Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 21 of 378
Found at i:5616435 original size:21 final size:20
Alignment explanation
Indices: 5616401--5616440 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5616391 ATTTTTTTAT
*
5616401 CATTTTAATAATTATTAATA
1 CATTTTAATAATTAATAATA
*
5616421 CATTTATAATTATTAATAAT
1 CATTT-TAATAATTAATAAT
5616441 GTTTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
CATTTTAATAATTAATAATA
Found at i:5626700 original size:9 final size:9
Alignment explanation
Indices: 5626654--5626715 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
5626644 AACTTTCAAC
5626654 ATTTAAAAA
1 ATTTAAAAA
*
5626663 TATGT-AAAA
1 -ATTTAAAAA
*
5626672 ATTTATTAAA
1 ATTTA-AAAA
*
5626682 ATGTATAAAA
1 ATTTA-AAAA
5626692 ATTTAAAAA
1 ATTTAAAAA
5626701 ATTTAAAAA
1 ATTTAAAAA
5626710 ATTTAA
1 ATTTAA
5626716 CATTTATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
8 3 0.07
9 23 0.52
10 18 0.41
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:5631159 original size:2 final size:2
Alignment explanation
Indices: 5631152--5631186 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5631142 TCCTTTGCAG
*
5631152 AT AT AT AT AT AA 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
5631187 AACCTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5636546 original size:16 final size:18
Alignment explanation
Indices: 5636514--5636549 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5636504 TATAATACTT
5636514 TATATTATGTTATATTTA
1 TATATTATGTTATATTTA
5636532 TATATTATG-TA-ATTTA
1 TATATTATGTTATATTTA
5636548 TA
1 TA
5636550 ACATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (18 bp):
TATATTATGTTATATTTA
Found at i:5643427 original size:17 final size:16
Alignment explanation
Indices: 5643386--5643434 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
5643376 TTTACTTAAT
5643386 TTTTTTTATTATTTCG
1 TTTTTTTATTATTTCG
5643402 TTTTCTTTATTATAATT-G
1 TTTT-TTTATTAT--TTCG
5643420 TTTTTTTATATATTT
1 TTTTTTTAT-TATTT
5643435 TCTTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.21
17 13 0.45
18 8 0.28
19 2 0.07
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (16 bp):
TTTTTTTATTATTTCG
Found at i:5643638 original size:3 final size:3
Alignment explanation
Indices: 5643632--5643671 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5643622 GACACTATAT
5643632 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5643672 ATACTATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5646367 original size:59 final size:59
Alignment explanation
Indices: 5646292--5646409 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
5646282 CTCTCAGGTC
*
5646292 AATGGACAACATGAATGAAAATAATAAAGTAAGAAGGTTTTGAAATTAAAAATTATAAT
1 AATGGACAACACGAATGAAAATAATAAAGTAAGAAGGTTTTGAAATTAAAAATTATAAT
*
5646351 AATGGACAACACGAATGAAAATAATAAAGTAAGGAGGTTTTGAAATTAAAAATTATAAT
1 AATGGACAACACGAATGAAAATAATAAAGTAAGAAGGTTTTGAAATTAAAAATTATAAT
5646410 TATAATTGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.26
Consensus pattern (59 bp):
AATGGACAACACGAATGAAAATAATAAAGTAAGAAGGTTTTGAAATTAAAAATTATAAT
Found at i:5651964 original size:39 final size:39
Alignment explanation
Indices: 5651863--5651964 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
5651853 TATGGTATTT
* * * *
5651863 AAAATATATATATATATATATATGTATATAATAGTATTTA
1 AAAATATATACATA-ATATATATATATATAATAGCATTAA
* * * *
5651903 AGAATATATACATAAGAAATATATA-ACTAATGGCATTAA
1 AAAATATATACATAATATATATATATA-TAATAGCATTAA
5651942 AAAATATATACATAATATATATA
1 AAAATATATACATAATATATATA
5651965 AAATACCTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.02
39 37 0.74
40 12 0.24
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATATATACATAATATATATATATATAATAGCATTAA
Found at i:5652537 original size:12 final size:11
Alignment explanation
Indices: 5652522--5652560 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5652512 TTGGGGTAGG
5652522 TTTTCTTTTTCT
1 TTTTCTTTTT-T
5652534 TTTTCTTTTTT
1 TTTTCTTTTTT
*
5652545 TCTTTGTTTTTT
1 T-TTTCTTTTTT
5652557 TTTT
1 TTTT
5652561 GGGTTAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:5652544 original size:14 final size:14
Alignment explanation
Indices: 5652521--5652559 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
5652511 TTTGGGGTAG
5652521 GTTTTCTTTTTCTTT
1 GTTTT-TTTTTCTTT
5652536 -TTCTTTTTTTCTTT
1 GTT-TTTTTTTCTTT
5652550 GTTTTTTTTT
1 GTTTTTTTTT
5652560 TGGGTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (14 bp):
GTTTTTTTTTCTTT
Found at i:5655882 original size:25 final size:25
Alignment explanation
Indices: 5655832--5655890 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5655822 TCAGATTATT
*
5655832 ATATAAAAATTTTAATAAATAAAAA
1 ATATATAAATTTTAATAAATAAAAA
* *
5655857 ATATATAAA-TTTATTAAATATTAAA
1 ATATATAAATTTTAATAAATA-AAAA
5655882 ATAATATAA
1 AT-ATATAA
5655891 TATAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.34
25 13 0.45
26 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATATAAATTTTAATAAATAAAAA
Found at i:5657045 original size:13 final size:13
Alignment explanation
Indices: 5657029--5657094 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
5657019 TTTAAACTAA
5657029 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
5657042 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
5657055 ACTTTTCTACAGC
1 ACTTTTCAAAAGC
*
5657068 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
5657081 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5657094 A
1 A
5657095 ATGAAGAACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5657068 original size:26 final size:26
Alignment explanation
Indices: 5657029--5657094 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
5657019 TTTAAACTAA
5657029 ACTTTTCAAAAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
* *
5657055 ACTTTTCTACAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
5657081 ACTTTTCAAAAGCA
1 ACTTTTCAAAAGCA
5657095 ATGAAGAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:5663211 original size:88 final size:85
Alignment explanation
Indices: 5663088--5663357 Score: 305
Period size: 88 Copynumber: 3.1 Consensus size: 85
5663078 TTATTTTAAA
* * * *
5663088 ACTCAATTGGATATTTGAACTGTCAAAATGTATCAAAAAGGCCCTCAAATTTTTTATTAAAAAAC
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGCCCTCAAATTTTTTA-TAAAAAAC
5663153 AATTAAGCCCCTGTTTTTTTTCC
65 AATTAAGCCCCT-TTTTTTTT-C
* * * *
5663176 ACTCAATTGGGTACTTGAATTATCAAAATGCATCAAAAAGACCCTCAAACTTTTTATAAAAAAAA
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGCCCTCAAATTTTTTAT-AAAAAAC
* *
5663241 AACTAAG--CTTTTTTTTTTC
65 AATTAAGCCCCTTTTTTTTTC
* * *
5663260 ACTCAACTGGGTACTTGAATTGTCAAAATGCAT-AAAAAGGATCCTCAAAATTTTTCA-AAAAAA
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGG-CCCTC-AAATTTTTTATAAAAAA
5663323 CCAATTAAGCCCCTACTTTTTCTTTC
64 -CAATTAAGCCCCT--TTTTT-TTTC
5663349 ACTCAATTG
1 ACTCAATTG
5663358 CCAAAATGCA
Statistics
Matches: 153, Mismatches: 20, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
83 12 0.08
84 42 0.27
85 16 0.10
86 4 0.03
87 1 0.01
88 66 0.43
89 12 0.08
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (85 bp):
ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGCCCTCAAATTTTTTATAAAAAACA
ATTAAGCCCCTTTTTTTTTC
Found at i:5663332 original size:84 final size:85
Alignment explanation
Indices: 5663088--5663332 Score: 284
Period size: 84 Copynumber: 2.9 Consensus size: 85
5663078 TTATTTTAAA
* * * * *
5663088 ACTCAATTGGATATTTGAACTGTCAAAATGTATCAAAAAGG-CCCTCAAATTTTTTATTAAAAAA
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGACCCTCAAAATTTTTA-TAAAAAA
5663152 CAATTAAGCCCCTGTTTTTTTTCC
65 CAATTAAG---CTGTTTTTTTTCC
* *
5663176 ACTCAATTGGGTACTTGAATTATCAAAATGCATCAAAAA-GACCCTCAAACTTTTTATAAAAAAA
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGACCCTCAAAATTTTTAT-AAAAAA
* * *
5663240 AAACTAAGCT-TTTTTTTTTC
65 CAATTAAGCTGTTTTTTTTCC
* *
5663260 ACTCAACTGGGTACTTGAATTGTCAAAATGCAT-AAAAAGGATCCTCAAAATTTTTCA-AAAAAA
1 ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGACCCTCAAAATTTTT-ATAAAAAA
5663323 CCAATTAAGC
65 -CAATTAAGC
5663333 CCCTACTTTT
Statistics
Matches: 137, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
83 11 0.08
84 61 0.45
85 3 0.02
87 2 0.01
88 60 0.44
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (85 bp):
ACTCAATTGGGTACTTGAATTGTCAAAATGCATCAAAAAGGACCCTCAAAATTTTTATAAAAAAC
AATTAAGCTGTTTTTTTTCC
Found at i:5663417 original size:20 final size:20
Alignment explanation
Indices: 5663381--5663418 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5663371 AAAAGGTCCT
*
5663381 TTGACCGTAAACTTTAACAG
1 TTGACCGTAAACGTTAACAG
5663401 TTGACCGTTAAA-GTTAAC
1 TTGACCG-TAAACGTTAAC
5663419 TGCCCCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
TTGACCGTAAACGTTAACAG
Found at i:5663676 original size:87 final size:86
Alignment explanation
Indices: 5663585--5663811 Score: 285
Period size: 87 Copynumber: 2.6 Consensus size: 86
5663575 TGCATTTTGG
* * ** *
5663585 CAATTGAGTGAAAAAAAAAAGAGAGCTTAATTGCTTTTTTTTTAAAGTTTGAAGGCATTTTTTAT
1 CAATTGAGTGAAAAAAAAAAG-GGGCTTAATTGCTTTTTCTGAAAAGTTTGAAGGCATTTTTGAT
