Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 38 of 770
Found at i:10945535 original size:21 final size:21
Alignment explanation
Indices: 10945519--10945592 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
10945509 TTTCTTGAAG
10945519 AATAA-CTTTAAAATCTTCAA
1 AATAATCTTTAAAATCTTCAA
*
10945539 AATAATTTTTAAAAT-TT-AA
1 AATAATCTTTAAAATCTTCAA
* * *
10945558 AAT-ATTTTTAGAAATTTTAAA
1 AATAATCTTTA-AAATCTTCAA
* *
10945579 AATTATATTTAAAA
1 AATAATCTTTAAAA
10945593 AAATATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.15
19 9 0.19
20 9 0.19
21 16 0.34
22 6 0.13
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
AATAATCTTTAAAATCTTCAA
Found at i:10945578 original size:20 final size:19
Alignment explanation
Indices: 10945525--10945579 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 19
10945515 GAAGAATAAC
10945525 TTTAAAATCTTCAAAATAATT
1 TTTAAAAT-TT-AAAATAATT
10945546 TTTAAAATTTAAAAT-ATT
1 TTTAAAATTTAAAATAATT
10945564 TTTAGAAATTTTAAAA
1 TTTA-AAA-TTTAAAA
10945580 ATTATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.22
19 8 0.25
20 9 0.28
21 8 0.25
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTAAAATTTAAAATAATT
Found at i:10945623 original size:31 final size:32
Alignment explanation
Indices: 10945569--10945633 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
10945559 ATATTTTTAG
** * *
10945569 AAATTTTAAAAATTATATTTAAAAAA-ATATA
1 AAATTTTAAAAAAAAAATCTAAAAAACATATA
10945600 AAATTTTAAAAAAAAAATCTAAAAAACATATA
1 AAATTTTAAAAAAAAAATCTAAAAAACATATA
10945632 AA
1 AA
10945634 GAACGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (32 bp):
AAATTTTAAAAAAAAAATCTAAAAAACATATA
Found at i:10950588 original size:10 final size:10
Alignment explanation
Indices: 10950573--10950597 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10950563 ATTTAATTAA
10950573 ATAAATTATT
1 ATAAATTATT
10950583 ATAAATTATT
1 ATAAATTATT
10950593 ATAAA
1 ATAAA
10950598 ATAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAAATTATT
Found at i:10953554 original size:20 final size:19
Alignment explanation
Indices: 10953529--10953589 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
10953519 ATGCTTTTGA
10953529 TTTAATATTTTTAATATAAT
1 TTTAATATTTTT-ATATAAT
* * *
10953549 TTTAATCATTTATATTTATT
1 TTTAAT-ATTTTTATATAAT
*
10953569 TTTAAGATTTTT-TATAAT
1 TTTAATATTTTTATATAAT
10953587 TTT
1 TTT
10953590 TTAGAATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 7 0.21
19 5 0.15
20 16 0.48
21 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTAATATTTTTATATAAT
Found at i:10957480 original size:98 final size:99
Alignment explanation
Indices: 10957271--10957568 Score: 517
Period size: 98 Copynumber: 3.0 Consensus size: 99
10957261 GTATTGGCCC
10957271 ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAACTTTCAGAT
1 ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAACTTTCAGAT
10957336 AATTTAGTGATTATTTCGTAATTTTTTAAATTTA
66 AATTTAGTGATTATTTCGTAATTTTTTAAATTTA
10957370 ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAAT-AAAACTTTCAGAT
1 ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAACTTTCAGAT
10957434 AATTTAGTGATTATTTCGTAATTTTTTAAATTTA
66 AATTTAGTGATTATTTCGTAATTTTTTAAATTTA
* * * *
10957468 ACCATATGAACCGTTGTTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAATTTTTAAAT
1 ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAACTTTCAGAT
* **
10957533 AATTTAGTGACTATTTTATAATTTTTTAAAATTTA
66 AATTTAGTGATTATTTCGTAATTTTTT-AAATTTA
10957568 A
1 A
10957569 TAAATGTAAA
Statistics
Matches: 190, Mismatches: 7, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
98 97 0.51
99 85 0.45
100 8 0.04
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.38
Consensus pattern (99 bp):
ACCATATGAACCGTTGCTTAAATAAAAACTTGATAACCCAATGACTTAAATAAAAACTTTCAGAT
AATTTAGTGATTATTTCGTAATTTTTTAAATTTA
Found at i:10958423 original size:21 final size:21
Alignment explanation
Indices: 10958397--10958436 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
10958387 ATAGCTCCAC
10958397 CAAGGTTTTCATTTGATGATT
1 CAAGGTTTTCATTTGATGATT
10958418 CAAGGTTTTCATTTGATGA
1 CAAGGTTTTCATTTGATGA
10958437 ACCAAGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (21 bp):
CAAGGTTTTCATTTGATGATT
Found at i:10958442 original size:21 final size:21
Alignment explanation
Indices: 10958395--10958442 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
10958385 ATATAGCTCC
10958395 ACCAAGGTTTTCATTTGATGA
1 ACCAAGGTTTTCATTTGATGA
**
10958416 TTCAAGGTTTTCATTTGATGA
1 ACCAAGGTTTTCATTTGATGA
10958437 ACCAAG
1 ACCAAG
10958443 AGCTTCTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (21 bp):
ACCAAGGTTTTCATTTGATGA
Found at i:10963406 original size:23 final size:25
Alignment explanation
Indices: 10963375--10963430 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
10963365 GTAAATTTAA
*
10963375 TTATTTATTTTAATTTAGTA-AA-T
1 TTATATATTTTAATTTAGTATAATT
*
10963398 TTATATATTTTAATTTATTATAATT
1 TTATATATTTTAATTTAGTATAATT
10963423 TTATATAT
1 TTATATAT
10963431 AATCACCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 18 0.62
24 2 0.07
25 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATATATTTTAATTTAGTATAATT
Found at i:10964379 original size:12 final size:12
Alignment explanation
Indices: 10964358--10964389 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
10964348 CATGATTATC
10964358 CTAATCCTAATG
1 CTAATCCTAATG
*
10964370 CTAATGCTAATG
1 CTAATCCTAATG
10964382 CTAATCCT
1 CTAATCCT
10964390 CTAATCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34
Consensus pattern (12 bp):
CTAATCCTAATG
Found at i:10971631 original size:100 final size:101
Alignment explanation
Indices: 10971456--10971660 Score: 349
Period size: 100 Copynumber: 2.0 Consensus size: 101
10971446 CATCAATACT
* *
10971456 AAATCATAACAAATACTAATCTGTAATCAATTAACACTATATCATCACAAATACAACAGCTAGCT
1 AAATCATAACAAATACTAATCTCTAATCAATTAACAATATATCATCACAAATACAACAGCTAGCT
* * *
10971521 CACTCCGAGT-AAATAAATTCATTAAATTAAACGCA
66 CACTCAGAGTAAAATAAATTCATCAAATTAAAAGCA
*
10971556 AAATCATAACAAATACTAATCTCTAATCAATTAACAATATATCATCACAAATACAACCGCTAGCT
1 AAATCATAACAAATACTAATCTCTAATCAATTAACAATATATCATCACAAATACAACAGCTAGCT
10971621 CACTCAGAGTAAAATAAATTCATCAAATTAAAAGCA
66 CACTCAGAGTAAAATAAATTCATCAAATTAAAAGCA
10971657 AAAT
1 AAAT
10971661 TCTACCTAAC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 71 0.72
101 27 0.28
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.25
Consensus pattern (101 bp):
AAATCATAACAAATACTAATCTCTAATCAATTAACAATATATCATCACAAATACAACAGCTAGCT
CACTCAGAGTAAAATAAATTCATCAAATTAAAAGCA
Found at i:10972711 original size:9 final size:9
Alignment explanation
Indices: 10972686--10972719 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
10972676 CAATTTAATA
10972686 TTTAAAATT
1 TTTAAAATT
*
10972695 TTT-TAATT
1 TTTAAAATT
10972703 TTTAAAATT
1 TTTAAAATT
10972712 TTTAAAAT
1 TTTAAAAT
10972720 AATTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAAAATT
Found at i:10977769 original size:5 final size:5
Alignment explanation
Indices: 10977759--10977783 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10977749 TCCCCTAAAT
10977759 GCCAA GCCAA GCCAA GCCAA GCCAA
1 GCCAA GCCAA GCCAA GCCAA GCCAA
10977784 AAAAACTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
GCCAA
Found at i:10983546 original size:11 final size:11
Alignment explanation
Indices: 10983530--10983555 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10983520 TCAGGTTTAA
10983530 TTTGCCTATTT
1 TTTGCCTATTT
10983541 TTTGCCTATTT
1 TTTGCCTATTT
10983552 TTTG
1 TTTG
10983556 AATAGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.12, T:0.65
Consensus pattern (11 bp):
TTTGCCTATTT
Found at i:10985996 original size:28 final size:30
Alignment explanation
Indices: 10985950--10986005 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
10985940 TTAAAATGTA
*
10985950 ATTTTTAAAGGATTAAATTAAAATTTTAAT
1 ATTTTTAAAGGATAAAATTAAAATTTTAAT
*
10985980 ATTTTT-AA-GATAAAATTATAATTTTA
1 ATTTTTAAAGGATAAAATTAAAATTTTA
10986006 CCATATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 16 0.67
29 2 0.08
30 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (30 bp):
ATTTTTAAAGGATAAAATTAAAATTTTAAT
Found at i:10994011 original size:35 final size:35
Alignment explanation
Indices: 10993972--10994041 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
10993962 AAATGGTGAG
10993972 GTGATAATGCTGAAGCATAAGAAGAAAACAGTTAC
1 GTGATAATGCTGAAGCATAAGAAGAAAACAGTTAC
10994007 GTGATAATGCTGAAGCATAAGAAGAAAACAGTTAC
1 GTGATAATGCTGAAGCATAAGAAGAAAACAGTTAC
10994042 ACGGGTCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (35 bp):
GTGATAATGCTGAAGCATAAGAAGAAAACAGTTAC
Found at i:10994845 original size:24 final size:24
Alignment explanation
Indices: 10994818--10994867 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
10994808 TTTGTCTGTG
*
10994818 TAATTAGTTCCATATTCATGCACA
1 TAATTAGTTCCATAGTCATGCACA
10994842 TAATTAGTTCCATAGTCATGCACA
1 TAATTAGTTCCATAGTCATGCACA
10994866 TA
1 TA
10994868 CATCGTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (24 bp):
TAATTAGTTCCATAGTCATGCACA
Found at i:11004656 original size:26 final size:25
Alignment explanation
Indices: 11004627--11004696 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 25
11004617 TGAGCTTTCT
11004627 AATGTGCAAGCTGCAAGCTCAGCAAA
1 AATGTGCAAGCTGCAAGCTCAG-AAA
