
1 AT
1719699 AATTTTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTTAAAATTAATT
Found at i:1722415 original size:2 final size:2
Alignment explanation
Indices: 1722408--1722441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1722398 TATTATCTTC
1722408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1722442 AAGGCAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1723192 original size:2 final size:2
Alignment explanation
Indices: 1723185--1723211 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1723175 GGTTACCTCA
1723185 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1723212 CTTAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1727620 original size:24 final size:23
Alignment explanation
Indices: 1727577--1727621 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1727567 TATTAACGTA
*
1727577 TTTAAAATATATTTATTAATATT
1 TTTAAAATATATATATTAATATT
1727600 TTTAACAATATA-ATATATAATA
1 TTTAA-AATATATATAT-TAATA
1727622 ATAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAAATATATATATTAATATT
Found at i:1727624 original size:3 final size:3
Alignment explanation
Indices: 1727609--1727642 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
1727599 TTTTAACAAT
1727609 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
1727643 TATAGTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1735032 original size:24 final size:26
Alignment explanation
Indices: 1734982--1735040 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
1734972 ACTGGACAAG
*
1734982 TATATAATAA-TATTTATATAAATAT
1 TATATAAAAAGTATTTATATAAATAT
1735007 TAT-TAAAAAGTATTTA-AT-AATAAT
1 TATATAAAAAGTATTTATATAAAT-AT
1735031 TATATAAAAA
1 TATATAAAAA
1735041 TTAACCGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 12 0.40
25 15 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TATATAAAAAGTATTTATATAAATAT
Found at i:1748355 original size:24 final size:24
Alignment explanation
Indices: 1748323--1748401 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
1748313 TTATAACAGC
1748323 AAAAA-AATAAAATAATTAAATAA
1 AAAAATAATAAAATAATTAAATAA
*
1748346 AAAAATAATACAATAATTAAATAA
1 AAAAATAATAAAATAATTAAATAA
* * *
1748370 AATACTAACAAAAT-ATTAAATATA
1 AAAAATAATAAAATAATTAAATA-A
1748394 ATAAAATA
1 A-AAAATA
1748402 TACCTTATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 13 0.28
24 29 0.63
25 4 0.09
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATAATAAAATAATTAAATAA
Found at i:1748457 original size:10 final size:10
Alignment explanation
Indices: 1748439--1748468 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1748429 TTTGGTTTTT
*
1748439 AGAGGATTTG
1 AGAGAATTTG
1748449 AGAGAATTTG
1 AGAGAATTTG
1748459 AGAGAATTTG
1 AGAGAATTTG
1748469 GTGTGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:1753734 original size:15 final size:15
Alignment explanation
Indices: 1753714--1753743 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1753704 GATTAGTATC
1753714 TTTCCTAACTTAGAG
1 TTTCCTAACTTAGAG
*
1753729 TTTCCTAATTTAGAG
1 TTTCCTAACTTAGAG
1753744 ACATAGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
TTTCCTAACTTAGAG
Found at i:1758389 original size:87 final size:87
Alignment explanation
Indices: 1758286--1758459 Score: 258
Period size: 87 Copynumber: 2.0 Consensus size: 87
1758276 CAAAAATTAC
* * * *
1758286 TACATATCCATATTTATGACTAGCAGAATGCATATCAATTGCCTCACACAATCAACCATACTACA
1 TACATAACCATATTTATGACTAGCAGAATGCATATCAATGGCATCACACAATCAACCATACAACA
*
1758351 AATTATTCAACACATATACAGA
66 AATTATTCAACACATAAACAGA
* * * *
1758373 TACATAACCATATTTATGATTAGTAGAATGCTTATCAATGGCATCACAGAATCAACCATACAACA
1 TACATAACCATATTTATGACTAGCAGAATGCATATCAATGGCATCACACAATCAACCATACAACA
*
1758438 AATTATTCAATACATAAACAGA
66 AATTATTCAACACATAAACAGA
1758460 ATTTGCTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.43, C:0.21, G:0.08, T:0.28
Consensus pattern (87 bp):
TACATAACCATATTTATGACTAGCAGAATGCATATCAATGGCATCACACAATCAACCATACAACA
AATTATTCAACACATAAACAGA
Found at i:1761157 original size:15 final size:16
Alignment explanation
Indices: 1761137--1761173 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1761127 CTCTGCTTTT
1761137 TCCTTTCTCTT-TTGC
1 TCCTTTCTCTTCTTGC
1761152 TCCTTT-TCTTCTTGC
1 TCCTTTCTCTTCTTGC
1761167 T-CTTTCT
1 TCCTTTCT
1761174 TCAATCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.00, C:0.32, G:0.05, T:0.62
Consensus pattern (16 bp):
TCCTTTCTCTTCTTGC
Found at i:1769608 original size:21 final size:21
Alignment explanation
Indices: 1769582--1769642 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1769572 AGTCGCTTGT
*