*
5663650 ACATTTTGATAGTTCAAGTACT
65 ACATTTTGATAGTTCAAGTACC
* *
5663672 CAATTGAGT-ACAAAAAAAACAGGGGCTTAATTGCTTTTTCTGAAAAGTTTGAGGGTATTTTTGA
1 CAATTGAGTGA-AAAAAAAA-AGGGGCTTAATTGCTTTTTCTGAAAAGTTTGAAGGCATTTTTGA
*
5663736 TGCATTTTGATAGTTCAAGTACC
64 TACATTTTGATAGTTCAAGTACC
* **
5663759 CAATTAAGTGCAAAAAAAATGGGGGGCTTAATTGCTTTTTCTGCAAAAGTTTG
1 CAATTGAGTG-AAAAAAAA-AAGGGGCTTAATTGCTTTTTCTG-AAAAGTTTG
5663812 GGAGCTTTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
86 1 0.01
87 81 0.66
88 30 0.25
89 10 0.08
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (86 bp):
CAATTGAGTGAAAAAAAAAAGGGGCTTAATTGCTTTTTCTGAAAAGTTTGAAGGCATTTTTGATA
CATTTTGATAGTTCAAGTACC
Found at i:5663864 original size:90 final size:88
Alignment explanation
Indices: 5663609--5663866 Score: 259
Period size: 87 Copynumber: 2.9 Consensus size: 88
5663599 AAAAAAGAGA
* ** * * * * * * *
5663609 GCTTAATTGCTTTTTTTTTAAAGTTTGAAGGCATTTTTTATACATTTTGATAGTTCAAGTACTCA
1 GCTTAATTGCTTTTTCTGAAAAGTTTGAGGGTATTTTTGATGCATTTTAAAAGTTCAAGTACCCA
* * * **
5663674 ATTGAGTACAAAAAAAA-CAGGG
66 ATTAAATAAAAAAAAAATGGGGG
* *
5663696 GCTTAATTGCTTTTTCTGAAAAGTTTGAGGGTATTTTTGATGCATTTTGATAGTTCAAGTACCCA
1 GCTTAATTGCTTTTTCTGAAAAGTTTGAGGGTATTTTTGATGCATTTTAAAAGTTCAAGTACCCA
* **
5663761 ATTAAGTGCAAAAAAAATGGGGG
66 ATTAAATAAAAAAAAAATGGGGG
* * * *
5663784 GCTTAATTGCTTTTTCTGCAAAAGTTTG-GGAGCTTTTTTTTATGCATTTTAAAAGTTTAAGTAT
1 GCTTAATTGCTTTTTCTG-AAAAGTTTGAGG-G-TATTTTTGATGCATTTTAAAAGTTCAAGTAC
5663848 CCAATTAAATAAAAAAAAA
63 CCAATTAAATAAAAAAAAA
5663867 CAGAAATTCA
Statistics
Matches: 146, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
87 72 0.49
88 23 0.16
89 10 0.07
90 41 0.28
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.39
Consensus pattern (88 bp):
GCTTAATTGCTTTTTCTGAAAAGTTTGAGGGTATTTTTGATGCATTTTAAAAGTTCAAGTACCCA
ATTAAATAAAAAAAAAATGGGGG
Found at i:5665672 original size:26 final size:28
Alignment explanation
Indices: 5665643--5665700 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
5665633 ATGAATATTG
* *
5665643 AAAACGTATGTACATAATAT-ATATG-A
1 AAAACATATATACATAATATAATATGTA
* *
5665669 AAAATATATATACATGATATAATATGTA
1 AAAACATATATACATAATATAATATGTA
5665697 AAAA
1 AAAA
5665701 TGTAATATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 16 0.62
27 5 0.19
28 5 0.19
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAACATATATACATAATATAATATGTA
Found at i:5666240 original size:12 final size:12
Alignment explanation
Indices: 5666220--5666249 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5666210 ACCATATACA
*
5666220 AATATTGATAAT
1 AATAATGATAAT
5666232 AATAATGATAAT
1 AATAATGATAAT
5666244 AATAAT
1 AATAAT
5666250 AACATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:5666369 original size:3 final size:3
Alignment explanation
Indices: 5666361--5666434 Score: 139
Period size: 3 Copynumber: 24.3 Consensus size: 3
5666351 CTAACATATC
5666361 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5666409 ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA -ATA A
5666435 AAAAAACAAG
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5667674 original size:18 final size:17
Alignment explanation
Indices: 5667637--5667676 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
5667627 TAGGTAATGT
**
5667637 ATTGGGTTGTGAGTTCA
1 ATTGGGTTGTGAGTAAA
5667654 ATTGGGCTTGTGAGTAAA
1 ATTGGG-TTGTGAGTAAA
5667672 ATTGG
1 ATTGG
5667677 TCTGTAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.05, G:0.35, T:0.38
Consensus pattern (17 bp):
ATTGGGTTGTGAGTAAA
Found at i:5668405 original size:56 final size:56
Alignment explanation
Indices: 5668324--5668437 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
5668314 GAAAAGTAGA
*
5668324 TTTTGAAAAATAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
5668380 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
5668436 TT
1 TT
5668438 GAAAACATGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (56 bp):
TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
Found at i:5668738 original size:13 final size:13
Alignment explanation
Indices: 5668720--5668749 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5668710 GATTTTTTGA
5668720 AAAACAGAAACTG
1 AAAACAGAAACTG
*
5668733 AAAACAGAAATTG
1 AAAACAGAAACTG
5668746 AAAA
1 AAAA
5668750 TACCTCAGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAACAGAAACTG
Found at i:5668879 original size:13 final size:13
Alignment explanation
Indices: 5668861--5668890 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5668851 GATTTTTTGA
5668861 AAAACAGAAACTG
1 AAAACAGAAACTG
*
5668874 AAAACAGAAATTG
1 AAAACAGAAACTG
5668887 AAAA
1 AAAA
5668891 TACCTCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAACAGAAACTG
Found at i:5669244 original size:141 final size:141
Alignment explanation
Indices: 5668345--5669226 Score: 1405
Period size: 141 Copynumber: 6.3 Consensus size: 141
5668335 AGAAATTAAA
* *
5668345 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAGGCTCAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAACAGAAATTAAAAGGTTCAAC
* * *
5668410 TCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAACATG-AA-TTAGAACAGAAATTGGAAATAC
64 TCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA-GAAACTGAAAACAGAAATTGAAAATAC
* * *
5668471 CTCAGCATG-GCCA
128 CTCAGCGTGCCCCG
* * *
5668484 AGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGTTCAACTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
* * *
5668549 ACCTCTAGCAATATGAGTTGATTTTTTTAAAAAACAGAAACTGAAAACAGGAATTGAAAATACCT
66 ACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCT
* *
5668614 TAGCATGCCCCG
130 CAGCGTGCCCCG
*
5668626 AGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
5668691 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
5668756 AGCGTGCCCCG
131 AGCGTGCCCCG
5668767 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
5668832 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
*
5668897 AGTGTGCCCCG
131 AGCGTGCCCCG
* * * *
5668908 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAAAAAAATTAAAAGGTTCAAGTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
* *
5668973 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAAAAACTGAAAATAGAAATTGAAAATACCTC
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
* *
5669038 AGCGTACTCCG
131 AGCGTGCCCCG
* * *
5669049 AGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTAAAAAACAAAAATTAAAAGGTTCAACCC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
* *
5669114 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAATAGAAATTGAAAATACTTC
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
5669179 AGCGTGCCCCG
131 AGCGTGCCCCG
*
5669190 AGGCTCAACTCACCTCTCGCAATATGAATTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5669227 GGAAAGTATA
Statistics
Matches: 694, Mismatches: 43, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
137 51 0.07
139 37 0.05
140 8 0.01
141 515 0.74
142 83 0.12
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (141 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGGTTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAACTGAAAACAGAAATTGAAAATACCTC
AGCGTGCCCCG
Found at i:5670155 original size:8 final size:8
Alignment explanation
Indices: 5670142--5670177 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
5670132 CTTGACCCCC
5670142 TTTTTCTT
1 TTTTTCTT
5670150 TTTTTC-T
1 TTTTTCTT
5670157 TTTTTCTT
1 TTTTTCTT
*
5670165 TTTCTCTT
1 TTTTTCTT
5670173 TTTTT
1 TTTTT
5670178 TAAAGATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:5670159 original size:7 final size:7
Alignment explanation
Indices: 5670142--5670176 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
5670132 CTTGACCCCC
5670142 TTTTTCTT
1 TTTTTC-T
5670150 TTTTTCT
1 TTTTTCT
5670157 TTTTTCT
1 TTTTTCT
5670164 TTTTCTCT
1 TTTT-TCT
5670172 TTTTT
1 TTTTT
5670177 TTAAAGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:5670162 original size:15 final size:15
Alignment explanation
Indices: 5670142--5670176 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5670132 CTTGACCCCC
*
5670142 TTTTTCTTTTTTTCT
1 TTTTTCTTTTTCTCT
5670157 TTTTTCTTTTTCTCT
1 TTTTTCTTTTTCTCT
5670172 TTTTT
1 TTTTT
5670177 TTAAAGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:5681892 original size:3 final size:3
Alignment explanation
Indices: 5681886--5681910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5681876 ACATTATTAT
5681886 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5681911 GGGTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5682047 original size:12 final size:12
Alignment explanation
Indices: 5682027--5682056 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5682017 ACCATATACA
*
5682027 AATATTGATAAT
1 AATAATGATAAT
5682039 AATAATGATAAT
1 AATAATGATAAT
5682051 AATAAT
1 AATAAT
5682057 AATATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AATAATGATAAT
Found at i:5682177 original size:3 final size:3
Alignment explanation
Indices: 5682169--5682222 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
5682159 CTAACATATC
5682169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5682217 ATA ATA