* *
11004653 AATGTGCAAGCTGCAAGCTTAGTAA
1 AATGTGCAAGCTGCAAGCTCAGAAA
*
11004678 GATGT-CAAAGCTGCAAGCT
1 AATGTGC-AAGCTGCAAGCT
11004697 TAGCGAGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 1 0.03
25 18 0.45
26 21 0.52
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
AATGTGCAAGCTGCAAGCTCAGAAA
Found at i:11004688 original size:25 final size:26
Alignment explanation
Indices: 11004627--11004700 Score: 98
Period size: 25 Copynumber: 2.9 Consensus size: 26
11004617 TGAGCTTTCT
*
11004627 AATGTGCAAGCTGCAAGCTCAGCAAA
1 AATGTGCAAGCTGCAAGCTTAGCAAA
*
11004653 AATGTGCAAGCTGCAAGCTTAG-TAA
1 AATGTGCAAGCTGCAAGCTTAGCAAA
*
11004678 GATGT-CAAAGCTGCAAGCTTAGC
1 AATGTGC-AAGCTGCAAGCTTAGC
11004701 GAGAAGTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 1 0.02
25 21 0.49
26 21 0.49
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
AATGTGCAAGCTGCAAGCTTAGCAAA
Found at i:11014592 original size:72 final size:72
Alignment explanation
Indices: 11014506--11014648 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
11014496 GGGCTTGCAT
* ** *
11014506 TTTGCTGCTCGCAACTATACACCTTTGACAGGCTCGCTTTTTTGCTTACTGTCTTCAACAGGTGT
1 TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
11014571 CTTCAAC
66 CTTCAAC
* ***
11014578 TTTGCTGCTTGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAGTTGGTGT
1 TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
11014643 CTTCAA
66 CTTCAA
11014649 TAGGCTCGCA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.37
Consensus pattern (72 bp):
TTTGCTGCTCGCAACCATACACCTTTGACAGGCTCGCACTTTGGCTTACTGTCTTCAACAGGTGT
CTTCAAC
Found at i:11014813 original size:31 final size:31
Alignment explanation
Indices: 11014778--11014840 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11014768 GCCTGTTTTG
11014778 GTGTCTTCATTTTAACCACCCATATGTGATA
1 GTGTCTTCATTTTAACCACCCATATGTGATA
11014809 GTGTCTTCATTTTAACCACCCATATGTGATA
1 GTGTCTTCATTTTAACCACCCATATGTGATA
11014840 G
1 G
11014841 CCTTTTCCAT
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:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (31 bp):
GTGTCTTCATTTTAACCACCCATATGTGATA
Found at i:11017713 original size:7 final size:7
Alignment explanation
Indices: 11017701--11017730 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
11017691 TCATTTGTTC
11017701 TTGATAT
1 TTGATAT
11017708 TTGATAT
1 TTGATAT
11017715 TTGATAT
1 TTGATAT
11017722 TTGATAT
1 TTGATAT
11017729 TT
1 TT
11017731 TTGAGTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (7 bp):
TTGATAT
Found at i:11025047 original size:21 final size:21
Alignment explanation
Indices: 11025022--11025061 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11025012 GACGAGTGAA
* *
11025022 ACTCCACAGCAGGTGGAGTGT
1 ACTCCAAAACAGGTGGAGTGT
11025043 ACTCCAAAACAGGTGGAGT
1 ACTCCAAAACAGGTGGAGT
11025062 TTGAGCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (21 bp):
ACTCCAAAACAGGTGGAGTGT
Found at i:11027612 original size:47 final size:47
Alignment explanation
Indices: 11027503--11027613 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
11027493 CCGGGATAAG
* *
11027503 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
11027550 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
11027597 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
11027614 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:11034864 original size:47 final size:47
Alignment explanation
Indices: 11034755--11034865 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
11034745 CCGGGATAAG
*
11034755 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
11034802 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
11034849 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
11034866 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:11039865 original size:31 final size:29
Alignment explanation
Indices: 11039830--11039889 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
11039820 TTTTTTAATC
11039830 GAGTCGAATAAAATGAAATTTGTGTCGAGTT
1 GAGTCGAATAAAATGAAA-TTGT-TCGAGTT
* *
11039861 GAGTCGAATCAAGTGAAATTGTTCGAGTT
1 GAGTCGAATAAAATGAAATTGTTCGAGTT
11039890 AAATTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 4 0.15
31 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (29 bp):
GAGTCGAATAAAATGAAATTGTTCGAGTT
Found at i:11047103 original size:21 final size:21
Alignment explanation
Indices: 11047078--11047146 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
11047068 TATAATGATT
11047078 ATTATTATGGTTTTATATTAA
1 ATTATTATGGTTTTATATTAA
**
11047099 ATTATTATAATTATTA-ATT-A
1 ATTATTATGGTT-TTATATTAA
* *
11047119 A-CATTATGGTTTTATATTAG
1 ATTATTATGGTTTTATATTAA
11047139 ATTATTAT
1 ATTATTAT
11047147 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.27
20 3 0.08
21 18 0.49
22 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTATTATGGTTTTATATTAA
Found at i:11047159 original size:15 final size:14
Alignment explanation
Indices: 11047133--11047163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
11047123 TATGGTTTTA
11047133 TATTAGATTATTAT
1 TATTAGATTATTAT
11047147 TATTAGCATTATTAT
1 TATTAG-ATTATTAT
11047162 TA
1 TA
11047164 AATAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.55
Consensus pattern (14 bp):
TATTAGATTATTAT
Found at i:11048603 original size:21 final size:23
Alignment explanation
Indices: 11048559--11048603 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11048549 AAATATTCTG
* *
11048559 GGTGTGTTTGGGTTGGACATTCT
1 GGTGTGTTTGGGTTAGACAATCT
11048582 GGTGTGTTTGGG-TAGA-AATCT
1 GGTGTGTTTGGGTTAGACAATCT
11048603 G
1 G
11048604 CGTATCTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.13, C:0.07, G:0.40, T:0.40
Consensus pattern (23 bp):
GGTGTGTTTGGGTTAGACAATCT
Found at i:11051165 original size:25 final size:25
Alignment explanation
Indices: 11051131--11051180 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
11051121 ACATGAAAGT
11051131 AAACTGAAACACCTTGACTATTAGG
1 AAACTGAAACACCTTGACTATTAGG
11051156 AAACTGAAACACCTTGACTATTAGG
1 AAACTGAAACACCTTGACTATTAGG
11051181 CGACTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
AAACTGAAACACCTTGACTATTAGG
Found at i:11054264 original size:29 final size:27
Alignment explanation
Indices: 11054231--11054284 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
11054221 AATAGTTTTA
11054231 ACTCTTGTAAAAATGTACAACTTAATTCT
1 ACTCTTG--AAAATGTACAACTTAATTCT
*
11054260 ACTCTTGAGAATGTACAACTTAATT
1 ACTCTTGAAAATGTACAACTTAATT
11054285 TTGAATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 17 0.71
29 7 0.29
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (27 bp):
ACTCTTGAAAATGTACAACTTAATTCT
Found at i:11062965 original size:113 final size:111
Alignment explanation
Indices: 11062745--11062956 Score: 264
Period size: 113 Copynumber: 1.8 Consensus size: 111
11062735 TAAAAAAAAA
* * * * *
11062745 GGACTGAATTTTAAATACTAAAAAATCACAGGGATTAGAAGAAGAGTTTGACCTATAAACAAAAA
1 GGACTAAATTTTAAATACTAAAAAACCAAAGGGATTAGAAGAAGAGTTTAACCCATAAACAAAAA
* *
11062810 AAATTCAAAGCTCTCCCGCGTTTTCTTTCCTCCATATTAAAAATAGAG
66 AAATTCAAAACTCTCCCGCGTTTTCGTTCCTCCA-A-TAAAAATAGAG
* *
11062858 GGACTAAATTTTAAATATTAAAAAACCAAAGGGATTAGATGAAG-GTTTAAACCCATCAAACAAA
1 GGACTAAATTTTAAATACTAAAAAACCAAAGGGATTAGAAGAAGAGTTT-AACCCAT-AAAC---
11062922 ACAAAAAAATTCAAAACTCTCCCGCGTTTTCGTTC
61 A-AAAAAAATTCAAAACTCTCCCGCGTTTTCGTTC
11062957 TTCAAAAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
112 4 0.05
113 44 0.52
114 4 0.05
117 1 0.01
118 31 0.37
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (111 bp):
GGACTAAATTTTAAATACTAAAAAACCAAAGGGATTAGAAGAAGAGTTTAACCCATAAACAAAAA
AAATTCAAAACTCTCCCGCGTTTTCGTTCCTCCAATAAAAATAGAG
Found at i:11065928 original size:1 final size:1
Alignment explanation
Indices: 11065924--11065948 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11065914 AAGCCCAGGT
11065924 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
11065949 CTAAGCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11071912 original size:23 final size:24
Alignment explanation
Indices: 11071851--11071936 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
11071841 ATTTTATTTT
11071851 TATAT-AAAGAAT-TTTAAAATATAA
1 TATATCAAA-AATATTTAAAATA-AA
11071875 TATATCAAAAATA-TTAAAATAAA
1 TATATCAAAAATATTTAAAATAAA
* * *
11071898 TATTTCCAAACTATTTGAAAATAAA
1 TATATCAAAAATATTT-AAAATAAA
11071923 T-T-T-AAAAATATTTA
1 TATATCAAAAATATTTA
11071937 TACTTAAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.02
22 8 0.15
23 13 0.25
24 19 0.36
25 12 0.23
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (24 bp):
TATATCAAAAATATTTAAAATAAA
Found at i:11072196 original size:23 final size:23
Alignment explanation
Indices: 11072135--11072197 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
11072125 TTAAAAATTA
11072135 TAAAAATATA-AATATTAAAATGG
1 TAAAAATATATAAT-TTAAAATGG
* * ** *
11072158 TAAAATTATAT-TTTTACTATTG
1 TAAAAATATATAATTTAAAATGG
11072180 TAAAAATATATAATTTAA
1 TAAAAATATATAATTTAA
11072198 TTTCAATCCC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAAAATATATAATTTAAAATGG
Found at i:11076258 original size:15 final size:15
Alignment explanation
Indices: 11076240--11076269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11076230 TATTCTATTT
*
11076240 ATATTAGGATAATTA
1 ATATTAAGATAATTA
11076255 ATATTAAGATAATTA
1 ATATTAAGATAATTA
