Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 110 of 125
Found at i:33511605 original size:17 final size:17
Alignment explanation
Indices: 33511583--33511616 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
33511573 CATCCTCCAT
33511583 TTTCATTCTCAT-TTCAA
1 TTTCATT-TCATATTCAA
33511600 TTTCATTTCATATTCAA
1 TTTCATTTCATATTCAA
33511617 ATTATTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTCATTTCATATTCAA
Found at i:33518522 original size:79 final size:80
Alignment explanation
Indices: 33518391--33518550 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 80
33518381 AGTCCGGATC
33518391 TCATCAGATAAGGATGCTATCACTTCATGTTCTTGGAATGAAACACCTGGCAAATGC-TTTCCTT
1 TCATCAGATAAGGATGCTATCACTTCATGTTCTTGGAATGAAACACCTGGCAAATGCTTTTCCTT
33518455 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
*
33518470 TCATCAGATAAGGATGCTATCACTTCATGTTCTTGGAGTGAAACACCTGGCAAATGCTTTTCCTT
1 TCATCAGATAAGGATGCTATCACTTCATGTTCTTGGAATGAAACACCTGGCAAATGCTTTTCCTT
33518535 GTTGATAAGCATTAG
66 GTTGATAAGCATTAG
33518550 T
1 T
33518551 TTTTCCGGAT
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 56 0.71
80 23 0.29
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (80 bp):
TCATCAGATAAGGATGCTATCACTTCATGTTCTTGGAATGAAACACCTGGCAAATGCTTTTCCTT
GTTGATAAGCATTAG
Found at i:33533612 original size:19 final size:18
Alignment explanation
Indices: 33533568--33533614 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
33533558 AAGAGCACTG
*
33533568 ACGTGCTAATAATTAAAA
1 ACGTGCTAATAATCAAAA
*
33533586 AGCATGCTAATAATCAGAAA
1 A-CGTGCTAATAATCA-AAA
33533606 ACGTGCTAA
1 ACGTGCTAA
33533615 AGTTCCTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 19 0.79
20 4 0.17
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (18 bp):
ACGTGCTAATAATCAAAA
Found at i:33539553 original size:4 final size:4
Alignment explanation
Indices: 33539544--33539569 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33539534 TACCTAATAA
33539544 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
33539570 ATAGGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:33540976 original size:119 final size:117
Alignment explanation
Indices: 33540765--33541042 Score: 391
Period size: 119 Copynumber: 2.4 Consensus size: 117
33540755 ATTAGGATTT
*
33540765 TTTTCTAGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACCCCCCCTTTTC
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACCCCCCCTTTTC
* *
33540830 TCGAGAAAAAATTCATTTTTTTGGGTGTTGGGCATCAAATGGCCGACACCCCC
66 TCGAGAAAAAATTCAATTTTTTGGGTGTTGGCCATCAAATGGCCGACA-CCCC
* * * * *
33540883 TTTTCTC-A-AAAAAAAATTCAATTTTTTTTGTGTTGGCCATCAAATGGTCGACACCCTCCTTTT
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGAC-CCC-CC-CTT
***
33540946 TTCTCGAGAAAAAATTCAAATTTTTT-GGTGTTGGCCATTGCATGGCCGACACCCC
63 TTCTCGAGAAAAAATTC-AATTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCC
33541001 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
33541043 TGCATGACAG
Statistics
Matches: 140, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
116 40 0.29
117 4 0.03
118 19 0.14
119 41 0.29
120 36 0.26
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (117 bp):
TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACCCCCCCTTTTC
TCGAGAAAAAATTCAATTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCC
Found at i:33541048 original size:59 final size:60
Alignment explanation
Indices: 33540765--33541042 Score: 338
Period size: 58 Copynumber: 4.7 Consensus size: 60
33540755 ATTAGGATTT
* ** *
33540765 TTTTCTAGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGATCGACCCCCCC
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
* *
33540825 TTTTCTCGAG-AAAAAA-TT-CATTTTTTTGGGTGTTGGGCATCAAATGGCCGACACCCCC
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTT-GGTGTTGGCCATCAAATGGCCGACACCCCC
* * * *
33540883 TTTTCTC-A-AAAAAAAATTCAATTTTTTTTGTGTTGGCCATCAAATGGTCGACACCCTCC
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCC-CC
* ***
33540942 TTTTTTCTCGAG-AAAAAATTCAAA-TTTTTTGGTGTTGGCCATTGCATGGCCGACA-CCCC
1 --TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
33541001 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
1 TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
33541043 TGCATGACAG
Statistics
Matches: 188, Mismatches: 19, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
57 25 0.13
58 73 0.39
59 36 0.19
60 11 0.06
61 33 0.18
62 10 0.05
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (60 bp):
TTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCC
Found at i:33541906 original size:30 final size:30
Alignment explanation
Indices: 33541871--33541935 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
33541861 CAACTTAACA
*
33541871 AACAAATGTCTCCAAAATAATAACAAAATT
1 AACAAATGCCTCCAAAATAATAACAAAATT
*
33541901 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCCAAAATAATAACAAAATT
33541931 AACAA
1 AACAA
33541936 TAAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.17, G:0.03, T:0.22
Consensus pattern (30 bp):
AACAAATGCCTCCAAAATAATAACAAAATT
Found at i:33552729 original size:20 final size:19
Alignment explanation
Indices: 33552689--33552729 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
33552679 TCTCAAATTT
* *
33552689 ATTTTATTTTATTATTCTA
1 ATTTTATTTTATTACTATA
33552708 ATTTTAATTTTATTACTATA
1 ATTTT-ATTTTATTACTATA
33552728 AT
1 AT
33552730 ATTTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATTTTATTACTATA
Found at i:33552747 original size:18 final size:18
Alignment explanation
Indices: 33552698--33552748 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
33552688 TATTTTATTT
33552698 TATTATTCTAAT-TTTAA
1 TATTATTCTAATATTTAA
* *
33552715 TTTTATTACTATAATATTTTA
1 TATTATT-C--TAATATTTAA
33552736 TATTATTCTAATA
1 TATTATTCTAATA
33552749 AACTTAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
20 5 0.19
21 10 0.37
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATTCTAATATTTAA
Found at i:33565725 original size:30 final size:30
Alignment explanation
Indices: 33565683--33565744 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
33565673 TCAATAACCG
* *
33565683 ACTGAATTAACCGATTAAATCAAAATCAAA
1 ACTGAATTAACCGATTAAACCAAAACCAAA
33565713 ACTG-ATTAAACCGATTAAACCAAAACCAAA
1 ACTGAATT-AACCGATTAAACCAAAACCAAA
33565743 AC
1 AC
33565745 ACCCTAACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.19
Consensus pattern (30 bp):
ACTGAATTAACCGATTAAACCAAAACCAAA
Found at i:33583961 original size:13 final size:13
Alignment explanation
Indices: 33583945--33583969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33583935 TATTAAATTA
33583945 ATAAATTAATAAC
1 ATAAATTAATAAC
33583958 ATAAATTAATAA
1 ATAAATTAATAA
33583970 ATTTCAAAAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAATTAATAAC
Found at i:33598262 original size:31 final size:31
Alignment explanation
Indices: 33598227--33598289 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
33598217 GTTGCCTGAA
33598227 ATATGGAGAGTAGATGGGATGATTTTAATAG
1 ATATGGAGAGTAGATGGGATGATTTTAATAG
33598258 ATATGGAGAGTAGATGGGATGATTTTAATAG
1 ATATGGAGAGTAGATGGGATGATTTTAATAG
33598289 A
1 A
33598290 CTCGTTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (31 bp):
ATATGGAGAGTAGATGGGATGATTTTAATAG
Found at i:33604709 original size:48 final size:48
Alignment explanation
Indices: 33604638--33604734 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
33604628 CTGTAACCTA
*
33604638 ATTTATGCTAAAAGATATTATAAGTACTCTATTTCGAGAGAAGTTAGG
1 ATTTATGCTAAAAGATATTATAAGTACTCTATTTCAAGAGAAGTTAGG
33604686 ATTTATGCTAAAAGATATTATAAGTACTCTATTTCAAGAGAAGTTAGG
1 ATTTATGCTAAAAGATATTATAAGTACTCTATTTCAAGAGAAGTTAGG
33604734 A
1 A
33604735 CTTTTAATCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (48 bp):
ATTTATGCTAAAAGATATTATAAGTACTCTATTTCAAGAGAAGTTAGG
Found at i:33615395 original size:15 final size:15
Alignment explanation