1 ATA ATA
5682223 GTATATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5685095 original size:23 final size:21
Alignment explanation
Indices: 5685046--5685098 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
5685036 ATTAGTTAAT
*
5685046 TTAATATTATCGTCTTTTTTA
1 TTAATATTATCCTCTTTTTTA
5685067 TT-ATATT-TCCTCTTTCGTTTCA
1 TTAATATTATCCTCTTT--TTT-A
5685089 TTAATATTAT
1 TTAATATTAT
5685099 TTGTTGCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 7 0.27
20 5 0.19
21 5 0.19
22 3 0.12
23 5 0.19
24 1 0.04
ACGTcount: A:0.23, C:0.13, G:0.04, T:0.60
Consensus pattern (21 bp):
TTAATATTATCCTCTTTTTTA
Found at i:5685301 original size:12 final size:13
Alignment explanation
Indices: 5685284--5685313 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5685274 CTTAATTTTA
5685284 TTTATAT-TATTT
1 TTTATATATATTT
5685296 TTTATATATATTT
1 TTTATATATATTT
5685309 TTTAT
1 TTTAT
5685314 TACAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATATATATTT
Found at i:5692098 original size:50 final size:49
Alignment explanation
Indices: 5692023--5692199 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 49
5692013 CCATGGCAAT
5692023 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAATGA
* *
5692073 AAGTGATAAGTAATAGCTTTGGCTACACTTATCTGATCAAGGAAAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAA-TGA
*
5692123 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAATGA
* * *
5692173 CAAGTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
5692200 CTGATCAGTG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
49 3 0.03
50 87 0.75
51 26 0.22
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (49 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAATGA
Found at i:5692213 original size:31 final size:31
Alignment explanation
Indices: 5692175--5692292 Score: 166
Period size: 31 Copynumber: 3.8 Consensus size: 31
5692165 ACAAATGACA
*
5692175 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
5692206 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
* * *
5692237 AGCGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
5692268 AGTGAATAGTGGTAGCTTTGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
5692293 AAGTGACAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
30 2 0.03
31 73 0.96
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5692387 original size:47 final size:46
Alignment explanation
Indices: 5692318--5692440 Score: 156
Period size: 47 Copynumber: 2.7 Consensus size: 46
5692308 AGTGATTTCC
* *
5692318 GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACT
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGAT-CT
* * * *
5692365 GTATAAGACCATATATGGGATATGGCATCAGTGAGATATGTGATTT
1 GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATCT
* * *
5692411 GTGTAAGACCATAGCTGGGCTATGGCATCG
1 GTATAAGACCATATCTGGGATATGGCATCG
5692441 ATATATGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
46 26 0.40
47 39 0.60
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (46 bp):
GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATCT
Found at i:5692475 original size:42 final size:42
Alignment explanation
Indices: 5692410--5692524 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
5692400 ATATGTGATT
* *
5692410 TGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATA
1 TGTGTAAGACCATAGCTGAGCTATGGCATC-ATTATATGAAGA
* *
5692452 TGTGTAAGACCATAACTGAGCTATGGCATCATTATGTGAAGA
1 TGTGTAAGACCATAGCTGAGCTATGGCATCATTATATGAAGA
* *
5692494 TGTGTAAGACCATAGTTGAACTATGGCATCA
1 TGTGTAAGACCATAGCTGAGCTATGGCATCA
5692525 AGAAAACGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.02
42 64 0.98
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTGTAAGACCATAGCTGAGCTATGGCATCATTATATGAAGA
Found at i:5692634 original size:25 final size:25
Alignment explanation
Indices: 5692600--5692656 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
5692590 GGAATTATGT
5692600 GATACAAGGAAGTACGAGTTGATAA
1 GATACAAGGAAGTACGAGTTGATAA
5692625 GATACAAGGAAGTACGAGTTGATAA
1 GATACAAGGAAGTACGAGTTGATAA
5692650 GATACAA
1 GATACAA
5692657 TGAATTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (25 bp):
GATACAAGGAAGTACGAGTTGATAA
Found at i:5699035 original size:13 final size:13
Alignment explanation
Indices: 5699019--5699057 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
5699009 TTTCCAAAAA
5699019 AAAAGAAAAAGAG
1 AAAAGAAAAAGAG
*
5699032 AAAA-AAAAAAAG
1 AAAAGAAAAAGAG
*
5699044 AAAAGAAAAGGAG
1 AAAAGAAAAAGAG
5699057 A
1 A
5699058 GGCCAAGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAG
Found at i:5699035 original size:14 final size:14
Alignment explanation
Indices: 5699018--5699057 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
5699008 TTTTCCAAAA
5699018 AAAAAGAAAAAGAG
1 AAAAAGAAAAAGAG
5699032 AAAAA-AAAAA-AG
1 AAAAAGAAAAAGAG
*
5699044 -AAAAGAAAAGGAG
1 AAAAAGAAAAAGAG
5699057 A
1 A
5699058 GGCCAAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
11 4 0.18
12 6 0.27
13 7 0.32
14 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGAG
Found at i:5699035 original size:17 final size:17
Alignment explanation
Indices: 5699014--5699052 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5699004 AAAGTTTTCC
5699014 AAAAAAAAAGAA-AAAGAG
1 AAAAAAAAA-AAGAAA-AG
5699032 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
5699049 AAAA
1 AAAA
5699053 GGAGAGGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:5699952 original size:46 final size:47
Alignment explanation
Indices: 5699840--5699965 Score: 175
Period size: 47 Copynumber: 2.7 Consensus size: 47
5699830 TGAAGAAGCC
* * * *
5699840 ACAAATCCTATACCCCTGAGCTGCACTAGAATGAATTGCAGTAGGAT
1 ACAAATCCTATACCCCTGAGCTGCAGTGGGATGAATTGAAGTAGGAT
*
5699887 ACAAATCCTATATCCCTGAGCTGCAGTGGGATGAATTGAAG-ATGG-T
1 ACAAATCCTATACCCCTGAGCTGCAGTGGGATGAATTGAAGTA-GGAT
*
5699933 ACAAATCCTATACCCCTGAGTTGCAGTGGGATG
1 ACAAATCCTATACCCCTGAGCTGCAGTGGGATG
5699966 GATGGAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
46 33 0.46
47 38 0.54
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (47 bp):
ACAAATCCTATACCCCTGAGCTGCAGTGGGATGAATTGAAGTAGGAT
Found at i:5700405 original size:45 final size:44
Alignment explanation
Indices: 5700327--5700588 Score: 156
Period size: 44 Copynumber: 5.9 Consensus size: 44
5700317 GAATCCACAA
* * ** **
5700327 ATCTCATCTCCCTGAAGCAGCAGTGGAGCAGATTGAAGTTATAG
1 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCATAG
** * *
5700371 ATCTTATCTCCTTGAAGTTTGCAGTGGAATAGATTGAA--AATGGTG
1 ATCTTATCTCCTTGAAG-TTGCAGTGGAGCAGATTGAAGCCAT--AG
* * * * *
5700416 AATCTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAG
1 -ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TAG
* * * *
5700462 -CCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGACAGT-G
1 ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TAG
* * * * * *
5700505 ATTCTTATCTCCTTGAAGTTTCAATGGAGTAGATTGAAGCTACAA
1 A-TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCATAG
* * * *
5700550 ATC-TATTCTCCTTGAAATTACATTGGAGCAGATCGAAGC
1 ATCTTA-TCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGC
5700589 ACCAACTTTA
Statistics
Matches: 166, Mismatches: 41, Indels: 22
0.72 0.18 0.10
Matches are distributed among these distances:
43 5 0.03
44 77 0.46
45 66 0.40
46 17 0.10
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCATAG
Found at i:5700496 original size:44 final size:44
Alignment explanation
Indices: 5700419--5700655 Score: 145
Period size: 44 Copynumber: 5.4 Consensus size: 44
5700409 AATGGTGAAT
* * * * *
5700419 CTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAAC
** * ** **
5700463 CTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGACAGTGATT
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCA-CCAAC
* * * * * *
5700508 CTTATCTCCTTGAAGTTTCAATGGAGTAGATTGAAGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAAC
* * * * *
5700552 C-TATTCTCCTTGAAATTACATTGGAGCAGATCGAAG-CACCAAC
1 CTTA-TCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAAC
* ** * * * * * * *
5700595 TTTATCTTTCTGATGTTGTAGTGAAACAGATTGAAGCCATCAGC
1 CTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAAC
5700639 CTTATCTCCCTGAAGTT
1 CTTATCTCCCTGAAGTT
5700656 ATAGCAGAGT
Statistics
Matches: 142, Mismatches: 47, Indels: 8
0.72 0.24 0.04
Matches are distributed among these distances:
43 27 0.19
44 82 0.58
45 33 0.23
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCCACCAAC
Found at i:5700523 original size:89 final size:89
Alignment explanation
Indices: 5700418--5700700 Score: 254
Period size: 89 Copynumber: 3.2 Consensus size: 89
5700408 AAATGGTGAA
*
5700418 TCTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTGCA
1 TCTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTACA
*
5700483 GCGGAGCAGATTGAAGACAGTGAT
66 GCGGAGCAGATTGAAGACAGTAAT
* * * * * * ** * *
5700507 TCTTATCTCCTTGAAGTTTCAATGGAGTAGATTGAAGCTACAAATC-TATTCTCCTTGAAATTAC
1 TCTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAGCCTTA-TCTCCCTGAAGTTAC
** * ** *
5700571 ATTGGAGCAGATCGAAG-CACCAAC
65 AGCGGAGCAGATTGAAGACAGTAAT