11076270 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:11079062 original size:46 final size:46
Alignment explanation
Indices: 11078998--11079147 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 46
11078988 ACACACTGTA
*
11078998 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
11079044 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
11079097 GCCATAGCCCAGCTATGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCACATTGAT
11079143 GCCAT
1 GCCAT
11079148 GGTCCAACCA
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
46 31 0.36
47 8 0.09
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 27 0.32
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
Found at i:11080295 original size:23 final size:21
Alignment explanation
Indices: 11080228--11080311 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
11080218 TGATCAGAAT
*
11080228 ACGACACATAA-GTGCCTGAA
1 ACGACACACAAGGTGCCTGAA
* *
11080248 ACAACACACGAGGTGCCTGAA
1 ACGACACACAAGGTGCCTGAA
11080269 ACGACACACAAGGTGCCTGAAA
1 ACGACACACAAGGTGCCTG-AA
* *
11080291 TACGACACATAAAGTGCCTGA
1 -ACGACACACAAGGTGCCTGA
11080312 TCAGTATAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 8 0.15
21 26 0.48
22 3 0.06
23 17 0.31
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.13
Consensus pattern (21 bp):
ACGACACACAAGGTGCCTGAA
Found at i:11080548 original size:28 final size:28
Alignment explanation
Indices: 11080516--11080628 Score: 163
Period size: 29 Copynumber: 4.0 Consensus size: 28
11080506 AACACACCAG
* *
11080516 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
11080544 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
* *
11080572 TATAATCTATCCACAACACACCAGAATAA
1 TATAATC-CTCCAAAACACACCAGAATAA
11080601 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
11080629 GCACAAAGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
28 32 0.43
29 43 0.57
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:11080571 original size:23 final size:23
Alignment explanation
Indices: 11080502--11080572 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 23
11080492 AAATGTCCAA
*
11080502 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
11080525 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
11080553 CCCAAACACACCAGAATAAT
1 CCAAAACACACCAGAATAAT
11080573 ATAATCTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 19 0.46
24 1 0.02
28 21 0.51
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:11080592 original size:57 final size:57
Alignment explanation
Indices: 11080516--11080628 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
11080506 AACACACCAG
* * * *
11080516 TATAATCCTCCAAAACACACCAGTATCATATAATCC-TCCCAAACACACCAGAATAA
1 TATAATCATCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATAA
*
11080572 TATAATCTATCCACAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATA
1 TATAATC-ATCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATA
11080629 GCACAAAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
56 7 0.14
57 25 0.50
58 18 0.36
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (57 bp):
TATAATCATCCAAAACACACCAGAATAATATAATCCATCCAAAACACACCAGAATAA
Found at i:11080696 original size:13 final size:13
Alignment explanation
Indices: 11080678--11080725 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
11080668 CATCAGCATA
*
11080678 TCCAAATCTCATC
1 TCCAAATCCCATC
*
11080691 TCCAAATCCCTTC
1 TCCAAATCCCATC
*
11080704 TCCAAATCCCTTC
1 TCCAAATCCCATC
*
11080717 TCAAAATCC
1 TCCAAATCC
11080726 TATGGCATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.42, G:0.00, T:0.29
Consensus pattern (13 bp):
TCCAAATCCCATC
Found at i:11092743 original size:30 final size:31
Alignment explanation
Indices: 11092709--11092768 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
11092699 AGGAATAAGA
*
11092709 TAAATAT-CAAATTT-ATAAATAAATTTTGAT
1 TAAATATGC-AATTTGATAAATAAACTTTGAT
11092739 TAAATATGCAATTTGATAAATAAACTTTGA
1 TAAATATGCAATTTGATAAATAAACTTTGA
11092769 ATTGGTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (31 bp):
TAAATATGCAATTTGATAAATAAACTTTGAT
Found at i:11098086 original size:13 final size:13
Alignment explanation
Indices: 11098068--11098092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11098058 TAGAAGTAAT
11098068 AAGAAATATATAA
1 AAGAAATATATAA
11098081 AAGAAATATATA
1 AAGAAATATATA
11098093 CATACATAAT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAGAAATATATAA
Found at i:11098528 original size:3 final size:3
Alignment explanation
Indices: 11098520--11098570 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
11098510 AATGGATATG
* *
11098520 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA GTTA AT- ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT-A
11098566 ATA AT
1 ATA AT
11098571 GCTACAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.85
4 4 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11100517 original size:16 final size:16
Alignment explanation
Indices: 11100496--11100527 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11100486 CTTCGACATG
11100496 TTCTCAATAAAAGAAA
1 TTCTCAATAAAAGAAA
*
11100512 TTCTCAATAATAGAAA
1 TTCTCAATAAAAGAAA
11100528 AAATAAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (16 bp):
TTCTCAATAAAAGAAA
Found at i:11104704 original size:45 final size:46
Alignment explanation
Indices: 11104565--11104708 Score: 184
Period size: 46 Copynumber: 3.2 Consensus size: 46
11104555 TTTGACATGA
* * * * *
11104565 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGC
*
11104611 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGC
* * *
11104657 TGCCATGGTATCTTTCAACCAT-GTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGC
11104702 TGCCATG
1 TGCCATG
11104709 CCATGGTCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
45 30 0.34
46 57 0.66
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGC
Found at i:11104759 original size:37 final size:37
Alignment explanation
Indices: 11104663--11104772 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 37
11104653 ACGCTGCCAT
11104663 GGTATCTTTCAACCAT-GTCTTACACATTTCATATCA
1 GGTATCTTTCAACCATGGTCTTACACATTTCATATCA
** *
11104699 GG---CTGCCATGCCATGGTCTTACACATTTCATATCA
1 GGTATCTTTCA-ACCATGGTCTTACACATTTCATATCA
11104734 GGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 GGTATCTTTCAACCATGGTCTTACACATTTCATATCA
11104771 GG
1 GG
11104773 AGCACACTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 4 0.06
34 4 0.06
35 22 0.35
36 2 0.03
37 27 0.43
38 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (37 bp):
GGTATCTTTCAACCATGGTCTTACACATTTCATATCA
Found at i:11104871 original size:54 final size:54
Alignment explanation
Indices: 11104804--11104940 Score: 256
Period size: 54 Copynumber: 2.5 Consensus size: 54
11104794 TCCTTACAGT
* *
11104804 GGGATTACTAGTCCAGACTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
11104858 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
11104912 GGGATTACCAGTCCAGGCTAAATCCCCTG
1 GGGATTACCAGTCCAGGCTAAATCCCCTG
11104941 CAACGACAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
Found at i:11106769 original size:21 final size:21
Alignment explanation
Indices: 11106745--11106791 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11106735 AAGCTTCACA
11106745 TCTTTGATTTTCCCTTTTT-TT
1 TCTTT-ATTTTCCCTTTTTCTT
* *
11106766 TCTTTCTTTTCTCTTTTTCTT
1 TCTTTATTTTCCCTTTTTCTT
11106787 TCTTT
1 TCTTT
11106792 CCTTCCCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (21 bp):
TCTTTATTTTCCCTTTTTCTT
Found at i:11106781 original size:20 final size:21
Alignment explanation
Indices: 11106752--11106792 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
11106742 ACATCTTTGA
11106752 TTTTCCCTTTTT-TTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
*
11106772 TTTTCTCTTTTTCTTTCTTTC
1 TTTTCCCTTTTTCTTTCTTTC
11106793 CTTCCCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCCCTTTTTCTTTCTTTC
Found at i:11109254 original size:20 final size:18
Alignment explanation
Indices: 11109229--11109265 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
11109219 ATTGCTAAGT
11109229 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
11109249 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
11109266 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:11109876 original size:47 final size:47
Alignment explanation
Indices: 11109822--11109998 Score: 211
Period size: 47 Copynumber: 3.8 Consensus size: 47
11109812 TGGTTGAGCA
*
11109822 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* * *
11109869 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA--A--CG
* *
11109916 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCG-AACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
* *
11109962 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11109999 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
43 2 0.02
44 5 0.05
45 1 0.01
46 37 0.33
47 58 0.52
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAACG
Found at i:11110466 original size:200 final size:204
Alignment explanation
Indices: 11110225--11110633 Score: 674
Period size: 208 Copynumber: 2.0 Consensus size: 204
11110215 GATCATGAAT
11110225 GAGTAATTTAGCCTGACAGATTTGAGTTACTGCAGTAGTGTAACTTTGAAAATACACT-AAAATA
1 GAGTAATTTAGCCTGACAGATTTGAGTTACTGCAGTAGTGTAACTTTGAAAATACACTAAAAATA