Indices: 33615377--33615409 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
33615367 GTCACCTTTG
*
33615377 GTTGAGTTTCCCATT
1 GTTGAGTCTCCCATT
33615392 GTTGAGTCTCCCATT
1 GTTGAGTCTCCCATT
33615407 GTT
1 GTT
33615410 CAAAGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (15 bp):
GTTGAGTCTCCCATT
Found at i:33617733 original size:18 final size:18
Alignment explanation
Indices: 33617707--33617751 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
33617697 TGCAAGTAAA
*
33617707 AATAAATAACTACAAAAT
1 AATAAATAAATACAAAAT
* *
33617725 AATACATAAATGCAAAAT
1 AATAAATAAATACAAAAT
*
33617743 AATATATAA
1 AATAAATAA
33617752 TTTCTCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAATAAATACAAAAT
Found at i:33619381 original size:6 final size:7
Alignment explanation
Indices: 33619356--33619380 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33619346 GAGAAGATTG
33619356 AAAAATA
1 AAAAATA
33619363 AAAAATA
1 AAAAATA
33619370 AAAAATA
1 AAAAATA
33619377 AAAA
1 AAAA
33619381 TGATTTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:33620458 original size:11 final size:12
Alignment explanation
Indices: 33620421--33620459 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
33620411 TCACTGTTTA
33620421 TTTTAAGTTATT
1 TTTTAAGTTATT
*
33620433 TTTTTA-TTAATT
1 TTTTAAGTT-ATT
33620445 TTTTAAGTTATT
1 TTTTAAGTTATT
33620457 TTT
1 TTT
33620460 GTCATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTAAGTTATT
Found at i:33620469 original size:24 final size:24
Alignment explanation
Indices: 33620421--33620471 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
33620411 TCACTGTTTA
*
33620421 TTTTAAGTTATTTTTTTATTAATT
1 TTTTAAGTTATTTTTTCATTAATT
33620445 TTTTAAGTTATTTTTGTCATT-ATT
1 TTTTAAGTTATTTTT-TCATTAATT
33620469 TTT
1 TTT
33620472 GAGGTTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTTAAGTTATTTTTTCATTAATT
Found at i:33625739 original size:30 final size:30
Alignment explanation
Indices: 33625672--33625739 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
33625662 TTTAAAGTAC
*
33625672 CCCAAAAAAATTTTACCAACTTTTAAGGGG
1 CCCAAAAAAATTTTACCAACTTTTAAGGGA
* * ** * *
33625702 TCTAAAAATTTTTTTCCGACTTTTAAGGGA
1 CCCAAAAAAATTTTACCAACTTTTAAGGGA
33625732 CCCAAAAA
1 CCCAAAAA
33625740 CTTAATTTAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (30 bp):
CCCAAAAAAATTTTACCAACTTTTAAGGGA
Found at i:33632568 original size:24 final size:24
Alignment explanation
Indices: 33632521--33632566 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
33632511 AGAATTAATC
*
33632521 TGTCAACGCAAATATAAAATAAAT
1 TGTCAAAGCAAATATAAAATAAAT
*
33632545 TGTCAAAGTAAAT-TAAAATAAA
1 TGTCAAAGCAAATATAAAATAAA
33632567 ATGAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (24 bp):
TGTCAAAGCAAATATAAAATAAAT
Found at i:33642732 original size:6 final size:6
Alignment explanation
Indices: 33642721--33642755 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
33642711 AAAACTCAGA
*
33642721 TATATG TATATG TATATG TATATG TACATG TATAT
1 TATATG TATATG TATATG TATATG TATATG TATAT
33642756 ATGATCCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:33644917 original size:2 final size:2
Alignment explanation
Indices: 33644910--33644934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33644900 GTTGAATAAT
33644910 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 T
33644935 TAATGATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33653726 original size:15 final size:14
Alignment explanation
Indices: 33653706--33653735 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
33653696 ATTACTTGCC
33653706 TTCTTTTTTTTCTTT
1 TTCTTTTTTTT-TTT
33653721 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
33653735 T
1 T
33653736 GTAGTTACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:33658827 original size:2 final size:2
Alignment explanation
Indices: 33658820--33658850 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33658810 AAGAGGTGGG
33658820 GA GA 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 GA GA G
33658851 CACCTTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33665352 original size:2 final size:2
Alignment explanation
Indices: 33665303--33665336 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
33665293 ATAAAAACAC
* *
33665303 AG AG AG AG AG AG AG AG AG AG AG AG TG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33665337 GATGGATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:33671151 original size:29 final size:30
Alignment explanation
Indices: 33671088--33671151 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
33671078 TGATTAGATT
*
33671088 AAAATTTTTAAATTATAAAAATATGAAGAC
1 AAAATTTTTAAATTATAAAAATATGAAAAC
* * *
33671118 TAAATTTTTAACTT-TTAAAATAT-AATAAC
1 AAAATTTTTAAATTATAAAAATATGAA-AAC
33671147 AAAAT
1 AAAAT
33671152 CTCATGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.07
29 14 0.50
30 12 0.43
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTTTTAAATTATAAAAATATGAAAAC
Found at i:33674384 original size:15 final size:15
Alignment explanation
Indices: 33674337--33674384 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
33674327 TTAAAAATAC
33674337 AAATTTCAAATGAAT
1 AAATTTCAAATGAAT
**
33674352 AAAAAT-AAATGAATT
1 AAATTTCAAATGAA-T
*
33674367 AAATTTCAAATGTAT
1 AAATTTCAAATGAAT
33674382 AAA
1 AAA
33674385 ATATACATCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 7 0.27
15 13 0.50
16 6 0.23
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (15 bp):
AAATTTCAAATGAAT
Found at i:33674386 original size:16 final size:16
Alignment explanation
Indices: 33674332--33674386 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
33674322 CACATTTAAA
33674332 AATACAAATTTCAAATG
1 AATA-AAATTTCAAATG
*
33674349 AATAAAA-AT-AAATG
1 AATAAAATTTCAAATG
*
33674363 AATTAAATTTCAAATG
1 AATAAAATTTCAAATG
*
33674379 TATAAAAT
1 AATAAAAT
33674387 ATACATCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.35
15 2 0.06
16 14 0.45
17 4 0.13
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (16 bp):
AATAAAATTTCAAATG
Found at i:33677199 original size:21 final size:21
Alignment explanation
Indices: 33677150--33677199 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
33677140 AAGCTCATGG
* *
33677150 TTGTAGTGCCTGGAGAAAAGC
1 TTGTAGTTCCTGGACAAAAGC
*
33677171 TTGTAGTTCCTGGACTAAAGC
1 TTGTAGTTCCTGGACAAAAGC
33677192 TTGTAGTT
1 TTGTAGTT
33677200 GTGCTGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (21 bp):
TTGTAGTTCCTGGACAAAAGC
Found at i:33689178 original size:3 final size:3
Alignment explanation
Indices: 33689170--33689194 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33689160 AATGGTTGTA
33689170 GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG G
33689195 TGTCGGTGGT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:33696419 original size:16 final size:16
Alignment explanation
Indices: 33696398--33696429 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33696388 AGTTACTAAT
33696398 GATTGATTTTATATAG
1 GATTGATTTTATATAG
33696414 GATTGATTTTATATAG
1 GATTGATTTTATATAG
33696430 AATAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (16 bp):
GATTGATTTTATATAG
Found at i:33696779 original size:30 final size:30
Alignment explanation
Indices: 33696743--33696811 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
33696733 GCCTTCTTTC
* * *
33696743 GCTCAAAACTTTCATGAAGATTTCTTGGTT
1 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
33696773 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
1 GCTCAAAACTTGCAAGAAGATTTCTTGGAT
33696803 GCTCAAAAC
1 GCTCAAAAC
33696812 AATGCTCGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (30 bp):
GCTCAAAACTTGCAAGAAGATTTCTTGGAT
Found at i:33701212 original size:4 final size:4
Alignment explanation
Indices: 33701203--33701233 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
33701193 TAGCCGTTGA