1769582 CGTCCTCCGACCATCGTCCGC
1 CGTCCTCCGACCACCGTCCGC
* * *
1769603 CGTCCTCCAACCACCGTTCGT
1 CGTCCTCCGACCACCGTCCGC
*
1769624 CGTCTTCCGACCACCGTCC
1 CGTCCTCCGACCACCGTCC
1769643 ACCGCCGCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.11, C:0.51, G:0.16, T:0.21
Consensus pattern (21 bp):
CGTCCTCCGACCACCGTCCGC
Found at i:1789991 original size:56 final size:56
Alignment explanation
Indices: 1789905--1790030 Score: 207
Period size: 56 Copynumber: 2.2 Consensus size: 56
1789895 AAAAAATTGT
*
1789905 ATATTAATGTAAAAGTGGGAGAAAGAAAATATATATAATGGATACACATATCCGTA
1 ATATTAATATAAAAGTGGGAGAAAGAAAATATATATAATGGATACACATATCCGTA
* * * *
1789961 ATATTAATATAAAAGTTGGAGGAATAAAATATATATAATGGATACCCATATCCGTA
1 ATATTAATATAAAAGTGGGAGAAAGAAAATATATATAATGGATACACATATCCGTA
1790017 ATATTAATATAAAA
1 ATATTAATATAAAA
1790031 CTGTGTATGC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.29
Consensus pattern (56 bp):
ATATTAATATAAAAGTGGGAGAAAGAAAATATATATAATGGATACACATATCCGTA
Found at i:1791287 original size:57 final size:57
Alignment explanation
Indices: 1791216--1791329 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
1791206 ATGAATCATA
1791216 GCTACTTTTGTAGACGTCCATGTGATGTAAGGACCACTTGGACATGATAATACAGGT
1 GCTACTTTTGTAGACGTCCATGTGATGTAAGGACCACTTGGACATGATAATACAGGT
* *
1791273 GCTACTTTTGTAGACTTCCATGTGATGTAAGGACCACTTGGACATGATAATCCAGGT
1 GCTACTTTTGTAGACGTCCATGTGATGTAAGGACCACTTGGACATGATAATACAGGT
1791330 AAGCATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (57 bp):
GCTACTTTTGTAGACGTCCATGTGATGTAAGGACCACTTGGACATGATAATACAGGT
Found at i:1800240 original size:15 final size:15
Alignment explanation
Indices: 1800222--1800264 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
1800212 CGAAAGGAGG
*
1800222 AATGTTAATAAAGGA
1 AATGCTAATAAAGGA
1800237 AATGCT-A-AAAGGA
1 AATGCTAATAAAGGA
1800250 AATGCTAATAAAGGA
1 AATGCTAATAAAGGA
1800265 TCAGTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 12 0.48
14 2 0.08
15 11 0.44
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (15 bp):
AATGCTAATAAAGGA
Found at i:1801623 original size:47 final size:46
Alignment explanation
Indices: 1801522--1801615 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 46
1801512 TCATTCAGCC
* * *
1801522 TACACAAATAAATTTTTACAAAGATATTCTGATTTATAAAAGTAAA
1 TACAAAAATAAAATTTTACAAAGATATTCTGACTTATAAAAGTAAA
*
1801568 TACAAAAATAAAAATTTTACAAAGATATTCTTACTTATAAAAGTAAA
1 TACAAAAAT-AAAATTTTACAAAGATATTCTGACTTATAAAAGTAAA
1801615 T
1 T
1801616 TAGAAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 8 0.19
47 35 0.81
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (46 bp):
TACAAAAATAAAATTTTACAAAGATATTCTGACTTATAAAAGTAAA
Found at i:1802469 original size:111 final size:109
Alignment explanation
Indices: 1802256--1802480 Score: 360
Period size: 111 Copynumber: 2.0 Consensus size: 109
1802246 CCTGGGTATT
*
1802256 TCCTGAATTGTTGATTTGTTGAATTTGAGCTGTTGAAGGTGTCTTTGATCCATAGATAGTGGTTT
1 TCCTGAATTGTTGATTCGTTGAATTTGAGCTGTTGAAGGTGTCTTTGATCCATAGATAGTGGTTT
* *
1802321 CCATAATATATTACTCTGATCTAATAGAATAAAGTTGGAAGAGA
66 CCATAATATATTACTCTGATCTAAGAGAAGAAAGTTGGAAGAGA
1802365 TCCTGAACTTTGTTGATTCGTTGAATTTGAGCTGTTGAAGGTGTCTTTGATCCATAGATAGTGGT
1 TCCTGAA--TTGTTGATTCGTTGAATTTGAGCTGTTGAAGGTGTCTTTGATCCATAGATAGTGGT
* * ** *
1802430 TTCCTTAATGTATTACTCTGATCTAAGAGAAGACGGTTGGAAGGGA
64 TTCCATAATATATTACTCTGATCTAAGAGAAGAAAGTTGGAAGAGA
1802476 TCCTG
1 TCCTG
1802481 CATTTGGTCT
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 7 0.07
111 99 0.93
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (109 bp):
TCCTGAATTGTTGATTCGTTGAATTTGAGCTGTTGAAGGTGTCTTTGATCCATAGATAGTGGTTT
CCATAATATATTACTCTGATCTAAGAGAAGAAAGTTGGAAGAGA
Found at i:1817385 original size:19 final size:20
Alignment explanation
Indices: 1817361--1817411 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1817351 AATGACCAAT
1817361 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1817380 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1817400 AAAATCGCAACG
1 AAAATCGCAACG
1817412 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1817405 original size:20 final size:20
Alignment explanation
Indices: 1817361--1817618 Score: 126
Period size: 20 Copynumber: 12.6 Consensus size: 20
1817351 AATGACCAAT
* *