11110289 GTGGAAAATGA-TTAGA-GCAGAAT-A-A-GGTGATTAAAGCTTAATGAG-TATTTTCA-ATGAG
66 GTGGAAAATGAGTTAGAGGCAGAATAATATGG-GATTAAAGCTTAATGAGCTATTTTCACAT--G
11110347 AAAGAAACAGAGAA-AGAAAAGAATTCCATATTATTTGATATTTGAATTCTTGTGAAACAGGGTC
128 AAAGAAACAGAGAAGA-AAAAGAATTCCATATTATTTGATATTTGAATTCTTGTGAAACAGGGTC
11110411 TGAATGAATTCGA
192 TGAATGAATTCGA
11110424 GAGTAATTTAGCCTTGACAGATTTGAGTTACTGCAGTAGTGTAACTTTGAAAATACACTAAAAAT
1 GAGTAATTTAGCC-TGACAGATTTGAGTTACTGCAGTAGTGTAACTTTGAAAATACACTAAAAAT
11110489 AGTGGAAAATGAGTTAGAGGCAGAATAAAATATGGGATTAAAGCTTAATGAGTCTATTTTCACAT
65 AGTGGAAAATGAGTTAGAGGCAGAAT--AATATGGGATTAAAGCTTAATGAG-CTATTTTCACAT
*
11110554 GAAAGAAACAGAGAAGAAAAAGAATTCCATATTGTTTGATATTTGAATTCTTGTGAAACAGGGTC
127 GAAAGAAACAGAGAAGAAAAAGAATTCCATATTATTTGATATTTGAATTCTTGTGAAACAGGGTC
11110619 TGAATGAATTCGA
192 TGAATGAATTCGA
11110632 GA
1 GA
11110634 TCCCCTGTTC
Statistics
Matches: 196, Mismatches: 1, Indels: 17
0.92 0.00 0.08
Matches are distributed among these distances:
199 13 0.07
200 45 0.23
201 17 0.09
202 5 0.03
203 7 0.04
206 1 0.01
207 18 0.09
208 79 0.40
209 9 0.05
210 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (204 bp):
GAGTAATTTAGCCTGACAGATTTGAGTTACTGCAGTAGTGTAACTTTGAAAATACACTAAAAATA
GTGGAAAATGAGTTAGAGGCAGAATAATATGGGATTAAAGCTTAATGAGCTATTTTCACATGAAA
GAAACAGAGAAGAAAAAGAATTCCATATTATTTGATATTTGAATTCTTGTGAAACAGGGTCTGAA
TGAATTCGA
Found at i:11112734 original size:46 final size:45
Alignment explanation
Indices: 11112632--11112801 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 45
11112622 GAGATTTGTG
* * * * *
11112632 TGCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGA
1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* *
11112679 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
* *
11112725 TAGCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-
1 T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA
*
11112770 TGCTAGTGTAAGACATGTCTGGGACATGCATC
1 TGCCAGTGTAAGACATGTCTGGGACATGCATC
11112802 AGCACGGTTA
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
44 28 0.26
45 3 0.03
46 52 0.49
47 12 0.11
48 11 0.10
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (45 bp):
TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:11112793 original size:44 final size:44
Alignment explanation
Indices: 11112681--11112841 Score: 184
Period size: 46 Copynumber: 3.6 Consensus size: 44
11112671 TGAGACGAGG
11112681 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATG-T
* * *
11112726 AGCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGT
1 -GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGT
* *
11112771 GCTAGTGTAAGACATGTCTGGGACATGCATCAGC-ACGGTTACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTAC-G--AGATGT
*
11112817 G-TCAGTGTAAGACCTGTCTGGGACA
1 GCT-AGTGTAAGACATGTCTGGGACA
11112842 CGGCATCGAC
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.02
44 31 0.31
45 4 0.04
46 64 0.63
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGT
Found at i:11119027 original size:26 final size:26
Alignment explanation
Indices: 11118991--11119100 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
11118981 CATGAATTTC
*
11118991 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
11119017 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
11119043 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
11119069 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
11119095 TTATCA
1 TTATCA
11119101 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:11120042 original size:3 final size:3
Alignment explanation
Indices: 11120034--11120219 Score: 72
Period size: 3 Copynumber: 62.3 Consensus size: 3
11120024 TAAAAATGAC
*
11120034 ATA ATA ATA TATA A-A ATA ATT ATA ATA TATA AT- ATA A-A AGT- ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA ATA
* * *
11120078 TATA ATA ATA ATA ATA ATTC GTGA AAA ATA ATA TATA ATAA ATA ATA
1 -ATA ATA ATA ATA ATA A-TA AT-A ATA ATA ATA -ATA AT-A ATA ATA
* *
11120125 AT- ATAA ATA AT- ATA ATT AT- ATA ATT AT- ATA AT- ATA AT- ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * * *
11120165 AAA ATA AGG TTA AAA ATA A-A ACGA ATA ACA AT- ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA
11120210 ATA ATA ATA A
1 ATA ATA ATA A
11120220 ATATATGTAG
Statistics
Matches: 137, Mismatches: 23, Indels: 46
0.67 0.11 0.22
Matches are distributed among these distances:
2 23 0.17
3 91 0.66
4 23 0.17
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11120045 original size:21 final size:19
Alignment explanation
Indices: 11120021--11120138 Score: 77
Period size: 18 Copynumber: 6.2 Consensus size: 19
11120011 ATGTGTGATA
11120021 ATATAAAAATGACATAATAAT
1 ATATAAAAAT-A-ATAATAAT
*
11120042 ATAT-AAAATAATTATAAT
1 ATATAAAAATAATAATAAT
*
11120060 ATAT-AATATAA-AAGT-AT
1 ATATAAAAATAATAA-TAAT
*
11120077 ATATAATAATAATAATAAT
1 ATATAAAAATAATAATAAT
*
11120096 -TCGTGAAAAATAATATATAAT
1 AT-AT-AAAAATAATA-ATAAT
* *
11120117 AAATAATAAT-ATAAATAAT
1 ATATAAAAATAAT-AATAAT
11120136 ATA
1 ATA
11120139 ATTATATAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
17 7 0.09
18 25 0.32
19 15 0.19
20 20 0.26
21 10 0.13
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (19 bp):
ATATAAAAATAATAATAAT
Found at i:11120139 original size:5 final size:5
Alignment explanation
Indices: 11120110--11120165 Score: 61
Period size: 5 Copynumber: 12.2 Consensus size: 5
11120100 GAAAAATAAT
11120110 ATATA ATA-A ATAATA ATATA A-ATA ATATA AT-T- ATATA AT-T- ATATA
1 ATATA ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
11120155 ATATA ATATA A
1 ATATA ATATA A
11120166 AAATAAGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
3 4 0.09
4 11 0.25
5 26 0.59
6 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:11120145 original size:8 final size:8
Alignment explanation
Indices: 11120105--11120156 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
11120095 TTCGTGAAAA
11120105 ATAA-TAT
1 ATAATTAT
*
11120112 ATAA-TAA
1 ATAATTAT
*
11120119 ATAATAAT
1 ATAATTAT
*
11120127 ATAAATAAT
1 AT-AATTAT
11120136 ATAATTAT
1 ATAATTAT
11120144 ATAATTAT
1 ATAATTAT
11120152 ATAAT
1 ATAAT
11120157 ATAATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
7 10 0.26
8 21 0.54
9 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATTAT
Found at i:11120170 original size:8 final size:8
Alignment explanation
Indices: 11120034--11120157 Score: 77
Period size: 7 Copynumber: 15.8 Consensus size: 8
11120024 TAAAAATGAC
11120034 ATAATAAT
1 ATAATAAT
*
11120042 AT-ATAAA
1 ATAATAAT
11120049 ATAAT--T
1 ATAATAAT
11120055 ATAAT-AT
1 ATAATAAT
11120062 ATAAT-AT
1 ATAATAAT
*
11120069 AAAAGTATAT
1 ATAA-TA-AT
11120079 ATAATAAT
1 ATAATAAT
11120087 AATAATAATT
1 -ATAATAA-T
*
11120097 CGTGAA-AA-
1 -AT-AATAAT
11120105 ATAAT-AT
1 ATAATAAT
11120112 ATAATAA-
1 ATAATAAT
11120119 ATAATAAT
1 ATAATAAT
11120127 ATAAATAAT
1 AT-AATAAT
*
11120136 ATAATTAT
1 ATAATAAT
*
11120144 ATAATTAT
1 ATAATAAT
11120152 ATAATA
1 ATAATA
11120158 TAATATAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
6 8 0.09
7 30 0.32
8 28 0.30
9 17 0.18
10 9 0.10
11 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:11130148 original size:15 final size:15
Alignment explanation
Indices: 11130107--11130156 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
11130097 ATAACTTTGA
*
11130107 ATGCAAATG-ATGTG
1 ATGCAAATGTATGAG
11130121 ATG-AAATGCTATGAG
1 ATGCAAATG-TATGAG
11130136 ATGCAAATGTATGA-
1 ATGCAAATGTATGAG
11130150 ATGCAAA
1 ATGCAAA
11130157 AAGAATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 12 0.38
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (15 bp):
ATGCAAATGTATGAG
Found at i:11134165 original size:3 final size:3
Alignment explanation
Indices: 11134157--11134350 Score: 74
Period size: 3 Copynumber: 64.3 Consensus size: 3
11134147 TAAACATGAC
*
11134157 ATA ATA ATA TATA A-A ATA ATT ATA ATA TATA AT- ATA A-A AGTA TATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA -ATA
* *
11134203 TATA ATA ATA ACA TATA AT- ATGT ATA TATA ATTA ATA A-A CAT- ATA
1 -ATA ATA ATA ATA -ATA ATA AT-A ATA -ATA A-TA ATA ATA -ATA ATA
* * *
11134248 AT- ATA ATA ATA AAA ATA ATTC GTA A-A A-A ATA ATA TATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA AT-A ATA
* *
11134293 ATA ATA ATA AT- ATAA ATA AT- ATA ATT AT- ATA ATT AT- ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
11134335 TATA AT- ATA AGA ATA A
1 -ATA ATA ATA ATA ATA A
11134351 GGTTAAAAAT
Statistics
Matches: 149, Mismatches: 15, Indels: 54
0.68 0.07 0.25
Matches are distributed among these distances:
2 27 0.18
3 86 0.58
4 35 0.23
5 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:11134170 original size:21 final size:18
Alignment explanation
Indices: 11134157--11134350 Score: 94
Period size: 20 Copynumber: 10.4 Consensus size: 18
11134147 TAAACATGAC
11134157 ATAATAATATATAAAATA
1 ATAATAATATATAAAATA
* *
11134175 ATTATAATATATAATATA
1 ATAATAATATATAAAATA
11134193 A-AAGTATATATATAATAATA
1 ATAA-TA-ATATATAA-AATA
* * *
11134213 ACATATAATATGTATATATA
1 ATA-ATAATATATA-AAATA
* *
11134233 ATTAATAAACATATAATATA
1 A-TAAT-AATATATAAAATA
* **
11134253 ATAATAA-AAATAATTCGTAA
1 ATAATAATATATAA--AAT-A
*
11134273 AAAATAATATATAATAAATA
1 ATAATAATATAT-A-AAATA
11134293 ATAATAATA-ATATAAATA
1 ATAATAATATATA-AAATA
* *