33701203 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
33701234 ACGAGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:33703175 original size:19 final size:19
Alignment explanation
Indices: 33703151--33703191 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
33703141 GATATTTTAT
33703151 AATATATAAAAATTT-TAAA
1 AATATA-AAAAATTTGTAAA
*
33703170 AATATAAAATATTTGTAAA
1 AATATAAAAAATTTGTAAA
33703189 AAT
1 AAT
33703192 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATATAAAAAATTTGTAAA
Found at i:33703176 original size:17 final size:18
Alignment explanation
Indices: 33703142--33703191 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
33703132 ATATATCTGG
*
33703142 ATATTTTATAATATATAAA
1 ATATTTTA-AAAATATAAA
33703161 A-ATTTTAAAAATATAAA
1 ATATTTTAAAAATATAAA
33703178 ATATTTGTAAAAAT
1 ATATTT-TAAAAAT
33703192 TTTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.36
18 10 0.36
19 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATTTTAAAAATATAAA
Found at i:33705649 original size:23 final size:23
Alignment explanation
Indices: 33705605--33705650 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33705595 AAAAAAAATT
**
33705605 TAACTCAATTCGTTTAACTCGAA
1 TAACTCAATTCGAATAACTCGAA
* *
33705628 TAACTCTATTCGAATAATTCGAA
1 TAACTCAATTCGAATAACTCGAA
33705651 ATTCGAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (23 bp):
TAACTCAATTCGAATAACTCGAA
Found at i:33706057 original size:36 final size:36
Alignment explanation
Indices: 33705969--33706060 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 36
33705959 TAATGGCTTG
* * * *
33705969 TTACAACTAATGAAAAAATAAAAGCAGATAAAATAT
1 TTACAACTAATGAAAAGACAAAAACAAATAAAATAT
** *
33706005 TT--AGTTAATGAAAAGACAAAAATAAATAAAATAT
1 TTACAACTAATGAAAAGACAAAAACAAATAAAATAT
33706039 TTACAACTAATGAAAAGACAAA
1 TTACAACTAATGAAAAGACAAA
33706061 CCAAGTAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
34 27 0.60
36 18 0.40
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.23
Consensus pattern (36 bp):
TTACAACTAATGAAAAGACAAAAACAAATAAAATAT
Found at i:33706531 original size:28 final size:28
Alignment explanation
Indices: 33706494--33706553 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
33706484 TCTTATTGTA
33706494 TTTTCAATTTGTTTGTTGTTTTAGA-ATT
1 TTTTCAATTTGTTTGTTGTTTTA-ATATT
*
33706522 TTTTTAATTTGTTTGTTGTTTTAATATT
1 TTTTCAATTTGTTTGTTGTTTTAATATT
33706550 TTTT
1 TTTT
33706554 AAGTGTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.17, C:0.02, G:0.12, T:0.70
Consensus pattern (28 bp):
TTTTCAATTTGTTTGTTGTTTTAATATT
Found at i:33706564 original size:28 final size:28
Alignment explanation
Indices: 33706505--33706564 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
33706495 TTTCAATTTG
* *
33706505 TTTGTTGTTTTAGAATTTTTTTAATTTG
1 TTTGTTGTTTTAGAATTTTTTTAATGTA
33706533 TTTGTTGTTTT--AATATTTTTTAAGTGTA
1 TTTGTTGTTTTAGAAT-TTTTTTAA-TGTA
33706561 TTTG
1 TTTG
33706565 ATATATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 8 0.29
28 17 0.61
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (28 bp):
TTTGTTGTTTTAGAATTTTTTTAATGTA
Found at i:33714380 original size:25 final size:24
Alignment explanation
Indices: 33714324--33714370 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
33714314 GAGTTAATAA
33714324 AATTCTTTTTGAGTTTTCCTTTTAAG
1 AATT-TTTTTGAGTTTT-CTTTTAAG
33714350 AATTTTTTTGAGTTTT-TTTTA
1 AATTTTTTTGAGTTTTCTTTTA
33714371 GAAGAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (24 bp):
AATTTTTTTGAGTTTTCTTTTAAG
Found at i:33720202 original size:12 final size:13
Alignment explanation
Indices: 33720179--33720205 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33720169 TCATCTAGCA
33720179 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
33720192 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
33720205 T
1 T
33720206 CAATATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCCTTTTTTTT
Found at i:33737648 original size:23 final size:23
Alignment explanation
Indices: 33737605--33737658 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
33737595 AAAAGTAAAT
* *
33737605 TATAATTTTTACGATAATAAAAA
1 TATAATTTTTACAAAAATAAAAA
* *
33737628 TATAATTTTTA-AAAAATTAAAT
1 TATAATTTTTACAAAAATAAAAA
*
33737650 TAAAATTTT
1 TATAATTTT
33737659 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATAATTTTTACAAAAATAAAAA
Found at i:33737666 original size:30 final size:31
Alignment explanation
Indices: 33737632--33737692 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
33737622 TAAAAATATA
33737632 ATTTTTAAAAAA-TTAAATTAAAATTTTATT
1 ATTTTTAAAAAAGTTAAATTAAAATTTTATT
*
33737662 ATTTTTAAAAAAGTTAAATTATAATTTTATT
1 ATTTTTAAAAAAGTTAAATTAAAATTTTATT
33737693 TTTACAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
ATTTTTAAAAAAGTTAAATTAAAATTTTATT
Found at i:33737721 original size:18 final size:18
Alignment explanation
Indices: 33737698--33737732 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33737688 TTATTTTTAC
*
33737698 AATTTTAAAATTTTAAAA
1 AATTTTAAAAATTTAAAA
33737716 AATTTTAAAAATTTAAA
1 AATTTTAAAAATTTAAA
33737733 TGAAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTTTAAAAATTTAAAA
Found at i:33748049 original size:6 final size:6
Alignment explanation
Indices: 33748038--33748067 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33748028 CATCCGTCCT
33748038 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
33748068 TCTCCCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCTC
Found at i:33749507 original size:98 final size:98
Alignment explanation
Indices: 33749335--33749535 Score: 348
Period size: 98 Copynumber: 2.1 Consensus size: 98
33749325 TAAACTAACT
* * *
33749335 AAATATATTACAAATATAATATATTTGTTGAGGAAGAAATTATAAACAAAGGAGATACTGATTCA
1 AAATATAATACAAATATAATATATTTGTTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCA
*
33749400 CATGGTGGTGATGTGTTACGAGAGAAATTGAAC
66 CATGATGGTGATGTGTTACGAGAGAAATTGAAC
*
33749433 AAATATAATACAAATATAATATATTTGTTGAGGAAGAAATGATAAACAAAAGAGATAGTGATTCA
1 AAATATAATACAAATATAATATATTTGTTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCA
*
33749498 CATGATGGTGATGTGTTACGAGAGAAATTGAGC
66 CATGATGGTGATGTGTTACGAGAGAAATTGAAC
33749531 AAATA
1 AAATA
33749536 CTAGCATAAG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (98 bp):
AAATATAATACAAATATAATATATTTGTTGAGGAAGAAATGATAAACAAAAGAGATACTGATTCA
CATGATGGTGATGTGTTACGAGAGAAATTGAAC
Found at i:33753715 original size:18 final size:18
Alignment explanation
Indices: 33753692--33753741 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
33753682 AAAATGCAGG
33753692 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
*
33753710 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACACTTC
33753728 AAATGATGTTAACA
1 AAATGATGTTAACA
33753742 TTGATGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:33754260 original size:72 final size:72
Alignment explanation
Indices: 33754175--33754565 Score: 578
Period size: 72 Copynumber: 5.5 Consensus size: 72
33754165 GTTAAACTAG
* *
33754175 TTTTATCATTAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754240 AATTTAT
66 AATTTAA
* * *
33754247 TTTTATCAATAGTTGTTTATGTTTGGTTCTT-GA-A-T--ATTTATATTCTACTTATTTATGTGC
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754307 AATCTAA
66 AATTTAA
* *
33754314 TTTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTTTGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754379 AATTTAG
66 AATTTAA
* * * *
33754386 TTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATATTCTACTTATTTATGTGC
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754451 AATCTAA
66 AATTTAA
33754458 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754523 ATTTTAA
66 AATTTAA
* *
33754530 TTTTATCAATAGTTGTTTATATTT-GATTTTGGATAT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATAT
33754566 AAAATTTGTT
Statistics
Matches: 284, Mismatches: 30, Indels: 11
0.87 0.09 0.03