* * * *
5700595 T-TTATCTT-TCTGATGTTGTAGT-GA-AACAGATTGAAGCCATCAGCCTTATCTCCCTGAAGTT
1 TCTTATCTTCT-TGAAGTTGCAATGGAGAA-A-ATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * *
5700656 ATAGCAGAGTAGACTGAAGACAGTAAT
63 ACAGCGGAGCAGATTGAAGACAGTAAT
5700683 TCTTATCTTCTTGAAGTT
1 TCTTATCTTCTTGAAGTT
5700701 TCGGTGGAGT
Statistics
Matches: 143, Mismatches: 43, Indels: 16
0.71 0.21 0.08
Matches are distributed among these distances:
85 1 0.01
86 3 0.02
87 48 0.34
88 13 0.09
89 77 0.54
90 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (89 bp):
TCTTATCTTCTTGAAGTTGCAATGGAGAAAATTGAAGCCACCAGCCTTATCTCCCTGAAGTTACA
GCGGAGCAGATTGAAGACAGTAAT
Found at i:5701040 original size:44 final size:44
Alignment explanation
Indices: 5700978--5701114 Score: 152
Period size: 44 Copynumber: 3.1 Consensus size: 44
5700968 CCTGACGTCG
* * *
5700978 CAGTGGAACAAATCAAAGCTACAAGTCTAATCTCCCTGTAGTTA
1 CAGTGGAGCAAATTAAAGCTACAAGTCTAATCTCCCTGAAGTTA
* * *
5701022 CAGTAGG-GCAAATTAAAGCTACGAA-TCTTATTTCCCTGAAGTTG
1 CAGT-GGAGCAAATTAAAGCTAC-AAGTCTAATCTCCCTGAAGTTA
* * * *
5701066 CAATGGAGCAGATTAAAGCTATAAGTCTAATCTCTCTGAAGTTA
1 CAGTGGAGCAAATTAAAGCTACAAGTCTAATCTCCCTGAAGTTA
5701110 CAGTG
1 CAGTG
5701115 AAGTAGATTG
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
43 4 0.05
44 67 0.89
45 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (44 bp):
CAGTGGAGCAAATTAAAGCTACAAGTCTAATCTCCCTGAAGTTA
Found at i:5701123 original size:44 final size:44
Alignment explanation
Indices: 5700992--5701158 Score: 126
Period size: 44 Copynumber: 3.8 Consensus size: 44
5700982 GGAACAAATC
* * * *
5700992 AAAGCTACAAGTCTAATCTCCCTGTAGTTACAGT-AGGGCAAATT
1 AAAGCTATAAGTCTAATCTCCCTGAAGTTACAGTGA-AGCAGATT
* * * * * *
5701036 AAAGCTACGAA-TCTTATTTCCCTGAAGTTGCAATGGAGCAGATT
1 AAAGCTA-TAAGTCTAATCTCCCTGAAGTTACAGTGAAGCAGATT
* *
5701080 AAAGCTATAAGTCTAATCTCTCTGAAGTTACAGTGAAGTAGATT
1 AAAGCTATAAGTCTAATCTCCCTGAAGTTACAGTGAAGCAGATT
* * * *
5701124 GAAGCGATAATTCCT-ATAC-CCCTGAAGTTGCAGTG
1 AAAGCTATAAGT-CTAAT-CTCCCTGAAGTTACAGTG
5701159 GGTTGGAATG
Statistics
Matches: 96, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
43 2 0.02
44 89 0.93
45 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
AAAGCTATAAGTCTAATCTCCCTGAAGTTACAGTGAAGCAGATT
Found at i:5701352 original size:13 final size:12
Alignment explanation
Indices: 5701323--5701357 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
5701313 TCATTTTAAA
5701323 CAAAAATAAAAC
1 CAAAAATAAAAC
5701335 CAAAAATAAAAC
1 CAAAAATAAAAC
5701347 CAAAAAATAAA
1 C-AAAAATAAA
5701358 GTCCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (12 bp):
CAAAAATAAAAC
Found at i:5703623 original size:42 final size:42
Alignment explanation
Indices: 5703574--5703658 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
5703564 AATCAACATT
5703574 AAAAAAGAGAGGATCGTATTTTAAATTCTTTTCGAGCTTTCA
1 AAAAAAGAGAGGATCGTATTTTAAATTCTTTTCGAGCTTTCA
*
5703616 AAAAAAGAGAGGATCGTATTTTAAATTCTTTTCTAGCTTTCA
1 AAAAAAGAGAGGATCGTATTTTAAATTCTTTTCGAGCTTTCA
5703658 A
1 A
5703659 CTTTCGACGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (42 bp):
AAAAAAGAGAGGATCGTATTTTAAATTCTTTTCGAGCTTTCA
Found at i:5711088 original size:17 final size:17
Alignment explanation
Indices: 5711050--5711095 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5711040 ACATTATAAG
5711050 ATTATTTTATTATAAAT
1 ATTATTTTATTATAAAT
* **
5711067 GTTATTTTATTATATGT
1 ATTATTTTATTATAAAT
5711084 ATTATTATTATT
1 ATTATT-TTATT
5711096 TATTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTATTTTATTATAAAT
Found at i:5711104 original size:30 final size:29
Alignment explanation
Indices: 5711068--5711223 Score: 87
Period size: 30 Copynumber: 5.3 Consensus size: 29
5711058 ATTATAAATG
5711068 TTATTTTATTATATGTATTATTATTATTTA
1 TTATTTTATTATAT-TATTATTATTATTTA
*
5711098 TTATTTT-TCTCAAATTATTATT-TTA--TA
1 TTATTTTAT-T-ATATTATTATTATTATTTA
* *
5711125 TCATTTT-TATATATATATTGTTA-TATTT-
1 TTATTTTAT-TATAT-TATTATTATTATTTA
* * *
5711153 TCACATATATTATATTATTATTATTTATATATA
1 TTA-TTTTATTATATTATTATTA-TTAT-T-TA
5711186 TTATTTTA-TAT-TTATTATTATTTATATATA
1 TTATTTTATTATATTATTATTA-TTAT-T-TA
5711216 TTATTTTA
1 TTATTTTA
5711224 CATATAAACT
Statistics
Matches: 102, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
26 3 0.03
27 18 0.18
28 10 0.10
29 12 0.12
30 46 0.45
31 7 0.07
32 4 0.04
33 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATTTTATTATATTATTATTATTATTTA
Found at i:5711187 original size:10 final size:10
Alignment explanation
Indices: 5711119--5711217 Score: 51
Period size: 10 Copynumber: 9.2 Consensus size: 10
5711109 AAATTATTAT
*
5711119 TTTATATCATT
1 TTTATAT-ATA
5711130 TTTATATATA
1 TTTATATATA
*
5711140 TATTGT-TATA
1 T-TTATATATA
*
5711150 TTTTCACATATA
1 -TTT-ATATATA
5711162 TTATATTATTATTA
1 TT-TA-TA-TA-TA
5711176 TTTATATATA
1 TTTATATATA
*
5711186 -TTATTTTATA
1 TTTA-TATATA
5711196 TTTAT-TATTA
1 TTTATATA-TA
5711206 TTTATATATA
1 TTTATATATA
5711216 TT
1 TT
5711218 ATTTTACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
9 5 0.07
10 28 0.40
11 21 0.30
12 8 0.11
13 4 0.06
14 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTATATATA
Found at i:5711197 original size:20 final size:21
Alignment explanation
Indices: 5711130--5711200 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
5711120 TTATATCATT
*
5711130 TTTATATATA-TATTGTTATA
1 TTTATATATATTATTATTATA
*
5711150 TTTTCACATATATTATATTATTATTA
1 -TTT-ATATATA-T-TATTATTA-TA
5711176 TTTATATATATTATT-TTATA
1 TTTATATATATTATTATTATA
5711196 TTTAT
1 TTTAT
5711201 TATTATTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
20 7 0.17
21 6 0.14
22 10 0.24
23 1 0.02
24 6 0.14
25 10 0.24
26 2 0.05
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (21 bp):
TTTATATATATTATTATTATA
Found at i:5711215 original size:20 final size:20
Alignment explanation
Indices: 5711130--5711217 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 20
5711120 TTATATCATT
*
5711130 TTTATATATATATTGTTA-TA
1 TTTATATATAT-TTATTATTA
*
5711150 TTTTCACATATATTATATTATTA
1 -TTT-ATATATATT-TATTATTA
*
5711173 -TTAT-T-TATATA-TATTA
1 TTTATATATATTTATTATTA
5711189 -TT-T-TATATTTATTATTA
1 TTTATATATATTTATTATTA
5711206 TTTATATATATT
1 TTTATATATATT
5711218 ATTTTACATA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
15 2 0.04
16 12 0.22
17 7 0.13
18 5 0.09
19 2 0.04
20 7 0.13
21 6 0.11
22 11 0.20
23 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTATATATATTTATTATTA
Found at i:5711218 original size:46 final size:46
Alignment explanation
Indices: 5711121--5711222 Score: 122
Period size: 46 Copynumber: 2.2 Consensus size: 46
5711111 ATTATTATTT
*
5711121 TATATCATTTTTATATATATATTGTTATATTTTCACATATATTATA
1 TATATTATTTTTATATATATATTGTTATATTTTCACATATATTATA
* *
5711167 T-TATTATTATTTATATATATTATT-TTATATTTATTA-TTAT-TTATA
1 TATATTATT-TTTATATATA-TATTGTTATATTT-TCACATATATTATA
5711212 TATATTATTTT
1 TATATTATTTT
5711223 ACATATAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
45 14 0.29
46 29 0.59
47 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (46 bp):
TATATTATTTTTATATATATATTGTTATATTTTCACATATATTATA
Found at i:5711223 original size:14 final size:16
Alignment explanation
Indices: 5711162--5711220 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
5711152 TTCACATATA
5711162 TTATAT-TATTATTAT
1 TTATATATATTATTAT
5711177 TTATATATATTA-T-T
1 TTATATATATTATTAT
*
5711191 TTATATTTATTATTAT
1 TTATATATATTATTAT
5711207 TTATATATATTATT
1 TTATATATATTATT
5711221 TTACATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 12 0.31
15 8 0.21
16 19 0.49
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATATATATTATTAT
Found at i:5711228 original size:16 final size:14
Alignment explanation
Indices: 5711162--5711229 Score: 75
Period size: 14 Copynumber: 4.6 Consensus size: 14
5711152 TTCACATATA
5711162 TTATAT-TATTATTAT
1 TTATATATATTA-T-T
5711177 TTATATATATTATT
1 TTATATATATTATT
*
5711191 TTATATTTATTATTAT
1 TTATATATATTA-T-T
5711207 TTATATATATTATT
1 TTATATATATTATT
*
5711221 TTACATATA
1 TTATATATA
5711230 AACTTTCATT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
14 21 0.45
15 9 0.19
16 17 0.36
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATATATTATT
Found at i:5711229 original size:44 final size:44
Alignment explanation
Indices: 5711111--5711229 Score: 115
Period size: 46 Copynumber: 2.7 Consensus size: 44
5711101 TTTTTCTCAA
5711111 ATTATTATTT-TATATCA-T-TTTTATATATATATTGTTATATTT
1 ATTATTATTTATATAT-ATTATTTTATATATATATTGTTATATTT
* *
5711153 -TCACATATATTATAT-TATTATTATTTATATATATTATT-TTATATTT
1 ATTA-TTAT-TTATATATATTA-T-TTTATATATA-TATTGTTATATTT
*
5711199 ATTATTATTTATATATATTATTTTACATATA
1 ATTATTATTTATATATATTATTTTATATATA
5711230 AACTTTCATT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
41 2 0.03
42 4 0.06
43 4 0.06
44 12 0.19
45 8 0.13
46 26 0.42
47 6 0.10
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (44 bp):
ATTATTATTTATATATATTATTTTATATATATATTGTTATATTT
Found at i:5713320 original size:64 final size:63
Alignment explanation
Indices: 5713238--5713457 Score: 140
Period size: 64 Copynumber: 3.3 Consensus size: 63