11134311 AT-ATAAT-TATATAATT
1 ATAATAATATATAAAATA
*
11134327 AT-ATAATATATAATATA
1 ATAATAATATATAAAATA
*
11134344 AGAATAA
1 ATAATAA
11134351 GGTTAAAAAT
Statistics
Matches: 136, Mismatches: 23, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
16 10 0.07
17 21 0.15
18 34 0.25
19 15 0.11
20 38 0.28
21 15 0.11
22 2 0.01
23 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATAATATATAAAATA
Found at i:11134188 original size:28 final size:28
Alignment explanation
Indices: 11134157--11134341 Score: 76
Period size: 32 Copynumber: 6.2 Consensus size: 28
11134147 TAAACATGAC
11134157 ATAATAATATATAAAATAATTATAATAT
1 ATAATAATATATAAAATAATTATAATAT
* * * *
11134185 ATAATATAAAAGTATATATATAATAATAACAT
1 AT-A-ATAATA-TATA-AAATAATTATAATAT
* * *
11134217 ATAAT-ATGTAT-ATATAATTAATAAACAT
1 ATAATAATATATAAAATAATT-AT-AATAT
*
11134245 ATAAT-ATAATAATAAAAATAATTCGTAA-A-
1 ATAATAAT-AT-AT-AAAATAATT-ATAATAT
*
11134274 A-AATAATATATAATAAATAATAATAATAAT
1 ATAATAATATAT-A-AAATAATTATAAT-AT
* *
11134304 ATAAATAATATAATTATATAATTATATAATAT
1 AT-AATAATAT-ATAAAATAATTAT--AATAT
11134336 ATAATA
1 ATAATA
11134342 TAAGAATAAG
Statistics
Matches: 121, Mismatches: 16, Indels: 37
0.70 0.09 0.21
Matches are distributed among these distances:
26 7 0.06
27 9 0.07
28 29 0.24
29 7 0.06
30 11 0.09
31 19 0.16
32 34 0.28
33 5 0.04
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
ATAATAATATATAAAATAATTATAATAT
Found at i:11134228 original size:26 final size:28
Alignment explanation
Indices: 11134199--11134251 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
11134189 TATAAAAGTA
11134199 TATATATAA-TAAT-AACATATAATATG
1 TATATATAATTAATAAACATATAATATG
11134225 TATATATAATTAATAAACATATAATAT
1 TATATATAATTAATAAACATATAATAT
11134252 AATAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 12 0.48
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
TATATATAATTAATAAACATATAATATG
Found at i:11134239 original size:30 final size:26
Alignment explanation
Indices: 11134188--11134251 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 26
11134178 ATAATATATA
*
11134188 ATATAA-AAGTATATATATAATAATAAC
1 ATATAATATGTATATATATAAT-A-AAC
11134215 ATATAATATGTATATATAATTAATAAAC
1 ATATAATATGTATATAT-A-TAATAAAC
11134243 ATATAATAT
1 ATATAATAT
11134252 AATAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 6 0.18
28 21 0.64
29 2 0.06
30 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (26 bp):
ATATAATATGTATATATATAATAAAC
Found at i:11134282 original size:91 final size:89
Alignment explanation
Indices: 11134160--11134350 Score: 210
Period size: 91 Copynumber: 2.1 Consensus size: 89
11134150 ACATGACATA
* * *
11134160 ATAAT-ATATAAAATAATTATAATATATAATATAAAAGTATATATATAATAATAACAT-ATAATA
1 ATAATAATA-AAAATAATTATAAAAAATAATATAAAA-TAAATA-ATAATAATAACATAATAATA
*
11134223 T-GTATATATAATTA-ATAAACATATAAT
63 TAAT-TATATAATTATAT-AACATATAAT
* * *
11134250 ATAATAATAAAAATAATTCGTAAAAAATAATATATAATAAATAATAATAATAATATAAATAATAT
1 ATAATAATAAAAATAATT-ATAAAAAATAATATAAAATAAATAATAATAATAACAT-AATAATAT
*
11134315 AATTATATAATTATATAATATATAAT
64 AATTATATAATTATATAACATATAAT
*
11134341 ATAAGAATAA
1 ATAATAATAA
11134351 GGTTAAAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
89 12 0.14
90 19 0.22
91 52 0.60
92 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (89 bp):
ATAATAATAAAAATAATTATAAAAAATAATATAAAATAAATAATAATAATAACATAATAATATAA
TTATATAATTATATAACATATAAT
Found at i:11134340 original size:43 final size:43
Alignment explanation
Indices: 11134160--11134349 Score: 138
Period size: 46 Copynumber: 4.2 Consensus size: 43
11134150 ACATGACATA
*
11134160 ATAAT-ATATAAAATAATTATAATATATAATATAAAAGTATATAT
1 ATAATAATAT-AAATAATTATAATATATAATATATAA-TATATAT
* *
11134204 ATAATAATA-ACATATAA-TATGTATATATAAT-TAATAAACATATAAT
1 ATAATAATATA-A-ATAATTAT-AATATATAATAT-AT-AATATAT-AT
* * * * *
11134250 ATAATAATAAAAATAATTCGTAAAAAATAATATATAATAAATAAT
1 ATAATAATATAAATAATT-ATAATATATAATATATAATATAT-AT
11134295 AATAATAATATAAATAA-TATAATTATATAATTATATAATATATAAT
1 -ATAATAATATAAATAATTATAA-TATATAA-TATATAATATAT-AT
*
11134341 ATAAGAATA
1 ATAATAATA
11134350 AGGTTAAAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 13 0.11
45 47 0.40
46 53 0.45
47 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (43 bp):
ATAATAATATAAATAATTATAATATATAATATATAATATATAT
Found at i:11134344 original size:28 final size:25
Alignment explanation
Indices: 11134158--11134343 Score: 129
Period size: 26 Copynumber: 7.4 Consensus size: 25
11134148 AAACATGACA
*
11134158 TAATAATATATAAAATAAT-TATAA
1 TAATAATATATAATATAATATATAA
*
11134182 TATATAATATAAAAGTAT-ATATATAA
1 TA-ATAATATATAA-TATAATATATAA
* *
11134208 TAATAACATATAATATGTATATATAA
1 TAATAATATATAATAT-AATATATAA
*
11134234 TTAATAAACATATAATATAATA-ATAA
1 -TAAT-AATATATAATATAATATATAA
* * * *
11134260 AAATAATTCGTAAAAAATAATATATAA
1 TAATAA-T-ATATAATATAATATATAA
11134287 T-A-AATA-ATAATAATAATATA-AA
1 TAATAATATATAAT-ATAATATATAA
*
11134309 TAAT-ATA-ATTATATAATTATATAA
1 TAATAATATATAATATAA-TATATAA
11134333 TATATAATATA
1 TA-ATAATATA
11134344 AGAATAAGGT
Statistics
Matches: 129, Mismatches: 15, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
22 10 0.08
23 20 0.16
24 12 0.09
25 28 0.22
26 35 0.27
27 12 0.09
28 12 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
TAATAATATATAATATAATATATAA
Found at i:11139408 original size:37 final size:37
Alignment explanation
Indices: 11139358--11139430 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
11139348 AAAGAGAATG
11139358 GCTCTTGTTGGATGGGATTCAGTGTGCCAACCTAAAA
1 GCTCTTGTTGGATGGGATTCAGTGTGCCAACCTAAAA
11139395 GCTCTTGTTGGATGGGATTCAGTGTGCCAACCTAAA
1 GCTCTTGTTGGATGGGATTCAGTGTGCCAACCTAAA
11139431 GCTAATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (37 bp):
GCTCTTGTTGGATGGGATTCAGTGTGCCAACCTAAAA
Found at i:11142513 original size:34 final size:34
Alignment explanation
Indices: 11142456--11142531 Score: 118
Period size: 34 Copynumber: 2.3 Consensus size: 34
11142446 TAAATTTTAA
*
11142456 GACAAAA-TTACCTTTTGCACGAAATAGAGTGGT
1 GACAAAAGTTACCTTTTACACGAAATAGAGTGGT
* *
11142489 GACAAAAGTTGCCTTTTACTCGAAATAGAGTGGT
1 GACAAAAGTTACCTTTTACACGAAATAGAGTGGT
11142523 GACAAAAGT
1 GACAAAAGT
11142532 GGAATGCTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 7 0.18
34 32 0.82
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (34 bp):
GACAAAAGTTACCTTTTACACGAAATAGAGTGGT
Found at i:11146727 original size:29 final size:29
Alignment explanation
Indices: 11146694--11146824 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 29
11146684 GTGACGAGAT
11146694 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
11146723 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
11146752 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
11146781 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
11146810 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
11146825 GAAATCGAGT
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.02
29 79 0.96
30 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:11154862 original size:29 final size:29
Alignment explanation
Indices: 11154829--11154959 Score: 122
Period size: 29 Copynumber: 4.5 Consensus size: 29
11154819 GTGACGAGAT
11154829 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
11154858 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
11154887 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
11154916 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
11154945 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
11154960 GAAATCGAGT
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
28 2 0.02
29 79 0.96
30 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:11160115 original size:19 final size:19
Alignment explanation
Indices: 11160052--11160116 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 19
11160042 TATACCTTTT
11160052 TTTTTAAATTTC-ATAACTAA
1 TTTTTAAATTTCTATAA--AA
*
11160072 TTTTATATATTT-TAATTATAAA
1 TTTT-TAAATTTCT-A-TA-AAA
11160094 TTTTTAAATTTCTATAAAA
1 TTTTTAAATTTCTATAAAA
11160113 TTTT
1 TTTT
11160117 ATAAGATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 7 0.19
20 6 0.16
21 13 0.35
22 8 0.22
23 2 0.05
24 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTAAATTTCTATAAAA
Found at i:11163175 original size:28 final size:26
Alignment explanation
Indices: 11163120--11163207 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
11163110 AGCATGGCTG
* *
11163120 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
11163146 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
11163174 CCAGAACAGATATATGTGGTATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
11163201 CCAGAAC
1 CCAGAAC
11163208 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 5 0.09
27 31 0.58
28 17 0.32
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:11164860 original size:26 final size:25
Alignment explanation
Indices: 11164824--11164907 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
11164814 CATGAAATTC
11164824 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAAC-CA
11164850 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
*
11164876 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACC-A
11164902 TTATCA
1 TTATCA
11164908 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
25 2 0.04
26 52 0.95