Matches are distributed among these distances:
67 57 0.20
68 2 0.01
69 2 0.01
70 2 0.01
71 13 0.05
72 208 0.73
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.57
Consensus pattern (72 bp):
TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
AATTTAA
Found at i:33754508 original size:144 final size:139
Alignment explanation
Indices: 33754175--33754554 Score: 643
Period size: 144 Copynumber: 2.7 Consensus size: 139
33754165 GTTAAACTAG
* *
33754175 TTTTATCATTAGTTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754240 AATTTATTTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTTATATTCTACTTATTTATGT
66 AATTTAATTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTTATATTCTACTTATTTATGT
33754305 GCAATCTAA
131 GCAATCTAA
* *
33754314 TTTTATCAATAATTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTTTGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
*
33754379 AATTTAGTTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTGAATTTATATTCTACTTATT
66 AATTTAATTTTATCAATAGTTGTTTATGTTTGGTTCTTG-A-A-T--ATTTATATTCTACTTATT
33754444 TATGTGCAATCTAA
126 TATGTGCAATCTAA
33754458 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
1 TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
* *
33754523 ATTTTAATTTTATCAATAGTTGTTTATATTTG
66 AATTTAATTTTATCAATAGTTGTTTATGTTTG
33754555 ATTTTGGATA
Statistics
Matches: 226, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
139 99 0.44
140 1 0.00
141 1 0.00
142 1 0.00
144 124 0.55
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.57
Consensus pattern (139 bp):
TTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTATGTGT
AATTTAATTTTATCAATAGTTGTTTATGTTTGGTTCTTGAATATTTATATTCTACTTATTTATGT
GCAATCTAA
Found at i:33762595 original size:28 final size:28
Alignment explanation
Indices: 33762563--33762622 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
33762553 CTAAAAAAAA
33762563 AATTGGTAGGATTAATAAATACTCAAAT
1 AATTGGTAGGATTAATAAATACTCAAAT
33762591 AATTGGTAGGATTAATAAATACTCAAAT
1 AATTGGTAGGATTAATAAATACTCAAAT
33762619 AATT
1 AATT
33762623 TTATGTGGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (28 bp):
AATTGGTAGGATTAATAAATACTCAAAT
Found at i:33763169 original size:18 final size:16
Alignment explanation
Indices: 33763132--33763180 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
33763122 TTCAAATGGG
33763132 ATTAGAATAAATTTTTA
1 ATTA-AATAAATTTTTA
33763149 ATTAAATAAA--TTTA
1 ATTAAATAAATTTTTA
*
33763163 ATTAATTAAAATTTTTA
1 ATTAAAT-AAATTTTTA
33763180 A
1 A
33763181 ACCTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 6 0.21
17 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTAAATAAATTTTTA
Found at i:33796334 original size:42 final size:42
Alignment explanation
Indices: 33796284--33796365 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
33796274 ATAAGTATAA
33796284 TACATCACAGACAGATAATGTTGGGGAGGAATTGATAAATAT
1 TACATCACAGACAGATAATGTTGGGGAGGAATTGATAAATAT
33796326 TACATCACAGACAGATAATGTTGGGGAGGAATTGATAAAT
1 TACATCACAGACAGATAATGTTGGGGAGGAATTGATAAAT
33796366 CCACGTGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (42 bp):
TACATCACAGACAGATAATGTTGGGGAGGAATTGATAAATAT
Found at i:33797822 original size:14 final size:15
Alignment explanation
Indices: 33797803--33797831 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33797793 ATGTCATATT
33797803 AATAAAT-TTAACAA
1 AATAAATATTAACAA
33797817 AATAAATATTAACAA
1 AATAAATATTAACAA
33797832 TGTTAACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAATATTAACAA
Found at i:33806849 original size:18 final size:17
Alignment explanation
Indices: 33806828--33806875 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
33806818 TAATTTTTAA
*
33806828 AAAAAATTAAAATATTAT
1 AAAAAATTAAAATA-CAT
*
33806846 AAAAATATAAAAATACAT
1 AAAAA-ATTAAAATACAT
*
33806864 AGAAAATTAAAA
1 AAAAAATTAAAA
33806876 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
18 11 0.44
19 8 0.32
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAAATTAAAATACAT
Found at i:33806876 original size:18 final size:18
Alignment explanation
Indices: 33806829--33806876 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
33806819 AATTTTTAAA
*
33806829 AAAAATT-AAAATATTAT
1 AAAAATTAAAAATATCAT
33806846 AAAAATATAAAAATA-CAT
1 AAAAAT-TAAAAATATCAT
33806864 AGAAAATTAAAAA
1 A-AAAATTAAAAA
33806877 AAATTAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 11 0.41
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATTAAAAATATCAT
Found at i:33810224 original size:31 final size:31
Alignment explanation
Indices: 33810189--33810265 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
33810179 TTAACTAAAT
*
33810189 AATTATTCTCATATT-GAGGTTTGAACTTGAC
1 AATTATTCTCATATTGGA-GCTTGAACTTGAC
* *
33810220 AATTATTCTTATATTGGAGCTTGAACTTGAT
1 AATTATTCTCATATTGGAGCTTGAACTTGAC
*
33810251 AATTATTCCCATATT
1 AATTATTCTCATATT
33810266 AAAACTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (31 bp):
AATTATTCTCATATTGGAGCTTGAACTTGAC
Found at i:33814170 original size:19 final size:19
Alignment explanation
Indices: 33814146--33814182 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
33814136 TTTTTTGGTG
33814146 AGAAACCCAGTTTAAGAAA
1 AGAAACCCAGTTTAAGAAA
33814165 AGAAACCCAGTTTAAGAA
1 AGAAACCCAGTTTAAGAA
33814183 TGGTGTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.16
Consensus pattern (19 bp):
AGAAACCCAGTTTAAGAAA
Found at i:33814986 original size:16 final size:16
Alignment explanation
Indices: 33814942--33814986 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
33814932 ATGAAATTTA
33814942 TTTATTAAAATAATAAT
1 TTTATTAAAA-AATAAT
* *
33814959 TTTATGATAAAATAAT
1 TTTATTAAAAAATAAT
33814975 TTTATTAAAAAA
1 TTTATTAAAAAA
33814987 AATCCCCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTATTAAAAAATAAT
Found at i:33815624 original size:25 final size:25
Alignment explanation
Indices: 33815596--33815644 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
33815586 GCTTTATGCC
* * *
33815596 TTGTTTGAACATCTGTTTGGACATA
1 TTGTTGGAACAACAGTTTGGACATA
*
33815621 TTGTTGGGACAACAGTTTGGACAT
1 TTGTTGGAACAACAGTTTGGACAT
33815645 CTATTTAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (25 bp):
TTGTTGGAACAACAGTTTGGACATA
Found at i:33815655 original size:25 final size:25
Alignment explanation
Indices: 33815610--33815659 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
33815600 TTGAACATCT
*
33815610 GTTTGGACATATTGTTGGGACAACA
1 GTTTGGACATATTGTTAGGACAACA
*
33815635 GTTTGGACATCTAT-TTAGGACAACA
1 GTTTGGACATAT-TGTTAGGACAACA
33815660 TAAGTGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (25 bp):
GTTTGGACATATTGTTAGGACAACA
Found at i:33822890 original size:26 final size:26
Alignment explanation
Indices: 33822847--33822900 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
33822837 TTTTTATTTG
33822847 AAAATATATTTAATAATTGAAATAAATA
1 AAAATATATTTAATAATT-AAA-AAATA
*
33822875 AAAATAT-TTTGA-AATTAAAAAATA
1 AAAATATATTTAATAATTAAAAAATA
33822899 AA
1 AA
33822901 TGAGTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 3 0.12
26 4 0.16
27 4 0.16
28 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAATATATTTAATAATTAAAAAATA
Found at i:33826424 original size:12 final size:12
Alignment explanation
Indices: 33826407--33826434 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
33826397 AAGTGAAAGT
33826407 GAAAAAAAAAAA
1 GAAAAAAAAAAA
33826419 GAAAAAAAAAAA
1 GAAAAAAAAAAA
33826431 GAAA
1 GAAA
33826435 CTGTGTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:33828727 original size:71 final size:71
Alignment explanation
Indices: 33828606--33828746 Score: 194
Period size: 71 Copynumber: 2.0 Consensus size: 71
33828596 TTTTAGTCAC
* * * * * *
33828606 CTGCTAGTAATTTAATGTTATTGTATATTTATTTCAGTCACTTAATTTTAATAAATTTTCATTTT
1 CTGCTAATAATTTAATGTTATTGTATACTCATCTCAATCACTTAACTTTAATAAATTTTCATTTT
33828671 GATCAG
66 GATCAG
* *