1817361 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1817380 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1817400 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1817420 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1817440 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1817461 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1817484 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1817504 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1817524 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1817547 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1817567 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1817587 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1817607 AGAATCGCAACG
1 AAAATCGCAACG
1817619 TTAAAAAGAT
Statistics
Matches: 186, Mismatches: 41, Indels: 23
0.74 0.16 0.09
Matches are distributed among these distances:
19 17 0.09
20 126 0.68
21 14 0.08
23 29 0.16
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1817548 original size:63 final size:63
Alignment explanation
Indices: 1817465--1817603 Score: 224
Period size: 63 Copynumber: 2.2 Consensus size: 63
1817455 GCTTCCAAGT
* * *
1817465 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* *
1817528 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
*
1817591 TCGCAATGCGATT
1 TCGCAACGCGATT
1817604 GAGAGAATCG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:1817553 original size:43 final size:40
Alignment explanation
Indices: 1817486--1817618 Score: 176
Period size: 40 Copynumber: 3.2 Consensus size: 40
1817476 TTTAGAAGAA
* * *
1817486 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTTAAAGAATCGCAATGCGATTGAGAG
* *
1817526 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTA-AAG--AATCGCAATGCGATTGAGAG
* *
1817569 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTTAAAGAATCGCAATGCGATTGAGAG
1817609 AATCGCAACG
1 AATCGCAACG
1817619 TTAAAAAGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
40 42 0.52
41 2 0.03
42 2 0.03
43 34 0.43
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGATTTAAAGAATCGCAATGCGATTGAGAG
Found at i:1817716 original size:6 final size:6
Alignment explanation
Indices: 1817705--1817799 Score: 162
Period size: 6 Copynumber: 16.5 Consensus size: 6
1817695 GACACGTATT
1817705 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1817753 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1817797 ACC
1 ACC
1817800 CGAGACGAGA
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 20 0.22
6 69 0.78
ACGTcount: A:0.31, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1818503 original size:6 final size:6
Alignment explanation
Indices: 1818487--1818654 Score: 315
Period size: 6 Copynumber: 28.5 Consensus size: 6
1818477 TCTCGTCTCG
1818487 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1818534 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1818582 GGTCGT GGTCGT GGTCGT GG--GT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1818628 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1818655 AATACGTGTC
Statistics
Matches: 160, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.03
5 5 0.03
6 151 0.94
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1818756 original size:20 final size:20
Alignment explanation
Indices: 1818731--1818843 Score: 109
Period size: 20 Copynumber: 5.3 Consensus size: 20
1818721 TCTTTTAACT
* *
1818731 ATTGCGATTCTCTCAGTCGC
1 ATTGCGATTCTCTAAATCGC
1818751 ATTGCGATTTTCTTCTAAATCGC
1 ATTGCGA--TTC-TCTAAATCGC
* * *
1818774 GTTGCGACTCTCTCAATCGC
1 ATTGCGATTCTCTAAATCGC
*
1818794 ATTGCGATTCTATAAATCGC
1 ATTGCGATTCTCTAAATCGC
1818814 ATTGCGATTTTCTTCTAAATCGC
1 ATTGCGA--TTC-TCTAAATCGC
*
1818837 GTTGCGA
1 ATTGCGA
1818844 ACTTGGAAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
20 39 0.51
21 2 0.03
22 6 0.08
23 29 0.38
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (20 bp):
ATTGCGATTCTCTAAATCGC
Found at i:1818920 original size:20 final size:20
Alignment explanation
Indices: 1818763--1818928 Score: 93
Period size: 20 Copynumber: 8.1 Consensus size: 20
1818753 TGCGATTTTC
*
1818763 TTCTAAATCGCGTTGCGACT
1 TTCTAAATCGCGTTGCGATT
* * *
1818783 CTCTCAATCGCATTGCGATT
1 TTCTAAATCGCGTTGCGATT
* * *
1818803 CTATAAATCGCATTGCGATTTT
1 TTCTAAATCGCGTTGCGA--TT
**
1818825 CTTCTAAATCGCGTTGCGAAC
1 -TTCTAAATCGCGTTGCGATT
** *
1818846 TTGGAAGCTCGCGTTGCGATT
1 TTCTAA-ATCGCGTTGCGATT
* *
1818867 TTCT--TTTGACCGTTGCGATT
1 TTCTAAATCG--CGTTGCGATT
*** **
1818887 TTCTTTTTAACGTTGCGATT
1 TTCTAAATCGCGTTGCGATT
1818907 TTCTAAATCGCGTTGCGATT
1 TTCTAAATCGCGTTGCGATT
1818927 TT
1 TT
1818929 ATTGGTCATT
Statistics
Matches: 111, Mismatches: 27, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
18 2 0.02
20 77 0.69
21 13 0.12
22 4 0.04
23 15 0.14
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (20 bp):
TTCTAAATCGCGTTGCGATT