5713228 ACAGTGGTAC
*
5713238 TGGCCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
1 TGGCCCAGAGCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
* * ** * * ***
5713301 TGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATG-C-AAGCCCATT-TGGG
1 TGGCCCAGA-GCCCATTTC-AGAT---T-----A-CAATAAAC-TGGGCCTTAGCCCCTTATTCA
***
5713363 GAATAGTGGTA
54 G-ATAACAGTA
* *
5713374 TTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
1 -TGGCCCAGAGCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
*
5713438 TGGCCCATAGGCCCATTTCA
1 TGGCCCAGA-GCCCATTTCA
5713458 AAATACATGC
Statistics
Matches: 109, Mismatches: 30, Indels: 35
0.63 0.17 0.20
Matches are distributed among these distances:
62 2 0.02
63 24 0.22
64 31 0.28
65 5 0.05
68 1 0.01
69 1 0.01
72 5 0.05
73 22 0.20
74 16 0.15
75 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGGCCCAGAGCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTA
Found at i:5713459 original size:137 final size:137
Alignment explanation
Indices: 5713230--5713501 Score: 517
Period size: 137 Copynumber: 2.0 Consensus size: 137
5713220 TTCAGGTAAC
5713230 AGTGGTACTGGCCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATA
1 AGTGGTACTGGCCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATA
5713295 ACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCCATTT
66 ACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCCATTT
5713360 GGGGAAT
131 GGGGAAT
* *
5713367 AGTGGTATTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATA
1 AGTGGTACTGGCCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATA
*
5713432 ACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCATTT
66 ACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCCATTT
5713497 GGGGA
131 GGGGA
5713502 GACTACTCAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AGTGGTACTGGCCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATA
ACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAACATATGCAAGCCCATTT
GGGGAAT
Found at i:5715320 original size:26 final size:26
Alignment explanation
Indices: 5715284--5715365 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
5715274 TGAAATTCTC
5715284 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5715310 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5715336 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5715362 ATCA
1 ATCA
5715366 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5718725 original size:27 final size:27
Alignment explanation
Indices: 5718659--5718712 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5718649 AAGCCCCCCT
5718659 AAAA-AAAAACCTAACCCAAAAAAAAA
1 AAAAGAAAAACCTAACCCAAAAAAAAA
5718685 AAAAGAAAAACCTAACCCAAAAAAAAA
1 AAAAGAAAAACCTAACCCAAAAAAAAA
5718712 A
1 A
5718713 CTAAGAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.76, C:0.19, G:0.02, T:0.04
Consensus pattern (27 bp):
AAAAGAAAAACCTAACCCAAAAAAAAA
Found at i:5721242 original size:12 final size:12
Alignment explanation
Indices: 5721225--5721260 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5721215 ATTCATTTGA
5721225 CATTCATGCATT
1 CATTCATGCATT
5721237 CATTCATGCATT
1 CATTCATGCATT
*
5721249 CATTCATACATT
1 CATTCATGCATT
5721261 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:5729780 original size:74 final size:75
Alignment explanation
Indices: 5729674--5729983 Score: 241
Period size: 74 Copynumber: 3.9 Consensus size: 75
5729664 TTTTTCAAAA
* * *
5729674 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAAT
1 AAAAAAATCAACTCATATTGCGAGCGGCGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAAT
5729738 TTCTGTTGTC
66 TTCTGTTGTC
* *
5729748 AAAAAAATCAACTCATATTGCGAGCGGCGAGTTGAGCCTCAGGTCACACACCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGCGGCGAGTTGAGCCTCAGG-CACACGCCGAGGTAATTTCAA
* *
5729813 TTTCCGTTTTC
65 TTTCTGTTGTC
** * * * ** *
5729824 AATTTCTGCCTTTCAAAAAAAAAATCA-ACT-CATATTGCGAGAGGTGAGTTGAGCCTCAGG-AC
1 AA------------AAAAATCAACTCATATTGC-GAGCG-GCG-----AGTTGAGCCTCAGGCAC
*
5729886 ACGCTGAGGTAATTTCAATTTCTGTTGTC
47 ACGCCGAGGTAATTTCAATTTCTGTTGTC
* *
5729915 AAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGCGGCGAGTTGAGCCTCAGG-CACACGCCGAGGTAATTTCAA
5729980 TTTC
65 TTTC
5729984 CGTTTTTCAA
Statistics
Matches: 180, Mismatches: 31, Indels: 48
0.69 0.12 0.19
Matches are distributed among these distances:
74 55 0.31
76 50 0.28
79 11 0.06
80 4 0.02
81 1 0.01
86 1 0.01
87 4 0.02
88 12 0.07
91 28 0.16
93 14 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (75 bp):
AAAAAAATCAACTCATATTGCGAGCGGCGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAAT
TTCTGTTGTC
Found at i:5729936 original size:167 final size:169
Alignment explanation
Indices: 5729652--5730315 Score: 925
Period size: 167 Copynumber: 3.9 Consensus size: 169
5729642 GAGTTGAGCC
**
5729652 TTTT-AATTTCTGTTTTTCAAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTTTCAATTTCTGCCTTTC-AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AG
* *
5729716 G-ACACGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAAATCAACTCATATTGCGAGCGGCGAG
64 GCACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAG
*
5729779 TTGAGCCTCAGGTCACACACCGAGGTATTTTCAATTTCCG-
129 TTGAGCCTCAGATCACACACCGAGGTATTTTCAATTTCCGT
5729819 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGG
* * *
5729884 -ACACGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAAAATCAACTCGTATTGCGAGCGGCGAGT
65 CACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGT
* *
5729947 TGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGT
130 TGAGCCTCAGATCACACACCGAGGTATTTTCAATTTCCGT
* * *
5729987 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTAAGCCTTGGC
1 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-
* * * *
5730052 TCACGCGCTGAGCTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAG
65 -CACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAG
* *
5730117 TTGAGCCTCAGATCACACGCCGAGGTATTTTCAATTTTCGT
129 TTGAGCCTCAGATCACACACCGAGGTATTTTCAATTTCCGT
** *
5730158 TTTTCAATTTCTGCCTTTC--AAAAAAAATCGAA-TCATATTATGAGAGGTGAGTTGAGCCTTGG
1 TTTTCAATTTCTGCCTTTCAAAAAAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAGCCTAGG
* * * *
5730220 CTCACGCGCTGAGCTATTTTCAATTTCTGTCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGA
65 --CACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGA
* **
5730284 GTTGAGCTTCAGATCACACATTGAGGTATTTT
128 GTTGAGCCTCAGATCACACACCGAGGTATTTT
5730316 TTTTTTTTCG
Statistics
Matches: 466, Mismatches: 24, Indels: 13
0.93 0.05 0.03
Matches are distributed among these distances:
167 152 0.33
168 128 0.27
169 72 0.15
170 25 0.05
171 89 0.19
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (169 bp):
TTTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGC
ACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTT
GAGCCTCAGATCACACACCGAGGTATTTTCAATTTCCGT
Found at i:5730069 original size:94 final size:94
Alignment explanation
Indices: 5729915--5730087 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
5729905 TTCTGTTGTC
* * * *
5729915 AAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGGTCACACGCCGAGCTATTTTCAA
*
5729980 TTTCCGTTTTTCAATTTCTGCCTTTCAAA
66 TTTCCGTCTTTCAATTTCTGCCTTTCAAA
* * * * *
5730009 AAAAAAATCGACTCATATTGCGAGAGGTGAGTTAAGCCT-TGGCTCACGCGCTGAGCTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGG-TCACACGCCGAGCTATTTTCA
*
5730073 ATTTCTGTCTTTCAA
65 ATTTCCGTCTTTCAA
5730088 AAAAATCAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
93 2 0.03
94 65 0.97
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (94 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTAAGCCTCAGGTCACACGCCGAGCTATTTTCAA
TTTCCGTCTTTCAATTTCTGCCTTTCAAA
Found at i:5730117 original size:77 final size:78
Alignment explanation
Indices: 5729987--5730153 Score: 228
Period size: 77 Copynumber: 2.1 Consensus size: 78
5729977 CAATTTCCGT
* ** *
5729987 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTAAGCCTTGGC
1 TTTTCAATTTCTGCCTTTC--AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGA
* *
5730052 TCACGCGCTGAGCTA
64 TCACACGCCGAGCTA
* *
5730067 TTTTCAATTTCTGTCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATC
1 TTTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGATC
*
5730131 ACACGCCGAGGTA
66 ACACGCCGAGCTA
5730144 TTTTCAATTT
1 TTTTCAATTT
5730154 TCGTTTTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
77 60 0.77
80 18 0.23
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (78 bp):
TTTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGATC
ACACGCCGAGCTA
Found at i:5730238 original size:92 final size:91
Alignment explanation
Indices: 5730067--5730245 Score: 252
Period size: 92 Copynumber: 2.0 Consensus size: 91
5730057 CGCTGAGCTA
* *
5730067 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCA
1 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCA
*
5730132 CACGCCGAGGTATTTTCAATTTTCGT
66 CACGCCGAGCTATTTTCAATTTTCGT
* ** *
5730158 TTTTCAATTTCTGCCTTTCAAAAAAAATCGAA-TCATATTATGAGAGGTGAGTTGAGCCTTGGCT
1 TTTTCAATTTCTGCCTTTC-AAAAAAATC-AACTCATATTACGAGAGGTGAGTTGAGCCTCAGAT
* *
5730222 CACGCGCTGAGCTATTTTCAATTT