33828677 CTGCTAATAATTTAGTGTTATTGTATACTCATCTCAATCA-TCTAACTTTAATAAATTTTTATTT
1 CTGCTAATAATTTAATGTTATTGTATACTCATCTCAATCACT-TAACTTTAATAAATTTTCATTT
33828741 TGATCA
65 TGATCA
33828747 TTTATTTTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 1 0.02
71 60 0.98
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (71 bp):
CTGCTAATAATTTAATGTTATTGTATACTCATCTCAATCACTTAACTTTAATAAATTTTCATTTT
GATCAG
Found at i:33838494 original size:11 final size:11
Alignment explanation
Indices: 33838478--33838502 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33838468 GAGATTAACA
33838478 TTTAAAGCATG
1 TTTAAAGCATG
33838489 TTTAAAGCATG
1 TTTAAAGCATG
33838500 TTT
1 TTT
33838503 CTTCTGCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (11 bp):
TTTAAAGCATG
Found at i:33842329 original size:6 final size:6
Alignment explanation
Indices: 33842318--33842356 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
33842308 TGATCAAAAT
*
33842318 TGAAAG TGAAAG TGAAAG TG-AAG TTGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG -TGAAAG TGAAAG TGA
33842357 TATGAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 3 0.10
6 24 0.83
7 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:33843626 original size:18 final size:18
Alignment explanation
Indices: 33843600--33843647 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
33843590 CAAAAATAGA
* *
33843600 TTATGATTTTTTTAGTTT
1 TTATAATTTTTTAAGTTT
*
33843618 TTATAATTTTCTAAGTTT
1 TTATAATTTTTTAAGTTT
* *
33843636 TAATACTTTTTT
1 TTATAATTTTTT
33843648 GGTTTTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATAATTTTTTAAGTTT
Found at i:33850247 original size:15 final size:15
Alignment explanation
Indices: 33850227--33850286 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
33850217 AATATTCAAT
33850227 ATAAATATTTTAATA
1 ATAAATATTTTAATA
* *
33850242 ATAAATATTTATTATGGTT
1 ATAAATA-TT-TTA--ATA
*
33850261 ATAAATATATTAATA
1 ATAAATATTTTAATA
33850276 ATAAATATTTT
1 ATAAATATTTT
33850287 GTAGTATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 18 0.51
16 2 0.06
17 6 0.17
18 1 0.03
19 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAATATTTTAATA
Found at i:33853568 original size:31 final size:31
Alignment explanation
Indices: 33853530--33853599 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
33853520 TGCTTTTCGA
33853530 AGGCACACGGGCGTGTGTGTATACTATTTGG
1 AGGCACACGGGCGTGTGTGTATACTATTTGG
*
33853561 AGGCACACGGGCGTGTGTGTATACTGTTTGG
1 AGGCACACGGGCGTGTGTGTATACTATTTGG
33853592 AGGCACAC
1 AGGCACAC
33853600 TATTTGGCAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.26
Consensus pattern (31 bp):
AGGCACACGGGCGTGTGTGTATACTATTTGG
Found at i:33854059 original size:33 final size:33
Alignment explanation
Indices: 33854022--33854087 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
33854012 TTATATGATC
33854022 ATGTCTATTGGTAGATTATACATATCTGTCATA
1 ATGTCTATTGGTAGATTATACATATCTGTCATA
* *
33854055 ATGTCTATTGGTAGATTATATATATTTGTCATA
1 ATGTCTATTGGTAGATTATACATATCTGTCATA
33854088 TGTTTTCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (33 bp):
ATGTCTATTGGTAGATTATACATATCTGTCATA
Found at i:33858082 original size:28 final size:28
Alignment explanation
Indices: 33858042--33858097 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
33858032 CTTTAATAAA
33858042 ATAAAGGTGAATCATTGTAAATTTATTT
1 ATAAAGGTGAATCATTGTAAATTTATTT
33858070 ATAAAGGTGAATCATTGTAAATTTATTT
1 ATAAAGGTGAATCATTGTAAATTTATTT
33858098 TCTCATTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (28 bp):
ATAAAGGTGAATCATTGTAAATTTATTT
Found at i:33865828 original size:23 final size:24
Alignment explanation
Indices: 33865801--33865849 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
33865791 ATTTGAGAAA
*
33865801 TAATT-TTTCAGTTAAACTCTGTT
1 TAATTATTTCAATTAAACTCTGTT
33865824 TAATTATTTCAATTAAACTCTGTT
1 TAATTATTTCAATTAAACTCTGTT
33865848 TA
1 TA
33865850 TTTGTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (24 bp):
TAATTATTTCAATTAAACTCTGTT
Found at i:33865865 original size:24 final size:24
Alignment explanation
Indices: 33865801--33865865 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
33865791 ATTTGAGAAA
* *
33865801 TAATT-TTTCAGTTAAACTCTGTT
1 TAATTATTTCAATCAAACTCTGTT
*
33865824 TAATTATTTCAATTAAACTCTGTT
1 TAATTATTTCAATCAAACTCTGTT
* * *
33865848 TATTTGTTTGAATCAAAC
1 TAATTATTTCAATCAAAC
33865866 GTCTAGATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
TAATTATTTCAATCAAACTCTGTT
Found at i:33872691 original size:24 final size:24
Alignment explanation
Indices: 33872640--33872685 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
33872630 TTCATAAGTC
*
33872640 AAATAAATTATGCTAATAAATACA
1 AAATAAATTATACTAATAAATACA
*
33872664 AAATATATTATACTAATAAATA
1 AAATAAATTATACTAATAAATA
33872686 TTAAATCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:33873056 original size:22 final size:22
Alignment explanation
Indices: 33873033--33873073 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
33873023 TTGAAATTTA
*
33873033 AAATT-TGAAAAGTAAAAAACT
1 AAATTCTGAAAAATAAAAAACT
*
33873054 AAATTCTTAAAAATAAAAAA
1 AAATTCTGAAAAATAAAAAA
33873074 TATTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (22 bp):
AAATTCTGAAAAATAAAAAACT
Found at i:33877989 original size:18 final size:19
Alignment explanation
Indices: 33877966--33878003 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
33877956 AAAAGTTATG
* *
33877966 AATAATTTTG-TATTATTA
1 AATAATATTGCTATCATTA
33877984 AATAATATTGCTATCATTA
1 AATAATATTGCTATCATTA
33878003 A
1 A
33878004 CTATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
AATAATATTGCTATCATTA
Found at i:33882099 original size:25 final size:23
Alignment explanation
Indices: 33882054--33882099 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
33882044 CGAATCCCGA
*
33882054 TAAATATTAAAAAACCACATACC
1 TAAATATTAAAAAAACACATACC
33882077 TAAATATTTAAAAAAACAGCATA
1 TAAATA-TTAAAAAAACA-CATA
33882100 TACCTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (23 bp):
TAAATATTAAAAAAACACATACC
Found at i:33909008 original size:7 final size:7
Alignment explanation
Indices: 33908996--33909036 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
33908986 TTCAAAACAT
33908996 AATTAAA
1 AATTAAA
33909003 AATTAAA
1 AATTAAA
*
33909010 AACT-AA
1 AATTAAA
*
33909016 AATTTAA
1 AATTAAA
33909023 AATT-AA
1 AATTAAA
33909029 AATTAAA
1 AATTAAA
33909036 A
1 A
33909037 TCATATTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 11 0.37
7 19 0.63
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:33909019 original size:13 final size:13
Alignment explanation
Indices: 33909001--33909036 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
33908991 AACATAATTA
33909001 AAAATTAAAAACT
1 AAAATTAAAAACT
* *
33909014 AAAATTTAAAATT
1 AAAATTAAAAACT
33909027 AAAATTAAAA
1 AAAATTAAAA
33909037 TCATATTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAAACT
Found at i:33911192 original size:24 final size:24
Alignment explanation
Indices: 33911160--33911207 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
33911150 TTTGATATGC
33911160 GGGTTAGTGATGCAGTCGAAACTA
1 GGGTTAGTGATGCAGTCGAAACTA
33911184 GGGTTAGTGATGCAGTCGAAACTA
1 GGGTTAGTGATGCAGTCGAAACTA
33911208 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.25
Consensus pattern (24 bp):
GGGTTAGTGATGCAGTCGAAACTA
Found at i:33914577 original size:25 final size:25
Alignment explanation
Indices: 33914524--33914570 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
33914514 GTTGGATTCA
33914524 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
33914549 AATTAAA-TCTAAATA-ATAATTT
1 AATTAAATTCTAAAAAGATAATTT
33914571 CCTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:33917271 original size:63 final size:63
Alignment explanation
Indices: 33917172--33917297 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
33917162 TGTTGAAAAG
*