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:11166226 original size:56 final size:57
Alignment explanation
Indices: 11166154--11166262 Score: 184
Period size: 56 Copynumber: 1.9 Consensus size: 57
11166144 CATGTACCTT
*
11166154 AATGCTCACACAGAGCTATGACAGTCCACAACATATGCGGAA-TACTACCAATCCTC
1 AATGCTCACACAGAGCTACGACAGTCCACAACATATGCGGAATTACTACCAATCCTC
* *
11166210 AATGCTCACACAGAGCTACGATAGTCCACAACATATGTGGAATTACTACCAAT
1 AATGCTCACACAGAGCTACGACAGTCCACAACATATGCGGAATTACTACCAAT
11166263 TACTATACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
56 39 0.80
57 10 0.20
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.21
Consensus pattern (57 bp):
AATGCTCACACAGAGCTACGACAGTCCACAACATATGCGGAATTACTACCAATCCTC
Found at i:11166347 original size:126 final size:125
Alignment explanation
Indices: 11166117--11166396 Score: 425
Period size: 126 Copynumber: 2.2 Consensus size: 125
11166107 GGGCAATTCG
* *
11166117 TATGCGGAATTACTACCAATTACTATACATGTACCTTAATGCTCACACAGAGCTATGACAGTCCA
1 TATGTGGAATTACTACCAATTACTATACATGTACCTTAATGCTCACACAGAGCTACGACAGTCCA
* *
11166182 CAACATATGCGGAATACTACCAATCCTCAATGCTCACACAGAGCTACGATAGTCCACAAC
66 CAACATATGCAGAATACTACCAATCCTCAATGCTCACACAGAGCTACGACAGTCCACAAC
* **
11166242 ATATGTGGAATTACTACCAATTACTATACATGTACCTTGATGCTCACACAGAGCTACGGTAGTCC
1 -TATGTGGAATTACTACCAATTACTATACATGTACCTTAATGCTCACACAGAGCTACGACAGTCC
* * * * *
11166307 ACAACATATGCAGAATACTACCAATCCTCGATGCTCACACAGAGCTATGGCAGTTCGCAAC
65 ACAACATATGCAGAATACTACCAATCCTCAATGCTCACACAGAGCTACGACAGTCCACAAC
*
11166368 TCATGTGGTATTACTACCAATTACTATAC
1 T-ATGTGGAATTACTACCAATTACTATAC
11166397 CCATGGAACT
Statistics
Matches: 140, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
125 1 0.01
126 139 0.99
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (125 bp):
TATGTGGAATTACTACCAATTACTATACATGTACCTTAATGCTCACACAGAGCTACGACAGTCCA
CAACATATGCAGAATACTACCAATCCTCAATGCTCACACAGAGCTACGACAGTCCACAAC
Found at i:11167331 original size:3 final size:3
Alignment explanation
Indices: 11167323--11167504 Score: 109
Period size: 3 Copynumber: 62.0 Consensus size: 3
11167313 GTTTTATATT
*
11167323 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * * *
11167369 TTA TTA TAA T-A TTA TAA T-A TTA TAA T-A TAA T-A TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
11167412 TAT TATA TATT TTA TCAT TAA GTAA TAA TAA -AA T-G TACA TAA TAA
1 TAA TA-A TA-A TAA T-AA TAA -TAA TAA TAA TAA TAA TA-A TAA TAA
*
11167457 TAA -AA TAA TAA -AA T-A TAA TAA T-A TAA TAA T-C TAA TAA TCCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T--AA
11167499 TAA TAA
1 TAA TAA
11167505 AATCTATGAT
Statistics
Matches: 144, Mismatches: 16, Indels: 38
0.73 0.08 0.19
Matches are distributed among these distances:
2 22 0.15
3 107 0.74
4 12 0.08
5 3 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:11167383 original size:8 final size:8
Alignment explanation
Indices: 11167370--11167422 Score: 72
Period size: 8 Copynumber: 6.5 Consensus size: 8
11167360 AATATATTAT
11167370 TATTATAA
1 TATTATAA
11167378 TATTATAA
1 TATTATAA
11167386 TATTATAA
1 TATTATAA
11167394 TATAATATAA
1 TAT--TATAA
*
11167404 TATAATAA
1 TATTATAA
11167412 TATTAT-A
1 TATTATAA
11167419 TATT
1 TATT
11167423 TTATCATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
7 5 0.12
8 28 0.68
10 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATTATAA
Found at i:11167508 original size:21 final size:19
Alignment explanation
Indices: 11167454--11167510 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
11167444 ATGTACATAA
*
11167454 TAATAA-AATAATAAAATA
1 TAATAATAATAATAAAATC
11167472 TAATAAT-ATAAT--AATC
1 TAATAATAATAATAAAATC
11167488 TAATAATCCAATAATAAAATC
1 TAATAAT--AATAATAAAATC
11167509 TA
1 TA
11167511 TGATTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 10 0.31
18 11 0.34
19 5 0.16
21 6 0.19
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAATAATAATAAAATC
Found at i:11167581 original size:29 final size:29
Alignment explanation
Indices: 11167538--11167595 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
11167528 GCCGCCTCTA
11167538 CTTTTTTTATCGGCATAATTTCCTATTTG
1 CTTTTTTTATCGGCATAATTTCCTATTTG
*
11167567 CTTTTTTTATTGGCATAATTTCCTATTTG
1 CTTTTTTTATCGGCATAATTTCCTATTTG
11167596 GTCCTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.16, G:0.10, T:0.57
Consensus pattern (29 bp):
CTTTTTTTATCGGCATAATTTCCTATTTG
Found at i:11167603 original size:29 final size:29
Alignment explanation
Indices: 11167542--11167604 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
11167532 CCTCTACTTT
**
11167542 TTTTATCGGCATAATTTCCTATTTGCTTT
1 TTTTATCGGCATAATTTCCTATTTGCTCC
* *
11167571 TTTTATTGGCATAATTTCCTATTTGGTCC
1 TTTTATCGGCATAATTTCCTATTTGCTCC
11167600 TTTTA
1 TTTTA
11167605 ACTTTCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.16, G:0.11, T:0.56
Consensus pattern (29 bp):
TTTTATCGGCATAATTTCCTATTTGCTCC
Found at i:11171042 original size:28 final size:28
Alignment explanation
Indices: 11171010--11171067 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
11171000 TATCTTATCA
11171010 GATTCAACATGGAGCAATTCACCATTCT
1 GATTCAACATGGAGCAATTCACCATTCT
*
11171038 GATTCAACATGGAGTAATTCACCATTCT
1 GATTCAACATGGAGCAATTCACCATTCT
11171066 GA
1 GA
11171068 CATTTTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (28 bp):
GATTCAACATGGAGCAATTCACCATTCT
Found at i:11171159 original size:9 final size:9
Alignment explanation
Indices: 11171145--11171178 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
11171135 CCAAAAATCA
11171145 CATCAAATT
1 CATCAAATT
11171154 CATCAAATT
1 CATCAAATT
*
11171163 TATCAAATT
1 CATCAAATT
11171172 CATCAAA
1 CATCAAA
11171179 AGGAAATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (9 bp):
CATCAAATT
Found at i:11173931 original size:20 final size:20
Alignment explanation
Indices: 11173908--11173945 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11173898 TTAAATTCCA
*
11173908 AAAGATAAATACAAATAATT
1 AAAGATAAATAAAAATAATT
11173928 AAAGATAAATAAAAATAA
1 AAAGATAAATAAAAATAA
11173946 ATCCTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAGATAAATAAAAATAATT
Found at i:11175228 original size:56 final size:56
Alignment explanation
Indices: 11175138--11175306 Score: 239
Period size: 56 Copynumber: 3.0 Consensus size: 56
11175128 TATACATGTA
* *
11175138 CCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGCGGAATATTATCAAT
1 CCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGCGGAATACTACCAAT
* * * *
11175194 CCTTGATGCTTACACGGAGCTACGGTAGTGCACAACATATGCGGAATACTACCAAT
1 CCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGCGGAATACTACCAAT
* * * *
11175250 CCTCGATGCTCACACAGAGCTACGGTAGTCCGCAACTTATGCTGTATTACTACCAAT
1 CCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGC-GGAATACTACCAAT
11175307 TACTATACTC
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
56 86 0.88
57 12 0.12
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (56 bp):
CCTCGATGCTCACACAGAGCTACGGTAGTCCACAACATATGCGGAATACTACCAAT
Found at i:11176256 original size:3 final size:3
Alignment explanation
Indices: 11176248--11176297 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
11176238 GTTTTATATT
*
11176248 TAA TAA TAA TATA TTA TAA T-A TAA TAA T-A TAA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11176291 T-A TAA TA
1 TAA TAA TA
11176298 CTATTCTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 30 0.75
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:11176267 original size:16 final size:16
Alignment explanation
Indices: 11176242--11176297 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
11176232 TACTTTGTTT
11176242 TATATT-TAATAATAA
1 TATATTATAATAATAA
11176257 TATATTATAAT-ATAA
1 TATATTATAATAATAA
11176272 TA-A-TATAATAAT-A
1 TATATTATAATAATAA
*
11176285 TAATAATATAATA
1 T-ATATTATAATA
11176298 CTATTCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.22
14 4 0.11
15 13 0.36
16 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATTATAATAATAA
Found at i:11176274 original size:8 final size:8
Alignment explanation
Indices: 11176250--11176297 Score: 78
Period size: 8 Copynumber: 5.8 Consensus size: 8
11176240 TTTATATTTA
11176250 ATAATAAT
1 ATAATAAT
11176258 ATATTATAAT
1 ATA--ATAAT
11176268 ATAATAAT
1 ATAATAAT
11176276 ATAATAAT
1 ATAATAAT
11176284 ATAATAAT
1 ATAATAAT
11176292 ATAATA
1 ATAATA
11176298 CTATTCTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 30 0.79
10 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:11181002 original size:29 final size:28
Alignment explanation
Indices: 11180982--11181060 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
11180972 GGATTTTGCG
11180982 AGCCTACATGCGAACCTTAGGTACATGCA
1 AGCCTACATGCGAACC-TAGGTACATGCA
*
11181011 AGCCTACATGCGAACCCTAGGTACATGCG
1 AGCCTACATGCGAA-CCTAGGTACATGCA
* *
11181040 AGCCTACTTGCAAACCCTAGG
1 AGCCTACATGCGAA-CCTAGG
11181061 AACTTATGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (28 bp):
AGCCTACATGCGAACCTAGGTACATGCA
Found at i:11181040 original size:58 final size:57
Alignment explanation
Indices: 11180978--11181108 Score: 138
Period size: 58 Copynumber: 2.3 Consensus size: 57
11180968 CCTAGGATTT
* * * * * *
11180978 TGCGAGCCTACATGCGAACCTTAGGTAC-ATGCAAGCCTACATGCGAACCCTAGGTACA
1 TGCGAGCCTACATGCAAACCCTAGGAACTATG--AGCCTACATACGAACCCTAGGAAAA
* * *
11181036 TGCGAGCCTACTTGCAAACCCTAGGAACTTATGAGCCTATATATGAACCCTAGGAAAA