Found at i:1824098 original size:2 final size:2
Alignment explanation
Indices: 1824091--1824146 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1824081 CGGTAAGGGA
1824091 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1824133 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1824147 CTTTGCAGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1834003 original size:2 final size:2
Alignment explanation
Indices: 1833996--1834030 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1833986 GTAGAAAAGA
1833996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1834031 AAAGATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1834303 original size:17 final size:18
Alignment explanation
Indices: 1834273--1834307 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1834263 CATAAAATTT
1834273 TAAAAATATATTTTTAAA
1 TAAAAATATATTTTTAAA
1834291 TAAAAATAT-TTTTTAAA
1 TAAAAATATATTTTTAAA
1834308 AATTATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAAATATATTTTTAAA
Found at i:1842693 original size:75 final size:75
Alignment explanation
Indices: 1842614--1842763 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
1842604 TTAATAAGTT
* *
1842614 AAACCATCTTAATATAATGTTACTTTTTAAACATGTGATGATCATCAAATAAATGTCAAATTATA
1 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
1842679 TAAATAATCC
66 TAAATAATCC
1842689 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
1 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
1842754 TAAATAATCC
66 TAAATAATCC
1842764 CTATACTTGC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (75 bp):
AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
TAAATAATCC
Found at i:1854412 original size:22 final size:22
Alignment explanation
Indices: 1854382--1854423 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1854372 CTTAATTTTA
*
1854382 GAAATTTTCAAATAAA-AAATCT
1 GAAAATTTCAAA-AAATAAATCT
1854404 GAAAATTTCAAAAAATAAAT
1 GAAAATTTCAAAAAATAAAT
1854424 TGAGCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
GAAAATTTCAAAAAATAAATCT
Found at i:1855984 original size:32 final size:33
Alignment explanation
Indices: 1855924--1855989 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
1855914 ATCGCCTTAA
*
1855924 CATGAACAAATAATTTATAATGCCACCAGCCCT
1 CATGAAAAAATAATTTATAATGCCACCAGCCCT
*
1855957 CATGAAAAAATAA-TTACT-ATGCCACCAGTCCT
1 CATGAAAAAATAATTTA-TAATGCCACCAGCCCT
1855989 C
1 C
1855990 GTAACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (33 bp):
CATGAAAAAATAATTTATAATGCCACCAGCCCT
Found at i:1860054 original size:20 final size:20
Alignment explanation
Indices: 1859960--1860328 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1859950 GATTTTCCAT
* ** *
1859960 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1859980 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1860000 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1860020 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1860040 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1860060 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1860080 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1860100 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1860120 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1860140 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1860160 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1860180 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1860200 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1860220 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1860240 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1860260 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1860280 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1860300 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1860320 AATCACAAC
1 AATCGCAAC
1860329 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1861041 original size:24 final size:24
Alignment explanation
Indices: 1861002--1861048 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1860992 AAATTTGGTC
1861002 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1861026 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1861049 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1861240 original size:12 final size:12
Alignment explanation
Indices: 1861223--1861247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1861213 ATATAATCCT
1861223 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1861235 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1861247 G
1 G