64 CACACGCCGAGCTATTTTCAATTT
5730246 CTGTCTTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 18 0.23
92 57 0.74
93 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (91 bp):
TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGATCA
CACGCCGAGCTATTTTCAATTTTCGT
Found at i:5730314 original size:76 final size:77
Alignment explanation
Indices: 5730158--5730315 Score: 187
Period size: 76 Copynumber: 2.1 Consensus size: 77
5730148 CAATTTTCGT
* * *
5730158 TTTTCAATTTCTGCCTTTCAAAAAAAATCGAATCATATTATGAGAGGTGAGTTGAGCCTTGGCTC
1 TTTTCAATTTCTGCCTTTC-AAAAAAATCGAATCATATTACGAGAGGTGAGTTGAGCCTTAGATC
* *
5730223 ACGCGCTGAGCTA
65 ACACACTGAGCTA
* *
5730236 TTTTCAATTTCTGTCTTTC-AAAAAATC-AACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGAT
1 TTTTCAATTTCTGCCTTTCAAAAAAATCGAA-TCATATTACGAGAGGTGAGTTGAGCCTT-AGAT
* *
5730298 CACACATTGAGGTA
64 CACACACTGAGCTA
5730312 TTTT
1 TTTT
5730316 TTTTTTTTCG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
75 5 0.07
76 46 0.67
78 18 0.26
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (77 bp):
TTTTCAATTTCTGCCTTTCAAAAAAATCGAATCATATTACGAGAGGTGAGTTGAGCCTTAGATCA
CACACTGAGCTA
Found at i:5730689 original size:78 final size:77
Alignment explanation
Indices: 5730561--5730888 Score: 274
Period size: 78 Copynumber: 4.1 Consensus size: 77
5730551 ATTTCTGTTC
* * * *
5730561 TTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCTAGTGGTGAGTTGAGCCTTGACTCACG
1 TTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACG
*
5730626 CGCTGAGCTATT
66 CACTGAGCTATT
5730638 TTCAATTTCTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGA-TC
1 TTCAATTTCTGTCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT--GACTC
* *
5730701 ACACAC-GAAGGTATTTTT
63 ACGCACTG-AGCTA---TT
* * * * *
5730719 TTCAATTTATATTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAGTCACA
1 TTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACG
* *
5730782 TA-TCGAGGTATT
66 CACT-GAGCTATT
**
5730794 TTCAAAATCTG-CTTTTCAAGTTAAGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTCAATTTCTGTC-TTTC-----AA-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
5730858 CTTGGCTCACGCACTGAGCAATT
55 CTTGACTCACGCACTGAGCTATT
5730881 TTCAATTT
1 TTCAATTT
5730889 ATGTTTTTAA
Statistics
Matches: 202, Mismatches: 24, Indels: 40
0.76 0.09 0.15
Matches are distributed among these distances:
75 13 0.06
77 22 0.11
78 88 0.44
79 6 0.03
81 16 0.08
87 56 0.28
88 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (77 bp):
TTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCACG
CACTGAGCTATT
Found at i:5731893 original size:12 final size:12
Alignment explanation
Indices: 5731878--5731920 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5731868 TTCTTTCGAA
5731878 TCTTTTTTTCTT
1 TCTTTTTTTCTT
*
5731890 TCTTTTTTTGTGT
1 TCTTTTTTTCT-T
*
5731903 TGTTTTTTTTCTT
1 T-CTTTTTTTCTT
5731916 TCTTT
1 TCTTT
5731921 ATATATACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 13 0.52
13 4 0.16
14 8 0.32
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:5734810 original size:2 final size:2
Alignment explanation
Indices: 5734805--5734847 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
5734795 TATATTTTAA
* * *
5734805 AT AT AT AT TT AA AA AT AT -T 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
5734846 AT
1 AT
5734848 TTCTTATTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5734839 original size:42 final size:43
Alignment explanation
Indices: 5734760--5734841 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
5734750 AGGTGGTTAG
* * *
5734760 AAATATTATTTTTAAAAATATCTAAATATGTTGTATATATTTT
1 AAATATTATATTTAAAAATATCTAAATATATTATATATATTTT
*
5734803 AAATA-TATATTTAAAAATAT-TATATATATATATATATAT
1 AAATATTATATTTAAAAATATCTAAATATAT-TATATATAT
5734842 ATATATTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 7 0.21
42 22 0.65
43 5 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (43 bp):
AAATATTATATTTAAAAATATCTAAATATATTATATATATTTT
Found at i:5734845 original size:23 final size:23
Alignment explanation
Indices: 5734793--5734845 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5734783 AAATATGTTG
* *
5734793 TATATATTTTAAATATATATTTA
1 TATATATTATAAATATATATATA
* * *
5734816 AAAATATTATATATATATATATA
1 TATATATTATAAATATATATATA
5734839 TATATAT
1 TATATAT
5734846 ATTTCTTATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATATTATAAATATATATATA
Found at i:5736721 original size:2 final size:2
Alignment explanation
Indices: 5736714--5736758 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5736704 ATGATTACTG
*
5736714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5736756 AT A
1 AT A
5736759 CGTATGAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5737549 original size:29 final size:29
Alignment explanation
Indices: 5737507--5737564 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5737497 GCTAAAAAGA
5737507 TACGTTTGAGTCAAAATAAAGGACACACG
1 TACGTTTGAGTCAAAATAAAGGACACACG
5737536 TACGTTTGAGTCAAAATAAAGGACACACG
1 TACGTTTGAGTCAAAATAAAGGACACACG
5737565 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (29 bp):
TACGTTTGAGTCAAAATAAAGGACACACG
Found at i:5741574 original size:31 final size:31
Alignment explanation
Indices: 5741514--5741574 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
5741504 ACTATTTCTT
* * *
5741514 AATTTAGTACATAAGTTTTTTTTTTAAATTC
1 AATTTAGTACATAAATTTTTTTGTCAAATTC
* *
5741545 AATTTGGTACTTAAATTTTTTTGTCAAATT
1 AATTTAGTACATAAATTTTTTTGTCAAATT
5741575 TGATACCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (31 bp):
AATTTAGTACATAAATTTTTTTGTCAAATTC
Found at i:5742033 original size:15 final size:15
Alignment explanation
Indices: 5742013--5742042 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5742003 AGGAAACTTC
5742013 AAATAAATGTAATCA
1 AAATAAATGTAATCA
5742028 AAATAAATGTAATCA
1 AAATAAATGTAATCA
5742043 TTCTTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
AAATAAATGTAATCA
Found at i:5746828 original size:17 final size:17
Alignment explanation
Indices: 5746804--5746861 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
5746794 TAAAATTTTA
5746804 AATA-ATTAAATAAATT
1 AATATATTAAATAAATT
* *
5746820 AATATATT-ATTATAGTT
1 AATATATTAAATA-AATT
*
5746837 AA-ATTATTAAAGAAATT
1 AATA-TATTAAATAAATT
5746854 AATATATT
1 AATATATT
5746862 TTAATTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
16 8 0.25
17 21 0.66
18 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AATATATTAAATAAATT
Found at i:5759816 original size:13 final size:14
Alignment explanation
Indices: 5759791--5759823 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5759781 TTCTTTCATT
5759791 AAAAATAATTTTTA
1 AAAAATAATTTTTA
*
5759805 TAAAAT-ATTTTTA
1 AAAAATAATTTTTA
5759818 AAAAAT
1 AAAAAT
5759824 CTATCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:5761477 original size:12 final size:13
Alignment explanation
Indices: 5761440--5761478 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
5761430 TTCACATATA
5761440 AAAATAATGGTATTT
1 AAAATAAT--TATTT
5761455 AAAATAATTATTT
1 AAAATAATTATTT
5761468 AAAA-AATTATT
1 AAAATAATTATT
5761479 ATTTTTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 9 0.38
15 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (13 bp):
AAAATAATTATTT
Found at i:5761780 original size:33 final size:33
Alignment explanation
Indices: 5761743--5761866 Score: 121
Period size: 32 Copynumber: 3.7 Consensus size: 33
5761733 CAATGTAGGT
*
5761743 TAAAATATAATGATA-TTTAAAATATTTCACATA
1 TAAAA-ATAATGATATTTTGAAATATTTCACATA
*
5761776 TAAAAAGAATGATATTTTGAAATAGTTTACACATAA
1 TAAAAATAATGATATTTTGAAATA-TTT-CACAT-A
* *
5761812 TAATAAT-ATGATATTTTGAAATAATTT-ACACA
1 TAAAAATAATGATATTTTGAAAT-ATTTCACATA
* *
5761844 TAATAATAATGGTA-TTTGAAATA
1 TAAAAATAATGATATTTTGAAATA
5761867 ATTGAAATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
31 1 0.01
32 24 0.30
33 21 0.27
34 3 0.04
35 23 0.29
36 7 0.09
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (33 bp):
TAAAAATAATGATATTTTGAAATATTTCACATA
Found at i:5761862 original size:32 final size:33
Alignment explanation
Indices: 5761749--5761869 Score: 140
Period size: 35 Copynumber: 3.7 Consensus size: 33
5761739 AGGTTAAAAT
* * *
5761749 ATAATGATA-TTTAAAAT-ATTTCACATATAAAA
1 ATAATGATATTTTGAAATAATTT-ACACATAATA
* *
5761781 AGAATGATATTTTGAAATAGTTTACACATAATA
1 ATAATGATATTTTGAAATAATTTACACATAATA
5761814 ATAATATGATATTTTGAAATAATTTACACATAATA
1 AT-A-ATGATATTTTGAAATAATTTACACATAATA
*
5761849 ATAATGGTA-TTTGAAATAATT
1 ATAATGATATTTTGAAATAATT
5761870 GAAATATTAA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
32 20 0.26
33 21 0.27
34 5 0.06
35 31 0.40
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.39
Consensus pattern (33 bp):
ATAATGATATTTTGAAATAATTTACACATAATA
Found at i:5763227 original size:17 final size:19
Alignment explanation
Indices: 5763205--5763242 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
5763195 GTCCCAGATC
5763205 TATTTTTTT-AAAA-AAAT
1 TATTTTTTTCAAAACAAAT
5763222 TATTTTTTTCAAAACAAAT
1 TATTTTTTTCAAAACAAAT
5763241 TA
1 TA