1 TGCGAGCCTACATGCAAACCCTAGGAAC-TATGAGCCTACATACGAACCCTAGGAAAA
*
11181094 TGCGAGCCTATATGC
1 TGCGAGCCTACATGC
11181109 CATGTGAACC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 57 0.95
60 3 0.05
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (57 bp):
TGCGAGCCTACATGCAAACCCTAGGAACTATGAGCCTACATACGAACCCTAGGAAAA
Found at i:11181071 original size:29 final size:29
Alignment explanation
Indices: 11180980--11181108 Score: 96
Period size: 29 Copynumber: 4.4 Consensus size: 29
11180970 TAGGATTTTG
* * * *
11180980 CGAGCCTACATGCGAACCTTAGGTACATG
1 CGAGCCTACATGCAAACCCTAGGAACATA
* * * *
11181009 CAAGCCTACATGCGAACCCTAGGTACATG
1 CGAGCCTACATGCAAACCCTAGGAACATA
* *
11181038 CGAGCCTACTTGCAAACCCTAGGAACTTA
1 CGAGCCTACATGCAAACCCTAGGAACATA
* * *** * *
11181067 TGAGCCTATATATGAACCCTAGGAAAATG
1 CGAGCCTACATGCAAACCCTAGGAACATA
*
11181096 CGAGCCTATATGC
1 CGAGCCTACATGC
11181109 CATGTGAACC
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (29 bp):
CGAGCCTACATGCAAACCCTAGGAACATA
Found at i:11181131 original size:17 final size:17
Alignment explanation
Indices: 11181109--11181158 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
11181099 GCCTATATGC
11181109 CATGTGAACCATAGGAA
1 CATGTGAACCATAGGAA
11181126 CATGTGAACCATAGGAA
1 CATGTGAACCATAGGAA
*
11181143 CATGTGAACCCTAGGA
1 CATGTGAACCATAGGA
11181159 CTGTGTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (17 bp):
CATGTGAACCATAGGAA
Found at i:11183663 original size:4 final size:4
Alignment explanation
Indices: 11183654--11183678 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11183644 TTTTCCTTTA
11183654 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
11183679 CCTTATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:11183746 original size:3 final size:3
Alignment explanation
Indices: 11183738--11183832 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
11183728 TTATAGCCCC
11183738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11183786 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11183833 ATGTTTTGAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11187722 original size:19 final size:19
Alignment explanation
Indices: 11187698--11187744 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
11187688 TGACGCGTTT
11187698 TTTGCATT-CATCCCATACA
1 TTTGCATTACATCCCAT-CA
*
11187717 TTTGCATTACATCGCATCA
1 TTTGCATTACATCCCATCA
*
11187736 TATGCATTA
1 TTTGCATTA
11187745 AATTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (19 bp):
TTTGCATTACATCCCATCA
Found at i:11195942 original size:44 final size:44
Alignment explanation
Indices: 11195835--11196585 Score: 381
Period size: 44 Copynumber: 16.6 Consensus size: 44
11195825 TAATGGCGAG
* * *
11195835 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAA-ATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCTA-CAAA
* * *
11195880 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * *
11195924 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * *
11195968 TCTTATCTCCCTGAAGTTGCAGTGGAACAAACTAAAGATAGCGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAA
* * * **
11196013 TCTTATTTACCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT----A---CAAA
* * * * * * *
11196064 TCTTATCTCCCTAAAGTTACAGTGGAGTAAATTGAAGTTACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * ** *
11196108 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAA
** * * * *
11196153 TCTTATCTCTTTGAAGTTACAATAGAGCAGATTAAAG---CAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * * * *
11196194 -CCT-TCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGTTATAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * *
11196236 TCTTATCTCCCTGAAGCTGTAGTGGAGCAGATTAAAACCT-CTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAA
*** * * * * *
11196280 TCTTATCTCCCTGAAAACGCAGTGGAGTAGGTTGAAA-CGATAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAA
* * * * * *
11196324 TCCTATAC-CTCTGAAGTTGTAGTAGG-TC-GAATCAAATCTACCATGGCAA
1 TCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAG-ATTAAAGCTA-CA----AA
* * *
11196373 GTCTTATCTCCCTGAAGTTGCAGTGGAATAGACTAAAGCTACAGGCTACAAA
1 -TCTTATCTCCCTGAAGTTGCAGTGG---AG-C-AGA-TTA-AAGCTACAAA
** *
11196425 TCTTATCTCCCTGAAGTTGCAGCAGAGCAGATTAAAGCTACGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * * * **
11196469 CCTTATCTCCTTGAAGTTACAATGGAACAGGTTAAAAATCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-ACAAA
* * * * * *
11196514 TCTCATCTCCCTAAAGTTGCAGCGGAGCAGATTGAAGCTACGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
*
11196558 TCTTATCTCCCTGAAGTGGCATGTGGAG
1 TCTTATCTCCCTGAAGTTGCA-GTGGAG
11196586 TGGATCGAAG
Statistics
Matches: 521, Mismatches: 147, Indels: 76
0.70 0.20 0.10
Matches are distributed among these distances:
39 23 0.04
40 2 0.00
41 3 0.01
42 2 0.00
43 7 0.01
44 245 0.47
45 142 0.27
46 2 0.00
47 2 0.00
48 2 0.00
49 5 0.01
50 18 0.03
51 57 0.11
52 2 0.00
54 1 0.00
55 1 0.00
56 3 0.01
57 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
Found at i:11195943 original size:89 final size:88
Alignment explanation
Indices: 11195835--11196586 Score: 433
Period size: 89 Copynumber: 8.3 Consensus size: 88
11195825 TAATGGCGAG
* * * *
11195835 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAATAGCAAATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATA-CAAATCTTATCTCCCTGAAGTTGC
*
11195900 AGTAGAGCAGATTAAAGCTATAAA
65 AGTAGAGCAGATTAAAGCTACAAA
* * * ** *
11195924 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATACAAATCTTATCTCCCTGAAGTTGCA
* * * * * *
11195989 GTGGAACAAACTAAAGATAGCGAA
66 GTAGAGCAGATTAAAGCTA-CAAA
* * * * * *
11196013 TCTTATTTACCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTGCAAATCTTATCTCCCTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATT---G--A-AAA-TACAAATCTTATCTCCCTGA
* * * * * * *
11196078 AGTTACAGTGGAGTAAATTGAAGTTACAGA
59 AGTTGCAGTAGAGCAGATTAAAGCTACAAA
* * * ** *
11196108 TCTTATCTCCCTGAAGTTGCAGTAGAGTAGATCGAAGATAGCAAATCTTATCTCTTTGAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATA-CAAATCTTATCTCCCTGAAGTTGC
* *
11196173 AATAGAGCAGATTAAAG---CAGA
65 AGTAGAGCAGATTAAAGCTACAAA
* * * ** * * *
11196194 -CCT-TCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGTTATAAATCTTATCTCCCTGAAGCTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATACAAATCTTATCTCCCTGAAGTTGCA
* * *
11196257 GTGGAGCAGATTAAAACCT-CTAA
66 GTAGAGCAGATT-AAAGCTACAAA
*** * ** * * * * *
11196280 TCTTATCTCCCTGAAAACGCAGTGGAGTAGGTTGAAACGATAAGTCCTATAC-CTCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATACAAATCTTAT-CTCCCTGAAGTTGC
* *
11196344 AGTAG-GTC-GAATCAAATCTACCATGGCAA
65 AGTAGAG-CAG-ATTAAAGCTA-CA----AA
* * *
11196373 GTCTTATCTCCCTGAAGTTGCAGTGGAATAGACTAAAGCTACAGGCTACAAATCTTATCTCCCTG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAA---A-A---TACAAATCTTATCTCCCTG
* *
11196438 AAGTTGCAGCAGAGCAGATTAAAGCTACGAA
58 AAGTTGCAGTAGAGCAGATTAAAGCTACAAA
* * * * ** * * * *
11196469 CCTTATCTCCTTGAAGTTACAATGGAACAGGTTAAAAATCACAAATCTCATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAAT-ACAAATCTTATCTCCCTGAAGTTGC
** * * *
11196534 AGCGGAGCAGATTGAAGCTACGAG
65 AGTAGAGCAGATTAAAGCTACAAA
*
11196558 TCTTATCTCCCTGAAGTGGCATGTGGAGT
1 TCTTATCTCCCTGAAGTTGCA-GTGGAGT
11196587 GGATCGAAGC
Statistics
Matches: 506, Mismatches: 121, Indels: 71
0.72 0.17 0.10
Matches are distributed among these distances:
83 29 0.06
84 33 0.07
85 2 0.00
86 6 0.01
87 9 0.02
88 92 0.18
89 160 0.32
90 5 0.01
91 1 0.00
92 3 0.01
93 2 0.00
94 30 0.06
95 59 0.12
96 39 0.08
97 1 0.00
100 2 0.00
101 31 0.06
102 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAAATACAAATCTTATCTCCCTGAAGTTGCA
GTAGAGCAGATTAAAGCTACAAA
Found at i:11196119 original size:140 final size:133
Alignment explanation
Indices: 11195833--11196261 Score: 399
Period size: 140 Copynumber: 3.2 Consensus size: 133
11195823 CATAATGGCG
* * *
11195833 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAAATAGCAAATCTTATCTCTCTGAAGTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAAACTGAAAATAGCAAATCTTATCTCTCTGAAGTT
* * * **
11195898 GCAGTAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTT
66 GCAGTAGAACAGATTAAAGCTATAAACCTTATCTCCCTAAAGTTACAGTGGAGCAAATTGAAGTT
11195963 ACA
131 ACA
* *
11195966 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAAACT-AAAGATAGCGAATCTTATTTAC-CTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAAACTGAAA-ATAGCAAATCTTATCT-CTCTGAAG
* * * * *
11196029 TTGTAGTGGAATAGATTAAAGCTACAAATTGCAAATCTTATCTCCCTAAAGTTACAGTGGAGTAA
64 TTGCAGTAGAACAGATTAAAGCT----A-T--AAACCTTATCTCCCTAAAGTTACAGTGGAGCAA
11196094 ATTGAAGTTAC-
122 ATTGAAGTTACA
* ** * * *
11196105 AGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-TCGAAGATAGCAAATCTTATCTCTTTGAAG
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAACAAACT-GAAAATAGCAAATCTTATCTCTCTGAAG
* * * * * * **
11196169 TTACAATAGAGCAGATTAAAGC---AGACC-T-TCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAG
64 TTGCAGTAGAACAGATTAAAGCTATAAACCTTATCTCCCTAAAGTTACAGTGGAGCAAATTGAAG
*
11196229 TTATA
129 TTACA
* * *
11196234 AATCTTATCTCCCTGAAGCTGTAGTGGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGA
11196262 GCAGATTAAA
Statistics
Matches: 243, Mismatches: 39, Indels: 33
0.77 0.12 0.10
Matches are distributed among these distances:
128 55 0.23
129 2 0.01
130 3 0.01
132 3 0.01
133 71 0.29
134 1 0.00
137 1 0.00