33917172 AATCCAAGTACTAAACCAACTACCATCGTCTATGCTCGTCGCCAAGGAGATGGTAAGGAATAT
1 AATCCAAGGACTAAACCAACTACCATCGTCTATGCTCGTCGCCAAGGAGATGGTAAGGAATAT
33917235 AATCCAAGGACTAAACCAACTACCATCGTCTATGCTCGTCGCCAAGGAGATGGTAAGGAATAT
1 AATCCAAGGACTAAACCAACTACCATCGTCTATGCTCGTCGCCAAGGAGATGGTAAGGAATAT
33917298 TTTGGGTATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (63 bp):
AATCCAAGGACTAAACCAACTACCATCGTCTATGCTCGTCGCCAAGGAGATGGTAAGGAATAT
Found at i:33929511 original size:17 final size:17
Alignment explanation
Indices: 33929489--33929525 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
33929479 TTACCTATGA
33929489 ATAAAAAAAACTATTCT
1 ATAAAAAAAACTATTCT
33929506 ATAAAAAAAACTATTCT
1 ATAAAAAAAACTATTCT
33929523 ATA
1 ATA
33929526 TCTGTTTATG
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAAAAAACTATTCT
Found at i:33934091 original size:5 final size:5
Alignment explanation
Indices: 33934066--33934107 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
33934056 TTTTATCTTA
* * *
33934066 TTATT TTCTT TTCTT TGATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
33934108 GTCTTGTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:33934092 original size:15 final size:15
Alignment explanation
Indices: 33934051--33934107 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
33934041 ACTTTGAGTC
* *
33934051 TTTGTTTTTATCTTA
1 TTTGATTTTATTTTA
* *
33934066 -TT-ATTTTCTTTTC
1 TTTGATTTTATTTTA
33934079 TTTGATTTTATTTTA
1 TTTGATTTTATTTTA
*
33934094 TTTTATTTTATTTT
1 TTTGATTTTATTTT
33934108 GTCTTGTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 22 0.67
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTGATTTTATTTTA
Found at i:33938933 original size:16 final size:16
Alignment explanation
Indices: 33938914--33938977 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
33938904 ATGTCATATG
33938914 AAAAATATAAATTTTA
1 AAAAATATAAATTTTA
* * *
33938930 AAAATTAAAAACTTTA
1 AAAAATATAAATTTTA
33938946 AAAATATATAAATTAATT-
1 AAAA-ATATAAATT--TTA
33938964 AAAAATAT-AATTTT
1 AAAAATATAAATTTT
33938978 TTTCATAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 2 0.05
16 21 0.54
17 10 0.26
18 4 0.10
19 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATAAATTTTA
Found at i:33958066 original size:21 final size:21
Alignment explanation
Indices: 33958024--33958067 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
33958014 TTTACGGATT
* *
33958024 TTTTTTGCATTTTTTTATGAA
1 TTTTTTGCATTTTTTAAGGAA
33958045 TTTTTTG-ATATTTTTAAGGAA
1 TTTTTTGCAT-TTTTTAAGGAA
33958066 TT
1 TT
33958068 CTGAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (21 bp):
TTTTTTGCATTTTTTAAGGAA
Found at i:33962505 original size:3 final size:3
Alignment explanation
Indices: 33962497--33962524 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33962487 ACAATATTCA
33962497 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33962525 TAGTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33962553 original size:21 final size:21
Alignment explanation
Indices: 33962529--33962568 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33962519 ATAATATAGT
*
33962529 AAAATTACAACAAAATAATGA
1 AAAATAACAACAAAATAATGA
**
33962550 AAAATAACAGTAAAATAAT
1 AAAATAACAACAAAATAAT
33962569 TTATTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAACAACAAAATAATGA
Found at i:33964005 original size:10 final size:9
Alignment explanation
Indices: 33963985--33964023 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
33963975 TTTTAAAATT
33963985 TTAATTAAA
1 TTAATTAAA
33963994 TTAATATAAA
1 TTAAT-TAAA
*
33964004 TTATTTTAAA
1 TTA-ATTAAA
33964014 TTAATTAAA
1 TTAATTAAA
33964023 T
1 T
33964024 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 11 0.42
10 14 0.54
11 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAATTAAA
Found at i:33964034 original size:19 final size:20
Alignment explanation
Indices: 33963989--33964028 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
33963979 AAAATTTTAA
33963989 TTAAATTAATATAAATTATT
1 TTAAATTAATATAAATTATT
33964009 TTAAATTAAT-TAAA-TATT
1 TTAAATTAATATAAATTATT
33964027 TT
1 TT
33964029 GTAATTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 4 0.20
20 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATTAATATAAATTATT
Found at i:33966519 original size:3 final size:3
Alignment explanation
Indices: 33966505--33966548 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
33966495 GACGGAATCC
* * *
33966505 AAG AAG AGG AAG AAG AAG CAAG ACG AGG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG A
33966549 GCCGGAGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33966532 original size:19 final size:19
Alignment explanation
Indices: 33966504--33966549 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
33966494 AGACGGAATC
33966504 CAAGAAGAGGAAGAAGAAG
1 CAAGAAGAGGAAGAAGAAG
*
33966523 CAAGACGAGGAAGAAGAAG
1 CAAGAAGAGGAAGAAGAAG
33966542 -AAGAAGAG
1 CAAGAAGAG
33966550 CCGGAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.57, C:0.07, G:0.37, T:0.00
Consensus pattern (19 bp):
CAAGAAGAGGAAGAAGAAG
Found at i:33987256 original size:116 final size:113
Alignment explanation
Indices: 33987129--33987351 Score: 281
Period size: 116 Copynumber: 1.9 Consensus size: 113
33987119 TTAGTTTGTC
* *
33987129 TAAAATCTAAAATTTAATTTTGA-CCTTTTCAAAAAT-GAAAATTATATAGTTTAATTCATTGAG
1 TAAAATCTAAAATTTAATTTTGATCC-CTTCAAAAATGGAAAATT-TATAATTTAATTCATTGA-
* * *
33987192 AAATTTTCGTAAAATTTGCATTGCTAC-AATGATAAAATTATATTTTATCCTTT
63 AAA-ATT-ATAAAATTTGCATTACT-CTAATGATAAAATTATATTTTATCCTTT
* * *
33987245 TAAAATTTAAAATTTAATTTTGATCCCTTCAAAAGTGGAAAGTTTATAATTTAATTCATTGAAAA
1 TAAAATCTAAAATTTAATTTTGATCCCTTCAAAAATGGAAAATTTATAATTTAATTCATTGAAAA
* *
33987310 ATTATAAAATTTGTATTACTCTAATGATAAAATTGTATTTTA
66 ATTATAAAATTTGCATTACTCTAATGATAAAATTATATTTTA
33987352 GCTATCTCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
112 1 0.01
113 33 0.35
114 2 0.02
115 3 0.03
116 47 0.50
117 8 0.09
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (113 bp):
TAAAATCTAAAATTTAATTTTGATCCCTTCAAAAATGGAAAATTTATAATTTAATTCATTGAAAA
ATTATAAAATTTGCATTACTCTAATGATAAAATTATATTTTATCCTTT
Found at i:33989057 original size:29 final size:30
Alignment explanation
Indices: 33989004--33989061 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
33988994 AGATTAAATC
* *
33989004 AAATTAAAATTTTATATATAGTATTATATA
1 AAATTAAAATTTCATATATAATATTATATA
33989034 AAATTAAAA-TTCATATATAATATTATAT
1 AAATTAAAATTTCATATATAATATTATAT
33989062 TTTTACATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
AAATTAAAATTTCATATATAATATTATATA
Found at i:33999138 original size:23 final size:23
Alignment explanation
Indices: 33999064--33999277 Score: 194
Period size: 23 Copynumber: 9.5 Consensus size: 23
33999054 TAAACGGAAC
* * *
33999064 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
33999086 GAACAGAGAGCACA-AAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
33999108 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
33999134 AAACAGAGAGTACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
33999157 ------A-AGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33999173 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33999196 AATAACAGAGAGTACACAAAGTACT
1 -A-AACAGAGAGCACACAAAGTGCT
*
33999221 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
33999244 AATCAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
33999267 AATCAGAGAGC
1 AAACAGAGAGC
33999278 GCGCTAGTGT
Statistics
Matches: 161, Mismatches: 17, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
16 14 0.09
17 1 0.01
22 18 0.11
23 87 0.54
24 2 0.01
25 31 0.19
26 8 0.05
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:33999143 original size:48 final size:45
Alignment explanation
Indices: 33999089--33999277 Score: 203
Period size: 48 Copynumber: 4.2 Consensus size: 45
33999079 AAGTACTGAA
*