5763243 ATTGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTTTTTCAAAACAAAT
Found at i:5764349 original size:29 final size:30
Alignment explanation
Indices: 5764297--5764374 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
5764287 GAATTGAATC
* * *
5764297 AAATCAAAATTTCGTTTATAAAATTACACA-
1 AAATCAAAATTT-ATGTACAAAATTACACAT
5764327 AAATCAAAATTTATGTACAAAATTACACATT
1 AAATCAAAATTTATGTACAAAATTACACA-T
* *
5764358 AAACCATAATTTATGTA
1 AAATCAAAATTTATGTA
5764375 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.34
30 12 0.29
31 15 0.37
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTTATGTACAAAATTACACAT
Found at i:5766070 original size:15 final size:16
Alignment explanation
Indices: 5766037--5766072 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5766027 ATGTTATTTC
5766037 AAAATTAAAACAATGA
1 AAAATTAAAACAATGA
5766053 AAAATTAAAACAAT-A
1 AAAATTAAAACAATGA
5766068 AAAAT
1 AAAAT
5766073 ATTATCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATTAAAACAATGA
Found at i:5766861 original size:8 final size:7
Alignment explanation
Indices: 5766845--5766932 Score: 56
Period size: 8 Copynumber: 12.0 Consensus size: 7
5766835 GTTAACAGCA
5766845 TAATAAT
1 TAATAAT
5766852 TAACTAAT
1 TAA-TAAT
5766860 TAA-AAT
1 TAATAAT
5766866 TAAATAATT
1 T-AATAA-T
5766875 TAATAA-
1 TAATAAT
* **
5766881 TATTTTT
1 TAATAAT
*
5766888 TAACAAT
1 TAATAAT
5766895 ATAATAAT
1 -TAATAAT
5766903 TAACTAAT
1 TAA-TAAT
5766911 TAA-AAT
1 TAATAAT
5766917 TAAATAAT
1 T-AATAAT
5766925 TAAATAAT
1 T-AATAAT
5766933 ATTTTGTTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
6 11 0.17
7 13 0.20
8 38 0.59
9 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATAAT
Found at i:5766919 original size:14 final size:14
Alignment explanation
Indices: 5766887--5766928 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5766877 ATAATATTTT
5766887 TTAAC-AATATAATAA
1 TTAACTAAT-TAA-AA
5766902 TTAACTAATTAAAA
1 TTAACTAATTAAAA
*
5766916 TTAAATAATTAAA
1 TTAACTAATTAAA
5766929 TAATATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 14 0.56
15 8 0.32
16 3 0.12
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAACTAATTAAAA
Found at i:5767085 original size:28 final size:27
Alignment explanation
Indices: 5767055--5767134 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
5767045 AAAGAACTAA
* *
5767055 AAAAAATTAGAATTGAGAATTTAGAAT
1 AAAAAATTAGAATTGAAAATTGAGAAT
5767082 AAAAAATTGAGAATT-AACAATTGAGAAT
1 AAAAAATT-AGAATTGAA-AATTGAGAAT
* *
5767110 CAAAAAGTAAGAATTGAAAATTGAG
1 -AAAAAATTAGAATTGAAAATTGAG
5767135 TTGAAAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
27 9 0.20
28 28 0.62
29 8 0.18
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (27 bp):
AAAAAATTAGAATTGAAAATTGAGAAT
Found at i:5767089 original size:14 final size:14
Alignment explanation
Indices: 5767072--5767134 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
5767062 TAGAATTGAG
*
5767072 AATTTAGAATAAAA
1 AATTGAGAATAAAA
* *
5767086 AATTGAGAATTAAC
1 AATTGAGAATAAAA
*
5767100 AATTGAGAATCAAA
1 AATTGAGAATAAAA
* * **
5767114 AAGTAAGAATTGAA
1 AATTGAGAATAAAA
5767128 AATTGAG
1 AATTGAG
5767135 TTGAAAAGAA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (14 bp):
AATTGAGAATAAAA
Found at i:5771092 original size:19 final size:19
Alignment explanation
Indices: 5771055--5771092 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5771045 AATAAATATA
*
5771055 TAATTAAAAACTAATTTTT
1 TAATTAAAAAATAATTTTT
5771074 TAATTAAAAAATAGATTTT
1 TAATTAAAAAATA-ATTTT
5771093 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TAATTAAAAAATAATTTTT
Found at i:5771098 original size:21 final size:19
Alignment explanation
Indices: 5771055--5771099 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5771045 AATAAATATA
* *
5771055 TAATTAAAAACTAATTTTT
1 TAATTAAAAAATAATTTTG
5771074 TAATTAAAAAATAGATTTTAG
1 TAATTAAAAAATA-ATTTT-G
5771095 TAATT
1 TAATT
5771100 TTTGAGTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 5 0.23
21 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (19 bp):
TAATTAAAAAATAATTTTG
Found at i:5778019 original size:21 final size:22
Alignment explanation
Indices: 5777993--5778051 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5777983 GTTTTAAGAA
*
5777993 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
5778014 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5778036 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5778052 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5778066 original size:26 final size:24
Alignment explanation
Indices: 5778022--5778071 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5778012 ATTTGTTTTA
*
5778022 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
5778046 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
5778072 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:5778649 original size:15 final size:16
Alignment explanation
Indices: 5778633--5778678 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
5778623 AAATTTTAAT
5778633 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
5778649 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
5778665 AAATAAAAAATATA
1 AAATAAAAAATATA
5778679 AATACATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:5778666 original size:27 final size:29
Alignment explanation
Indices: 5778600--5778670 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 29
5778590 TACTCTAATG
5778600 TAAATATTAAAATAACTATATAAAAATTT
1 TAAATATTAAAATAACTATATAAAAATTT
*
5778629 T-AATAAATAAAA-AA-TATAT-AAAATTAT
1 TAAAT-ATTAAAATAACTATATAAAAATT-T
5778656 TAAATATTAAAATAA
1 TAAATATTAAAATAA
5778671 AAAATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 6 0.17
27 13 0.36
28 10 0.28
29 7 0.19
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAATATTAAAATAACTATATAAAAATTT
Found at i:5781622 original size:27 final size:26
Alignment explanation
Indices: 5781592--5781653 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
5781582 AGATAATTAA
5781592 AATAAAATCCTAAAT-TTGAATAATCCT
1 AATAAAAT-CTAAATATT-AATAATCCT
* * *
5781619 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCTAAATATTAATAATCCT
5781646 AATAAAAT
1 AATAAAAT
5781654 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAAAATCTAAATATTAATAATCCT
Found at i:5783601 original size:130 final size:130
Alignment explanation
Indices: 5783430--5783681 Score: 391
Period size: 130 Copynumber: 1.9 Consensus size: 130
5783420 TATTTTAGCA
* *
5783430 TTTAAAGAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAATGAGAAATCGCAA
1 TTTAAAGAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAACGAGAAATCGCAA
* * *
5783495 CCCAGCACGATAGGGCACGATTCTCGAATTGCCAAACATCGAGTATTACCTTGGTTTTAAAGAGT
66 CCCAACACGATAGGGCACGATTCCCGAATTGCCAAACATCAAGTATTACCTT-GTTTTAAAGAGT
5783560 T
130 T
* *
5783561 TTTAAAG-ACATGAGTGAGATT-TCAAAGGAATATTCAATTATTTTGAACAAACGAGAAATTGCA
1 TTTAAAGAACATGAGTGAAATTCT-AAAGGAATATTCAATTATTTTGAACAAACGAGAAATCGCA
* *
5783624 ACCCAACATGATAGGGCACGATTCCCGAATTGCCAAACATCAAGTATTGCCTTGTTTT
65 ACCCAACACGATAGGGCACGATTCCCGAATTGCCAAACATCAAGTATTACCTTGTTTT
5783682 GGGGGAGTCC
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
129 6 0.05
130 98 0.88
131 7 0.06
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (130 bp):
TTTAAAGAACATGAGTGAAATTCTAAAGGAATATTCAATTATTTTGAACAAACGAGAAATCGCAA
CCCAACACGATAGGGCACGATTCCCGAATTGCCAAACATCAAGTATTACCTTGTTTTAAAGAGTT
Found at i:5784822 original size:2 final size:2
Alignment explanation
Indices: 5784815--5784859 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5784805 ACATACACAA
5784815 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
5784857 AT A
1 AT A
5784860 AATAGGTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5785843 original size:9 final size:9
Alignment explanation
Indices: 5785831--5785863 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
5785821 GAATTATTCG
5785831 AATCGAGTT
1 AATCGAGTT
5785840 AATCGAGTT
1 AATCGAGTT
*
5785849 AATCGAATT
1 AATCGAGTT
5785858 AATCGA
1 AATCGA
5785864 ATCAACTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (9 bp):
AATCGAGTT
Found at i:5785864 original size:9 final size:9
Alignment explanation
Indices: 5785831--5785876 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
5785821 GAATTATTCG
*
5785831 AATCGAGTT
1 AATCGAATT
*
5785840 AATCGAGTT
1 AATCGAATT
5785849 AATCGAATT
1 AATCGAATT
*
5785858 AATCGAATC
1 AATCGAATT
5785867 AACTCGAATT
1 AA-TCGAATT
5785877 TTTTTTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (9 bp):
AATCGAATT
Found at i:5786268 original size:24 final size:24
Alignment explanation
Indices: 5786239--5786286 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5786229 TTATTCAAAC
5786239 CCCTTACCCCCCATTTCAACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
*
5786263 CCCTTACCCCCCATTTCTACGAAA
1 CCCTTACCCCCCATTTCAACGAAA
5786287 GACGAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.46, G:0.04, T:0.23
Consensus pattern (24 bp):
CCCTTACCCCCCATTTCAACGAAA
Found at i:5793910 original size:36 final size:36
Alignment explanation
Indices: 5793869--5793941 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
