Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 166 of 175
Found at i:50060243 original size:26 final size:27
Alignment explanation
Indices: 50060206--50060270 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
50060196 GGCAGAGACA
50060206 CCATTGGCGCCTCT-CATGAGGCTCCT
1 CCATTGGCGCCTCTACATGAGGCTCCT
*
50060232 TCATTGGCGCCTCTACATGAGGCTCCT
1 CCATTGGCGCCTCTACATGAGGCTCCT
50060259 CCATTGGCGCCT
1 CCATTGGCGCCT
50060271 ACTAGACAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 13 0.36
27 23 0.64
ACGTcount: A:0.12, C:0.37, G:0.23, T:0.28
Consensus pattern (27 bp):
CCATTGGCGCCTCTACATGAGGCTCCT
Found at i:50065299 original size:13 final size:13
Alignment explanation
Indices: 50065281--50065306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50065271 TTTATTGTAA
50065281 ACAAATTTAATAG
1 ACAAATTTAATAG
50065294 ACAAATTTAATAG
1 ACAAATTTAATAG
50065307 TTGGACTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
ACAAATTTAATAG
Found at i:50070384 original size:14 final size:14
Alignment explanation
Indices: 50070345--50070386 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
50070335 TATATACAAA
*
50070345 TTTTTATTTATATT
1 TTTTTATTTAAATT
*
50070359 TTTCTA-TT-AATT
1 TTTTTATTTAAATT
50070371 TTTTTATTTAAATT
1 TTTTTATTTAAATT
50070385 TT
1 TT
50070387 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTATTTAAATT
Found at i:50070399 original size:13 final size:13
Alignment explanation
Indices: 50070345--50070401 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
50070335 TATATACAAA
*
50070345 TTTTTATTTATAT
1 TTTTTATTTAAAT
*
50070358 TTTTCTA-TTAATT
1 TTTT-TATTTAAAT
50070371 TTTTTATTTAAA-
1 TTTTTATTTAAAT
*
50070383 -TTTTATTAAAAT
1 TTTTTATTTAAAT
50070395 TTTTTAT
1 TTTTTAT
50070402 CTATTTTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 10 0.28
12 2 0.06
13 22 0.61
14 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATTTAAAT
Found at i:50075377 original size:24 final size:24
Alignment explanation
Indices: 50075343--50075390 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
50075333 TTCTTCTTAA
*
50075343 TTTTTAGTATTTTTAATTAAATTT
1 TTTTTAATATTTTTAATTAAATTT
*
50075367 TTTTTAATATTTTTAGTTAAATTT
1 TTTTTAATATTTTTAATTAAATTT
50075391 AAATTTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
TTTTTAATATTTTTAATTAAATTT
Found at i:50076152 original size:33 final size:33
Alignment explanation
Indices: 50076088--50076153 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
50076078 CAGACAATTT
* *
50076088 AACAAAGATACCAACATCTTAGTTTCGAGTAAC
1 AACAAAGATACCAACATCTGAGTTTCCAGTAAC
50076121 AACAAAGATACCAACATCCTGA-TTTCCAGTAAC
1 AACAAAGATACCAACAT-CTGAGTTTCCAGTAAC
50076154 CAAGGTATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (33 bp):
AACAAAGATACCAACATCTGAGTTTCCAGTAAC
Found at i:50077406 original size:15 final size:16
Alignment explanation
Indices: 50077386--50077415 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50077376 CCTTTAAAAA
50077386 TATTAAAAT-ATAAAT
1 TATTAAAATAATAAAT
50077401 TATTAAAATAATAAA
1 TATTAAAATAATAAA
50077416 ATTTGATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAAATAATAAAT
Found at i:50080396 original size:1 final size:1
Alignment explanation
Indices: 50080390--50080444 Score: 110
Period size: 1 Copynumber: 55.0 Consensus size: 1
50080380 TTATAATAGG
50080390 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50080445 TTTTGAAGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50103299 original size:108 final size:108
Alignment explanation
Indices: 50103112--50103521 Score: 655
Period size: 108 Copynumber: 3.8 Consensus size: 108
50103102 AAAATTCAAG
* * * * *
50103112 AGGATATTTGGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACGTTCCTCA
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
*
50103175 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAATTTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
*
50103218 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACTCAGCACCTTAGGGCACGTTCCTCG
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
50103283 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
50103326 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
50103391 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
66 AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
** * * *
50103434 AGGATATTTAGCCGTTTGGTTGAACGAGAAAGA-CAGACACCCAGCACCTTAGGGCATGTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATC-GACACCCAGCACCTTAGGGCACGTTCCTC
* * *
50103498 GAGTTTCCAAACGCTAAATATTGC
65 GAATTTCCAAACGCAAAACATTGC
50103522 ATCAATTAGA
Statistics
Matches: 285, Mismatches: 16, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
106 25 0.09
107 1 0.00
108 259 0.91
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (108 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTCCTCG
AATTTCCAAACGCAAAACATTGCCTTATTTTGTAAATTTTGAA
Found at i:50108667 original size:14 final size:14
Alignment explanation
Indices: 50108648--50108675 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50108638 AGCAGAAATC