33999089 CAGAGAGCACA-AAAGTGCTGGGCAACAGAGAGCACACAAAGTGCTAAA
1 CAGAGAGCACACAAAGTGCT----AACAGAGAGCACACAAAGTGCTAAT
*
33999137 CAGAGAGTACACAAAGTGCT-----A-AGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAACAGAGAGCACACAAAGTGCTAAT
* * *
33999176 CAGAGAGCACACACAGTGCTAATAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGC---TAACAGAGAGCACACAAAGTGCTAAT
*
33999224 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAA-CAGAGAGCACACAAAGTGCTAAT
33999270 CAGAGAGC
1 CAGAGAGC
33999278 GCGCTAGTGT
Statistics
Matches: 120, Mismatches: 10, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
39 34 0.28
40 1 0.01
42 1 0.01
45 3 0.03
46 28 0.23
47 1 0.01
48 44 0.37
49 8 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (45 bp):
CAGAGAGCACACAAAGTGCTAACAGAGAGCACACAAAGTGCTAAT
Found at i:33999173 original size:39 final size:39
Alignment explanation
Indices: 33999119--33999197 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
33999109 GGCAACAGAG
*
33999119 AGCACACAAAGTGCTAAACAGAGAGTACACAAAGTGCTA
1 AGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCTA
* *
33999158 AGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTA
1 AGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCTA
33999197 A
1 A
33999198 TAACAGAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13
Consensus pattern (39 bp):
AGCACACAAAGTGCTAAACAGAGAGCACACAAAGTGCTA
Found at i:34002409 original size:24 final size:24
Alignment explanation
Indices: 34002382--34002427 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
34002372 GAAATTTCAA
34002382 AAAAAAACAAAAAAAGACAAAATT
1 AAAAAAACAAAAAAAGACAAAATT
** *
34002406 AAAAAAAGGAAAAAAGAGAAAA
1 AAAAAAACAAAAAAAGACAAAA
34002428 AGAGAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (24 bp):
AAAAAAACAAAAAAAGACAAAATT
Found at i:34002427 original size:15 final size:15
Alignment explanation
Indices: 34002409--34002463 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
34002399 CAAAATTAAA
34002409 AAAAGGAAAAAAGAG
1 AAAAGGAAAAAAGAG
* *
34002424 AAAAAGAGAAAA-AG
1 AAAAGGAAAAAAGAG
34002438 AAAAGG-AAAAAGAAG
1 AAAAGGAAAAAAG-AG
34002453 AAAA-GAAAAAA
1 AAAAGGAAAAAA
34002464 AAGGGAGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 4 0.12
14 8 0.24
15 21 0.64
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGGAAAAAAGAG
Found at i:34002448 original size:12 final size:13
Alignment explanation
Indices: 34002425--34002462 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
34002415 AAAAAAGAGA
34002425 AAAAGAGAAAAAG
1 AAAAGAGAAAAAG
34002438 AAAAG-GAAAAAG
1 AAAAGAGAAAAAG
*
34002450 AAGAAAAGAAAAA
1 AA-AAGAGAAAAA
34002463 AAAGGGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 9 0.41
13 7 0.32
14 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAG
Found at i:34002448 original size:20 final size:21
Alignment explanation
Indices: 34002417--34002461 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
34002407 AAAAAAGGAA
34002417 AAAAGAGAAAAAG-AGAAAAAG
1 AAAAGAGAAAAAGAAG-AAAAG
34002438 AAAAG-GAAAAAGAAGAAAAG
1 AAAAGAGAAAAAGAAGAAAAG
34002458 AAAA
1 AAAA
34002462 AAAAGGGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AAAAGAGAAAAAGAAGAAAAG
Found at i:34002466 original size:29 final size:29
Alignment explanation
Indices: 34002409--34002464 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
34002399 CAAAATTAAA
*
34002409 AAAAGGAAAAAAGAGAAAAAGAGAAAAAG
1 AAAAGGAAAAAAGAGAAAAAGAAAAAAAG
34002438 AAAAGG-AAAAAGA-AGAAAAGAAAAAAA
1 AAAAGGAAAAAAGAGA-AAAAGAAAAAAA
34002465 AGGGAGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 1 0.04
28 18 0.72
29 6 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAAGGAAAAAAGAGAAAAAGAAAAAAAG
Found at i:34003504 original size:49 final size:49
Alignment explanation
Indices: 34003348--34003569 Score: 178
Period size: 49 Copynumber: 4.5 Consensus size: 49
34003338 TTTACAGGTT
* ** * **
34003348 TGAAGGGAAA-ATTTGAAGCCTCAACGGCAAATCTAATACCCTAGAGATA
1 TGAAGGGAAAGA-TTGAAGCCGCAACGGTGAACCTTGTACCCTAGAGATA
* * * ** * * **
34003397 AGAAGAGAAAGGTTGAAGCCGCAACGGCAAACCTTGTACCTTAGGGACG
1 TGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTGTACCCTAGAGATA
* * **
34003446 TGATA-GGAAAGATTGAAGCCGCGACGGTGAATCTTGTACCCTAGATTTA
1 TGA-AGGGAAAGATTGAAGCCGCAACGGTGAACCTTGTACCCTAGAGATA
* * * * *
34003495 TGGAGGGAAAGGTTGAAGCTGCAACGGTGAGCCTTGTACCCTAGAGATG
1 TGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTGTACCCTAGAGATA
* *
34003544 TGAAGGGAAAGATTGAGGCCCCAACG
1 TGAAGGGAAAGATTGAAGCCGCAACG
34003570 ACGAATCTTA
Statistics
Matches: 132, Mismatches: 38, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
48 1 0.01
49 130 0.98
50 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTGTACCCTAGAGATA
Found at i:34003700 original size:42 final size:43
Alignment explanation
Indices: 34003618--34003701 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
34003608 AAGCTGTAAA
*
34003618 GGTGAATCTTACATCTCTAAAGTTGAAGATGAGCAAATTGAAC
1 GGTGAATCTTACACCTCTAAAGTTGAAGATGAGCAAATTGAAC
* *
34003661 GGTGAATCTT-CTACCTC-AAAGTTGCAG-TGAAGCAGATTGAA
1 GGTGAATCTTAC-ACCTCTAAAGTTGAAGATG-AGCAAATTGAA
34003702 ACAAGTAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.06
42 20 0.56
43 14 0.39
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (43 bp):
GGTGAATCTTACACCTCTAAAGTTGAAGATGAGCAAATTGAAC
Found at i:34004039 original size:40 final size:39
Alignment explanation
Indices: 34003939--34004073 Score: 164
Period size: 39 Copynumber: 3.4 Consensus size: 39
34003929 ATTGAAGACC
* * * * *
34003939 ATCCAATCTCTTACCCCGATCATGCGGCAGATTGAAGCA
1 ATCCAATCTTTTACCCCAACCATGAGGCAGATTGAAGTA
34003978 ATCCAATCTTTTACCCCAACCATGAGGCAGATTGAAGTA
1 ATCCAATCTTTTACCCCAACCATGAGGCAGATTGAAGTA
* * **
34004017 ATTCAGATCTTCTACCTTAACCA-GAGGGCAGATTGAAGTA
1 ATCCA-ATCTTTTACCCCAACCATGA-GGCAGATTGAAGTA
34004057 ATCCAATCTTTTACCCC
1 ATCCAATCTTTTACCCC
34004074 TAAAGCTATG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 49 0.60
40 32 0.40
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (39 bp):
ATCCAATCTTTTACCCCAACCATGAGGCAGATTGAAGTA
Found at i:34004159 original size:50 final size:50
Alignment explanation
Indices: 34004104--34004201 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
34004094 TTGAAACTGT
*
34004104 AATGGCAAATGTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAGTCGC
1 AATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAGTCGC
* * * *
34004154 AATGGCAAATCTCATTCACCTAAAGTTGTAGAGGGGCAGATTGAAGTC
1 AATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAGTC
34004202 ATAAGGACGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (50 bp):
AATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGCAAAATGAAGTCGC
Found at i:34004301 original size:40 final size:40
Alignment explanation
Indices: 34004253--34004584 Score: 304
Period size: 40 Copynumber: 8.4 Consensus size: 40
34004243 AGTTACAACC
*
34004253 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * *
34004293 TCCGATCTCTTATCCC-AATCATG-GGGCAGATTGAAAACTA
1 TCCAATCTCTTA-CCCTAACCA-GAGGGCAGATTGAAGACAA
* *
34004333 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGATC-A
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGA-CAA
* * * *
34004373 TCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGGCAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* *
34004413 TCCAATCTCTTACCCCAATCATG-GGGCAGATTGAA-ACAA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* *
34004452 TCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG-CAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * * * * **
34004491 TCCAGTCTTTTACCCTAACCACAGAGTAGATTAAAGATTA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* ** *
34004531 TCAAATCTCTTACCCCGACCATG-GGGCAGATTGAA-ATAA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
34004570 TCCAATCGT-TTACCC
1 TCCAATC-TCTTACCC
34004585 CTAAAGTTAT
Statistics
Matches: 245, Mismatches: 35, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