1861248 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1863570 original size:19 final size:19
Alignment explanation
Indices: 1863548--1863871 Score: 378
Period size: 19 Copynumber: 18.4 Consensus size: 19
1863538 CGGAAAATAC
*
1863548 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1863567 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1863581 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1863601 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1863615 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1863634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1863653 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1863667 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1863686 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1863705 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1863719 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1863738 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1863757 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1863776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1863795 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1863814 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1863828 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1863846 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1863864 AATCGCAA
1 AATCGCAA
1863872 CGAGATAATC
Statistics
Matches: 266, Mismatches: 14, Indels: 51
0.80 0.04 0.15
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.05
18 30 0.11
19 145 0.55
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1863635 original size:33 final size:34
Alignment explanation
Indices: 1863548--1863853 Score: 301
Period size: 33 Copynumber: 8.8 Consensus size: 34
1863538 CGGAAAATAC
* *
1863548 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1863581 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
1863615 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1863653 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
1863686 AATCACAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1863719 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1863757 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1863795 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1863827 GAATCGCAATGCGAAATG-AAATCGCAA
1 -AATCGCAATGCGAAATGAAAATCGCAA
1863854 TGCGAAATGA
Statistics
Matches: 241, Mismatches: 14, Indels: 37
0.83 0.05 0.13
Matches are distributed among these distances:
32 11 0.05
33 99 0.41
34 32 0.13
35 7 0.03
36 6 0.02
37 3 0.01
38 83 0.34
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1863663 original size:52 final size:52
Alignment explanation
Indices: 1863576--1863893 Score: 523
Period size: 52 Copynumber: 6.0 Consensus size: 52
1863566 AAATCCCAAC
1863576 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1863629 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1863681 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1863733 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
1863790 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1863842 ATG-AAATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1863892 AT
1 AT
1863894 TATAAACGCA
Statistics
Matches: 251, Mismatches: 9, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
50 29 0.12
51 18 0.07
52 133 0.53
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1863704 original size:71 final size:69
Alignment explanation
Indices: 1863615--1863893 Score: 323
Period size: 71 Copynumber: 4.0 Consensus size: 69
1863605 GCAACGAGAG
1863615 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGA-AATCGCAATGCGA
1863680 AATGAA
64 AATGAA
* * * * * *
1863686 AATCACAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA-AAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAT-CGCAACGAGAAATCGCAATGCG
*
1863750 AAATTAA
63 AAATGAA
* * * * *
1863757 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT-GAAAAT-CGC
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAAATCG-CAATGCGA
*
1863820 AACGAAA
64 AATG-AA
1863827 GAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAATCGCAACGAGATAATCGCAATGCGA
1 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGA-AATCGCAATGCGA
1863891 AAT
64 AAT
1863894 TATAAACGCA
Statistics
Matches: 173, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
69 24 0.14
70 39 0.23
71 96 0.55
72 7 0.04
73 7 0.04
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (69 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGAAATCGCAATGCGAAA
TGAA
Done.