5793859 AGACTTCCAT
*
5793869 TAGTTCATTAACAATTAACCTTTACGTCGAACATTA
1 TAGTTCATTAACAATTAAACTTTACGTCGAACATTA
5793905 TAGTTCATTAACAATTAAACTTTACGTCGAACATTA
1 TAGTTCATTAACAATTAAACTTTACGTCGAACATTA
5793941 T
1 T
5793942 GTGCAAGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (36 bp):
TAGTTCATTAACAATTAAACTTTACGTCGAACATTA
Found at i:5797227 original size:18 final size:19
Alignment explanation
Indices: 5797204--5797244 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5797194 AATACATATG
5797204 TTTTTTATAG-TTTTAGAT
1 TTTTTTATAGTTTTTAGAT
5797222 TTTTTTATAGTTTTTAGAT
1 TTTTTTATAGTTTTTAGAT
5797241 TTTT
1 TTTT
5797245 ATATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTTTTATAGTTTTTAGAT
Found at i:5799929 original size:26 final size:26
Alignment explanation
Indices: 5799900--5799993 Score: 82
Period size: 26 Copynumber: 3.4 Consensus size: 26
5799890 CAAAATTTGT
5799900 ATAAATTTATACATAATTTTAATGAA
1 ATAAATTTATACATAATTTTAATGAA
* ** *
5799926 ATAAAATTATAAACTAAATAAAATT-ATGAGG
1 AT-AAATT-T--A-TACATAATTTTAATGA-A
5799957 ATAAATTTATACATAATTTTAATGAA
1 ATAAATTTATACATAATTTTAATGAA
*
5799983 ATAAAATTATA
1 ATAAATTTATA
5799994 AATTGAATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
26 20 0.38
27 10 0.19
28 1 0.02
29 1 0.02
30 10 0.19
31 10 0.19
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (26 bp):
ATAAATTTATACATAATTTTAATGAA
Found at i:5799976 original size:57 final size:57
Alignment explanation
Indices: 5799900--5800014 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
5799890 CAAAATTTGT
5799900 ATAAATTTATACATAATTTTAATGAAATAAAATTATAAACTAAATAAAATTATGAGG
1 ATAAATTTATACATAATTTTAATGAAATAAAATTATAAACTAAATAAAATTATGAGG
* *
5799957 ATAAATTTATACATAATTTTAATGAAATAAAATTATAAATTGAATAAAATTATGAGG
1 ATAAATTTATACATAATTTTAATGAAATAAAATTATAAACTAAATAAAATTATGAGG
5800014 A
1 A
5800015 ATTTTAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (57 bp):
ATAAATTTATACATAATTTTAATGAAATAAAATTATAAACTAAATAAAATTATGAGG
Found at i:5804406 original size:159 final size:158
Alignment explanation
Indices: 5804107--5804394 Score: 409
Period size: 159 Copynumber: 1.8 Consensus size: 158
5804097 TATGCACGAA
* * * *
5804107 AGTTTTAGTTAATTAAATGTCATACTTTATTTTGTTGAGTAAATTTATACGTAGAATTTGTAAAT
1 AGTTTTAATTAATTAAATGTAATACTTTATTTTGTTGAATAAATTTATACATAGAATTTGTAAAT
* * * * *
5804172 CCAGTATTGATTTTTCTATCTATAAGAAAAATATTAATTTGACTGAAGTTAAAGTCTTGCCTCTA
66 CAAGTATTAATTTTTCTATCTATAAG-AAAACATCAATTTGACTAAAGTTAAAGTCTTGCCTCTA
5804237 CCTCATCTTTTTTTTTTTTCTAGAGTGCT
130 CCTCATCTTTTTTTTTTTTCTAGAGTGCT
* * * *
5804266 AGTTTTAATTAATTGAATGTAATGCTTTTATTTTGTTGAATAATTTTATATATAGAATTTGTAAA
1 AGTTTTAATTAATTAAATGTAATAC-TTTATTTTGTTGAATAAATTTATACATAGAATTTGTAAA
* *
5804331 -CAAGTATTAATTTTTCTATCTATAAG-AAACATCAATTTGACTAAATTTAATGTCTTGCCTCTA
65 TCAAGTATTAATTTTTCTATCTATAAGAAAACATCAATTTGACTAAAGTTAAAGTCTTGCCTCTA
5804394 C
130 C
5804395 TTTCTCTCTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
157 33 0.29
159 45 0.40
160 35 0.31
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (158 bp):
AGTTTTAATTAATTAAATGTAATACTTTATTTTGTTGAATAAATTTATACATAGAATTTGTAAAT
CAAGTATTAATTTTTCTATCTATAAGAAAACATCAATTTGACTAAAGTTAAAGTCTTGCCTCTAC
CTCATCTTTTTTTTTTTTCTAGAGTGCT
Found at i:5807325 original size:22 final size:22
Alignment explanation
Indices: 5807299--5807341 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5807289 TGCCAATATA
5807299 CATAGTCGAAGCCATCTCGATG
1 CATAGTCGAAGCCATCTCGATG
*
5807321 CATAGTCGAAGCTATCTCGAT
1 CATAGTCGAAGCCATCTCGAT
5807342 AACTATCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (22 bp):
CATAGTCGAAGCCATCTCGATG
Found at i:5811428 original size:27 final size:27
Alignment explanation
Indices: 5811396--5811448 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5811386 GTGAAATTGT
* *
5811396 AGCAAAATAGTGAAAAAAAAAGAAAAC
1 AGCAAAAAAATGAAAAAAAAAGAAAAC
**
5811423 AGCAAAAAAATTTAAAAAAAAGAAAA
1 AGCAAAAAAATGAAAAAAAAAGAAAA
5811449 AAAAGCAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (27 bp):
AGCAAAAAAATGAAAAAAAAAGAAAAC
Found at i:5812281 original size:16 final size:15
Alignment explanation
Indices: 5812246--5812286 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
5812236 TATTATTCAA
*
5812246 AATAATAACT-AATT
1 AATAATAATTAAATT
5812260 AA-AATAATTAAATTT
1 AATAATAATTAAA-TT
5812275 AATAATAATTAA
1 AATAATAATTAA
5812287 GATGCTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 4 0.17
15 4 0.17
16 9 0.39
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATAATTAAATT
Found at i:5812527 original size:2 final size:2
Alignment explanation
Indices: 5812522--5812547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5812512 TTCTAAACTC
5812522 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
5812548 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5815465 original size:27 final size:24
Alignment explanation
Indices: 5815435--5815492 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
5815425 ATATTGTCTC
5815435 AAAATTTACAAATAGTTATAATAAAAT
1 AAAATTTA-AAATA--TATAATAAAAT
*
5815462 AAAATTTTAAAATATATATTAAAAT
1 AAAA-TTTAAAATATATAATAAAAT
*
5815487 TAAATT
1 AAAATT
5815493 GGAAGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 13 0.46
27 9 0.32
28 4 0.14
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAATTTAAAATATATAATAAAAT
Found at i:5819657 original size:31 final size:30
Alignment explanation
Indices: 5819618--5819677 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
5819608 ATAAAACTTC
* *
5819618 AAATATATATAAATTGAAATTGAAAATAAA
1 AAATATATATAAATTGAAAATAAAAATAAA
5819648 AAATAATATATAAATTGAAAATAAAAATAA
1 AAAT-ATATATAAATTGAAAATAAAAATAA
5819678 CAGTATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (30 bp):
AAATATATATAAATTGAAAATAAAAATAAA
Found at i:5819943 original size:8 final size:8
Alignment explanation
Indices: 5819926--5819998 Score: 55
Period size: 8 Copynumber: 9.4 Consensus size: 8
5819916 ATATTGACTA
*
5819926 TTTATTTT
1 TTTATATT
5819934 TTTATATT
1 TTTATATT
*
5819942 TTT-TAAAT
1 TTTAT-ATT
*
5819950 TTTATTTT
1 TTTATATT
5819958 TTATATATT
1 TT-TATATT
*
5819967 TTTAGATT
1 TTTATATT
*
5819975 TTAAT-TT
1 TTTATATT
5819982 TTTA-ATT
1 TTTATATT
5819989 TTT-TATT
1 TTTATATT
5819996 TTT
1 TTT
5819999 TAAGTTAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
7 17 0.33
8 26 0.51
9 8 0.16
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (8 bp):
TTTATATT
Found at i:5819953 original size:24 final size:23
Alignment explanation
Indices: 5819926--5819993 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 23
5819916 ATATTGACTA
5819926 TTTATTTTTTTATATTTTTTAAAT
1 TTTA-TTTTTTATATTTTTTAAAT
*
5819950 TTTATTTTTTATATATTTTTAGAT
1 TTTATTTTTTATAT-TTTTTAAAT
5819974 TTTAATTTTTTA-ATTTTTTA
1 TTT-ATTTTTTATATTTTTTA
5819994 TTTTTTAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 16 0.39
24 17 0.41
25 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTATTTTTTATATTTTTTAAAT
Found at i:5819985 original size:15 final size:15
Alignment explanation
Indices: 5819926--5820001 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
5819916 ATATTGACTA
*
5819926 TTTATTTTTTTATATTT
1 TTTAATTTTTTA-A-TT
* *
5819943 TTTAA-ATTTTATTT
1 TTTAATTTTTTAATT
5819957 TTTATATATTTTTAGA-T
1 TTTA-AT-TTTTTA-ATT
5819974 TTTAATTTTTTAATT
1 TTTAATTTTTTAATT
*
5819989 TTTTATTTTTTAA
1 TTTAATTTTTTAA
5820002 GTTAAATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
14 7 0.15
15 20 0.42
16 7 0.15
17 14 0.29
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTAATTTTTTAATT
Found at i:5820001 original size:23 final size:24
Alignment explanation
Indices: 5819926--5819993 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
5819916 ATATTGACTA
*
5819926 TTTATTTTTTTATATTTTTTAAAT
1 TTTAATTTTTTATATTTTTTAAAT
*
5819950 TTT-ATTTTTTATATATTTTTAGAT
1 TTTAATTTTTTATAT-TTTTTAAAT
5819974 TTTAATTTTTTA-ATTTTTTA
1 TTTAATTTTTTATATTTTTTA
5819994 TTTTTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 16 0.40
24 16 0.40
25 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTAATTTTTTATATTTTTTAAAT
Found at i:5820130 original size:19 final size:20
Alignment explanation
Indices: 5820095--5820158 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
5820085 GGAGTTTTAT
5820095 AATTTATAATATC-TTTTAAA
1 AATTT-TAATATCTTTTTAAA
*
5820115 AATTTTAA-ATCTTTTTTCAA
1 AATTTTAATATC-TTTTTAAA
*
5820135 AATTTTAAGATATTTTTTTAAA
1 AATTTT-A-ATATCTTTTTAAA
5820157 AA
1 AA
5820159 AATTGTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 17 0.47
21 1 0.03
22 10 0.28
23 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (20 bp):
AATTTTAATATCTTTTTAAA
Found at i:5820131 original size:20 final size:22
Alignment explanation
Indices: 5820108--5820158 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5820098 TTATAATATC
5820108 TTTTAAAAATTTTAA-AT-CTT
1 TTTTAAAAATTTTAAGATACTT
* *
5820128 TTTTCAAAATTTTAAGATATTT
1 TTTTAAAAATTTTAAGATACTT
5820150 TTTTAAAAA
1 TTTTAAAAA
5820159 AATTGTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 10 0.38
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTTAAGATACTT
Done.