138 1 0.00
139 4 0.02
140 100 0.41
141 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (133 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAACAAACTGAAAATAGCAAATCTTATCTCTCTGAAGTT
GCAGTAGAACAGATTAAAGCTATAAACCTTATCTCCCTAAAGTTACAGTGGAGCAAATTGAAGTT
ACA
Found at i:11196153 original size:96 final size:96
Alignment explanation
Indices: 11195968--11196153 Score: 205
Period size: 96 Copynumber: 1.9 Consensus size: 96
11195958 AAGTTACAAG
* * * *
11195968 TCTTATCTCCCTGAAGTTGCAGTGGAACAAACTAAAGATAGCGAATCTTATTTACCTGAAGTTGT
1 TCTTATCTCCCTAAAGTTACAGTGGAACAAACTAAAGATAGCGAATCTTATCTACCTGAAGTTGC
* * *
11196033 AGTGGAATAGATTAAAGCTACAAATTGCAAA
66 AGTAGAATAGATCAAAGATACAAATTGCAAA
** * * * *
11196064 TCTTATCTCCCTAAAGTTACAGTGGAGTAAATTGAAGTTA-C-AGATCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTAAAGTTACAGTGGAACAAACTAAAGATAGCGA-ATCTTATCTACCTGAAGTTG
* *
11196127 CAGTAGAGTAGATCGAAGATAGCAAAT
65 CAGTAGAATAGATCAAAGATA-CAAAT
11196154 CTTATCTCTT
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
94 1 0.01
95 34 0.47
96 38 0.52
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (96 bp):
TCTTATCTCCCTAAAGTTACAGTGGAACAAACTAAAGATAGCGAATCTTATCTACCTGAAGTTGC
AGTAGAATAGATCAAAGATACAAATTGCAAA
Found at i:11196265 original size:83 final size:84
Alignment explanation
Indices: 11196113--11196271 Score: 194
Period size: 83 Copynumber: 1.9 Consensus size: 84
11196103 ACAGATCTTA
* ** *
11196113 TCTCCCTGAAGTTGCAGTAGAGTAGATCGAAGATAGCAAATCTTATCTCTTTGAAGTTACAATAG
1 TCTCCCTAAAGTTGCAGTAGAGTAGATCGAAGATAGCAAATCTTATCTCCCTGAAGCTACAATAG
11196178 AGCAGATTAAAGCAGACCT
66 AGCAGATTAAAGCAGACCT
* * * * * ** * *
11196197 TCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGTTA-TAAATCTTATCTCCCTGAAGCTGTAGTGG
1 TCTCCCTAAAGTTGCAGTAGAGTAGATCGAAGATAGCAAATCTTATCTCCCTGAAGCTACAATAG
11196261 AGCAGATTAAA
66 AGCAGATTAAA
11196272 ACCTCTAATC
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
83 32 0.52
84 30 0.48
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (84 bp):
TCTCCCTAAAGTTGCAGTAGAGTAGATCGAAGATAGCAAATCTTATCTCCCTGAAGCTACAATAG
AGCAGATTAAAGCAGACCT
Found at i:11197138 original size:15 final size:15
Alignment explanation
Indices: 11197118--11197150 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11197108 CTTCTTACTA
*
11197118 CATCAATATCCATTT
1 CATCAATAACCATTT
11197133 CATCAATAACCATTT
1 CATCAATAACCATTT
11197148 CAT
1 CAT
11197151 AAATCATTAT
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:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (15 bp):
CATCAATAACCATTT
Found at i:11199613 original size:3 final size:3
Alignment explanation
Indices: 11199607--11199644 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11199597 AATAAGATTA
11199607 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11199645 AACAACAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11204200 original size:3 final size:3
Alignment explanation
Indices: 11204192--11204243 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
11204182 TTGTAGCCCC
11204192 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11204240 -TT AT
1 ATT AT
11204244 GTTTTGATTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11204538 original size:2 final size:2
Alignment explanation
Indices: 11204531--11204562 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11204521 TATTAGTAAG
11204531 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
11204563 TTGTATATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11208196 original size:23 final size:23
Alignment explanation
Indices: 11208146--11208198 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
11208136 ATTATAAACA
11208146 CTTTTT-TCTTTTCTTTTCCTTT
1 CTTTTTCTCTTTTCTTTTCCTTT
*
11208168 CCTTTTCTCTTATTC-TTTCCTTT
1 CTTTTTCTCTT-TTCTTTTCCTTT
*
11208191 TTTTTTCT
1 CTTTTTCT
11208199 TCATTTCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 18 0.69
24 3 0.12
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (23 bp):
CTTTTTCTCTTTTCTTTTCCTTT
Found at i:11210336 original size:27 final size:27
Alignment explanation
Indices: 11210295--11210348 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11210285 ACAAGATCTC
*
11210295 AACACCTATAAATATTGAATTTTTTTT
1 AACACCCATAAATATTGAATTTTTTTT
* **
11210322 AACACCCATAGATATTGGGTTTTTTTT
1 AACACCCATAAATATTGAATTTTTTTT
11210349 TTTTGTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (27 bp):
AACACCCATAAATATTGAATTTTTTTT
Found at i:11216872 original size:21 final size:20
Alignment explanation
Indices: 11216844--11216882 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11216834 CAAAACTTGT
11216844 ATAACTATCATCAAACATTA
1 ATAACTATCATCAAACATTA
*
11216864 ATAATCTATCCTCAAACAT
1 ATAA-CTATCATCAAACAT
11216883 CAAAACACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTATCATCAAACATTA
Found at i:11220252 original size:14 final size:15
Alignment explanation
Indices: 11220233--11220263 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11220223 AACTCTTTCA
11220233 ATTCTGT-CGGAGCT
1 ATTCTGTACGGAGCT
11220247 ATTCTGTACGGAGCT
1 ATTCTGTACGGAGCT
11220262 AT
1 AT
11220264 AGATATCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (15 bp):
ATTCTGTACGGAGCT
Found at i:11225526 original size:23 final size:22
Alignment explanation
Indices: 11225474--11225548 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
11225464 CCTGATCAGT
** *
11225474 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
11225495 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
11225516 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
11225539 ATACGACACA
1 ATACGACACA
11225549 TAAAGTGTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:11225560 original size:23 final size:23
Alignment explanation
Indices: 11225474--11225560 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
11225464 CCTGATCAGT
*
11225474 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
11225496 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
11225516 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
* *
11225539 ATACGACACATAAAGTGTCTGA
1 ATACGACACACAAAGTGCCTGA
11225561 TCAGTAAAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.63
22 1 0.02
23 18 0.33
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:11227080 original size:22 final size:22
Alignment explanation
Indices: 11227042--11227097 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
11227032 TGTTTGAATG
*
11227042 CTTTCTGTTCTCTTTTCTCTATT
1 CTTTTTGTT-TCTTTTCTCTATT
*
11227065 CTTTTTGTTTCTTTTCTTTATT
1 CTTTTTGTTTCTTTTCTCTATT
* *
11227087 CTATTTATTTC
1 CTTTTTGTTTC
11227098 ATTTACTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (22 bp):
CTTTTTGTTTCTTTTCTCTATT
Found at i:11233548 original size:6 final size:6
Alignment explanation
Indices: 11233514--11233561 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
11233504 TTATTGATAT
*
11233514 TTTAATA TTTAATA TTTAATA TTTGAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAA-A TTTAA-A TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTT
11233562 TTATATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 21 0.54
7 18 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:11237256 original size:46 final size:46
Alignment explanation
Indices: 11237203--11237294 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
11237193 ATTTTTTTTC
*
11237203 TAAGGATATAAGATGTGAAAAGCGTTGCTCTCTTATTGTGAGAGTG
1 TAAGGATATAAGATGTGAAAAGCGTCGCTCTCTTATTGTGAGAGTG
11237249 TAAGGATATAAGATGTGAAAAGCGTCGCTCTCTTATTGTGAGAGTG
1 TAAGGATATAAGATGTGAAAAGCGTCGCTCTCTTATTGTGAGAGTG
11237295 CAATTGATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (46 bp):
TAAGGATATAAGATGTGAAAAGCGTCGCTCTCTTATTGTGAGAGTG
Found at i:11237506 original size:24 final size:26
Alignment explanation
Indices: 11237479--11237538 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
11237469 ATCACAATAT
*
11237479 TTTTATAAAT-ATTTT-AATTATTTA
1 TTTTATAAATCATTTTAAACTATTTA
11237503 TTTTAT-AATCATTTTAAACTATTTA
1 TTTTATAAATCATTTTAAACTATTTA
*
11237528 TTATATTAAAT
1 TTTTA-TAAAT
11237539 GATAAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.10
24 11 0.37
25 12 0.40
26 1 0.03
27 3 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTATAAATCATTTTAAACTATTTA
Found at i:11237567 original size:22 final size:24
Alignment explanation
Indices: 11237523--11237593 Score: 58
Period size: 25 Copynumber: 3.0 Consensus size: 24
11237513 ATTTTAAACT
* *
11237523 ATTTATTATATTAAATGATAAATG
1 ATTTATTATATTAAATAAAAAATG
*
11237547 ATTT-TTA-ATTAAATAAAAAATAA
1 ATTTATTATATTAAATAAAAAAT-G
* *
11237570 ATAATATTAT-TTAAATAGAAAATG
1 AT-TTATTATATTAAATAAAAAATG
11237594 TACTCTTACT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
22 12 0.32
23 5 0.14
24 5 0.14
25 15 0.41
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (24 bp):
ATTTATTATATTAAATAAAAAATG
Found at i:11245973 original size:28 final size:28
Alignment explanation
Indices: 11245933--11245989 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
11245923 TCGTGTAGGG
*
11245933 ATTCGAACACAGGACCTTTAACACACTA
1 ATTCGAACACAGGACCTTCAACACACTA
11245961 ATTCGAACACAGGACCTTCAACACACTA
1 ATTCGAACACAGGACCTTCAACACACTA
11245989 A
1 A
11245990 CTCTTTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.19
Consensus pattern (28 bp):
ATTCGAACACAGGACCTTCAACACACTA
Done.