39 87 0.36
40 152 0.62
41 6 0.02
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
Found at i:34004554 original size:118 final size:118
Alignment explanation
Indices: 34004253--34004584 Score: 387
Period size: 118 Copynumber: 2.8 Consensus size: 118
34004243 AGTTACAACC
* * * * * * ** *
34004253 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTATCCCAATCATGGG
1 TCCAATCTTTTACCCTAACCACAGAGCAAATTAAAGACAATCAAATCTCTTACCCCAATCATGGG
* * *
34004318 GCAGATTGAAAACTATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGATCA
66 GCAGATTG-AAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGA-CA
* * * * * *
34004373 TCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAGGCAATCCAATCTCTTACCCCAATCATGGG
1 TCCAATCTTTTACCCTAACCACAGAGCAAATTAAAGACAATCAAATCTCTTACCCCAATCATGGG
34004438 GCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG-CAA
66 GCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGAC-A
* * * ** * *
34004491 TCCAGTCTTTTACCCTAACCACAGAGTAGATTAAAGATTATCAAATCTCTTACCCCGACCATGGG
1 TCCAATCTTTTACCCTAACCACAGAGCAAATTAAAGACAATCAAATCTCTTACCCCAATCATGGG
* *
34004556 GCAGATTGAAATAATCCAATCGTTTACCC
66 GCAGATTGAAACAATCCAATCTTTTACCC
34004585 CTAAAGTTAT
Statistics
Matches: 186, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
117 1 0.01
118 80 0.43
119 39 0.21
120 66 0.35
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (118 bp):
TCCAATCTTTTACCCTAACCACAGAGCAAATTAAAGACAATCAAATCTCTTACCCCAATCATGGG
GCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGACA
Found at i:34008700 original size:25 final size:23
Alignment explanation
Indices: 34008659--34008705 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
34008649 CCAATTAGGG
34008659 AATTATTGTTTAGATTTAATTTT
1 AATTATTGTTTAGATTTAATTTT
*
34008682 AATTATCTTTTTAGAATTTAATTT
1 AATTAT-TGTTTAG-ATTTAATTT
34008706 GGATCCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 6 0.29
25 9 0.43
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTT
Found at i:34013896 original size:15 final size:15
Alignment explanation
Indices: 34013846--34013896 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
34013836 AATATAAAAA
34013846 ATAAAAAAATTAAATT
1 ATAAAAAAA-TAAATT
34013862 ACTAAAAATAA-AAA-T
1 A-TAAAAA-AATAAATT
34013877 ATAAAAAAATAAATT
1 ATAAAAAAATAAATT
*
34013892 TTAAA
1 ATAAA
34013897 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 2 0.07
14 9 0.30
15 7 0.23
16 4 0.13
17 6 0.20
18 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAAAAAATAAATT
Found at i:34029863 original size:22 final size:22
Alignment explanation
Indices: 34029838--34029884 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
34029828 TAACAATATT
*
34029838 TAATTAAATATAAATTT-AAAAA
1 TAATAAAAT-TAAATTTCAAAAA
*
34029860 TAATAAAATTAAATTTCTAAAA
1 TAATAAAATTAAATTTCAAAAA
34029882 TAA
1 TAA
34029885 AATATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
TAATAAAATTAAATTTCAAAAA
Found at i:34029866 original size:21 final size:21
Alignment explanation
Indices: 34029842--34029892 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
34029832 AATATTTAAT
34029842 TAAATATAAATTT-AAAAATAA
1 TAAATATAAATTTCAAAAAT-A
*
34029863 TAAA-ATTAAATTTCTAAAATA
1 TAAATA-TAAATTTCAAAAATA
34029884 -AAATATAAA
1 TAAATATAAA
34029893 AATTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 8 0.31
21 13 0.50
22 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATATAAATTTCAAAAATA
Found at i:34029880 original size:14 final size:13
Alignment explanation
Indices: 34029863--34029910 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
34029853 TTAAAAATAA
34029863 TAAAATTAAATTT
1 TAAAATTAAATTT
* *
34029876 CTAAAATAAAATAT
1 -TAAAATTAAATTT
*
34029890 AAAAATTAAATTT
1 TAAAATTAAATTT
34029903 T-AAATTAA
1 TAAAATTAA
34029911 TAAAAATAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 7 0.25
13 10 0.36
14 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTAAATTT
Found at i:34029886 original size:27 final size:26
Alignment explanation
Indices: 34029856--34029906 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
34029846 TATAAATTTA
34029856 AAAATA-ATAAAATTAAATTTCTAAAAT
1 AAAATATA-AAAATTAAATTT-TAAAAT
34029883 AAAATATAAAAATTAAATTTTAAA
1 AAAATATAAAAATTAAATTTTAAA
34029907 TTAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.17
27 18 0.78
28 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATATAAAAATTAAATTTTAAAAT
Found at i:34029913 original size:22 final size:22
Alignment explanation
Indices: 34029843--34029917 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
34029833 ATATTTAATT
* *
34029843 AAATATAAATTTAAAAATAAT-A
1 AAAT-TAAATTTTAAATTAATAA
*
34029865 AAATTAAATTTCTAAAATAAAATATAA
1 AAATTAAATTT-T-AAAT--TA-ATAA
34029892 AAATTAAATTTTAAATTAATAA
1 AAATTAAATTTTAAATTAATAA
34029914 AAAT
1 AAAT
34029918 AGAACGTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 7 0.16
22 12 0.28
23 4 0.09
25 5 0.12
26 3 0.07
27 12 0.28
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTAAATTTTAAATTAATAA
Found at i:34032754 original size:2 final size:2
Alignment explanation
Indices: 34032747--34032771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34032737 AATCTCCCTC
34032747 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
34032772 AAGTTGGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:34033772 original size:21 final size:21
Alignment explanation
Indices: 34033748--34033788 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34033738 TGTTATAAAT
34033748 TATAATATAC-ATATAACATAA
1 TATAATATACTATA-AACATAA
34033769 TATAATATACTATAAACATA
1 TATAATATACTATAAACATA
34033789 TAAAATGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TATAATATACTATAAACATAA
Found at i:34036189 original size:61 final size:62
Alignment explanation
Indices: 34036094--34036231 Score: 167
Period size: 61 Copynumber: 2.3 Consensus size: 62
34036084 ATTGGGGTCT
** *
34036094 AAAGTTCAAGCCCCAATGTGGGAACAATTGCCAAGTTCAAGGAC-TAACTTGGA-CAAAAAAA
1 AAAGTTCAAGCCCCAATACGAGAACAATTGCCAAGTTC-AGGACTTAACTTGGACCAAAAAAA
* * * *
34036155 AAAGTTCAAGCTCCAATACGAGAACAATTGCCAAGTTCAGGGCTTAATTTGGACCCAAAAAA
1 AAAGTTCAAGCCCCAATACGAGAACAATTGCCAAGTTCAGGACTTAACTTGGACCAAAAAAA
*
34036217 AAA--TCAGGCCCCAAT
1 AAAGTTCAAGCCCCAAT
34036232 GTGAAAATAG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
60 14 0.21
61 42 0.64
62 10 0.15
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (62 bp):
AAAGTTCAAGCCCCAATACGAGAACAATTGCCAAGTTCAGGACTTAACTTGGACCAAAAAAA
Found at i:34037769 original size:89 final size:89
Alignment explanation
Indices: 34037618--34037789 Score: 301
Period size: 89 Copynumber: 1.9 Consensus size: 89
34037608 GAAACCTTGG
*
34037618 GATTAAAGCTCGTCATTTTTTGTAGCAATTTGCTTCATGCAGGACTTCTATGCATGAAA-TTTTG
1 GATTAAAGCTCGTCATTTTTTGTAGCAATTTGCTTCATGCAGGACTTCTATGCAAGAAATTTTTG
34037682 CATGAGTCAGAAATACCAACCATGT
66 C-TGAGTCAGAAATACCAACCATGT
* *
34037707 GATTAAAGCTCGTCATTTTTTGTAGTAATTTGCTTCATGCAGGACTTCTATGTAAGAAATTTTTG
1 GATTAAAGCTCGTCATTTTTTGTAGCAATTTGCTTCATGCAGGACTTCTATGCAAGAAATTTTTG
34037772 CTGAGTCAGAAATACCAA
66 CTGAGTCAGAAATACCAA
34037790 AGCAGCAGTG
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 73 0.92
90 6 0.08
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (89 bp):
GATTAAAGCTCGTCATTTTTTGTAGCAATTTGCTTCATGCAGGACTTCTATGCAAGAAATTTTTG
CTGAGTCAGAAATACCAACCATGT
Found at i:34050291 original size:28 final size:30
Alignment explanation
Indices: 34050260--34050316 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
34050250 TTTTAATATA
*
34050260 TAATT-TG-ATATATAAATTTGATT-TGGTG
1 TAATTATGCATATA-AAATTTAATTGTGGTG
34050288 TAATTATGCATATAAAATTTAATTGTGGT
1 TAATTATGCATATAAAATTTAATTGTGGT
34050317 TCGAATAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 9 0.36
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (30 bp):
TAATTATGCATATAAAATTTAATTGTGGTG
Done.