50108648 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
50108662 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
50108676 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:50108673 original size:19 final size:18
Alignment explanation
Indices: 50108651--50108695 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
50108641 AGAAATCTGG
50108651 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
50108670 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
50108687 AGAAAAGAA
1 AGAAAAGAA
50108696 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:50112506 original size:27 final size:27
Alignment explanation
Indices: 50112476--50112538 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
50112466 CAAGCCTTAT
* *
50112476 TCCAGGCTCTACAACTC-TGAGTTTTTC
1 TCCAGGCACTACAAC-CATGAGCTTTTC
50112503 TCCAGGCACTACAACCATGAGCTTTTC
1 TCCAGGCACTACAACCATGAGCTTTTC
50112530 TCCAGGCAC
1 TCCAGGCAC
50112539 CACAGCTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (27 bp):
TCCAGGCACTACAACCATGAGCTTTTC
Found at i:50113806 original size:24 final size:24
Alignment explanation
Indices: 50113772--50113818 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
50113762 TGCAGAATTT
*
50113772 GACCTTGTTTCGAGTATTTGAGTA
1 GACCTTATTTCGAGTATTTGAGTA
50113796 GACCTTATTTCGAGTATTTGAGT
1 GACCTTATTTCGAGTATTTGAGT
50113819 GGCATGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (24 bp):
GACCTTATTTCGAGTATTTGAGTA
Found at i:50116640 original size:53 final size:53
Alignment explanation
Indices: 50116577--50116678 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
50116567 TACTTTTTCT
* *
50116577 TTAGTAAATTTAGTCAATGT-ATTTTTATAGCTTTGTATATCTTAATCCAATCC
1 TTAGTAAATTTAATCAAT-TCATTTTTATAGCTTTGTAAATCTTAATCCAATCC
* * *
50116630 TTAGTGAATTTAATCACTTCATTTTTATAGGTTTGTAAATCTTAATCCA
1 TTAGTAAATTTAATCAATTCATTTTTATAGCTTTGTAAATCTTAATCCA
50116679 CTCATTACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 1 0.02
53 42 0.98
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (53 bp):
TTAGTAAATTTAATCAATTCATTTTTATAGCTTTGTAAATCTTAATCCAATCC
Found at i:50117913 original size:6 final size:6
Alignment explanation
Indices: 50117902--50117937 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
50117892 AAGATATTAT
50117902 AAAATA AAAATA AAAATA AAAATA AAAATA AGAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAAT
50117938 TCTATTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:50120386 original size:2 final size:2
Alignment explanation
Indices: 50120379--50120414 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
50120369 ACTTCCCATG
*
50120379 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
50120415 CTAATAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:50120659 original size:3 final size:3
Alignment explanation
Indices: 50120651--50120680 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
50120641 TTTTCATTGG
50120651 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
50120681 GTATTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:50127064 original size:18 final size:20
Alignment explanation
Indices: 50127022--50127064 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
50127012 CTTCTGTAAA
*
50127022 AAAATTCAAAATAATCTTCT
1 AAAATTCAAAATAATCTTAT
50127042 AAAATTCAAAAT-AT-TTAT
1 AAAATTCAAAATAATCTTAT
50127060 AAAAT
1 AAAAT
50127065 AAAATTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 2 0.09
20 12 0.55
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTCAAAATAATCTTAT
Found at i:50127990 original size:43 final size:42
Alignment explanation
Indices: 50127896--50128005 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 42
50127886 TAAACAAAAA
* *
50127896 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTTCATAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCATAAG
* *
50127938 CGCCTCTAAAGAACATGGTATTTAGCGGCGTCTTTTTTC-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG--TTTTTTCATAAG
50127981 CGCCGCTAAAGAACATGGTCTTTAG
1 CGCCGCTAAAGAACATGGTCTTTAG
50128006 TCTTTAGCGG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
42 26 0.43
43 27 0.45
44 7 0.12
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCATAAG
Found at i:50128407 original size:21 final size:21
Alignment explanation
Indices: 50128339--50128409 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
50128329 TTTTGCTCTG
*
50128339 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
50128360 CTCCGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
50128381 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
50128402 CTCTGCTT
1 CTCTGCTT
50128410 TAAGTTGTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.04, C:0.48, G:0.17, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:50130455 original size:25 final size:25
Alignment explanation
Indices: 50130421--50130495 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 25
50130411 TGATATATTT
50130421 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
50130446 TTATGTATTATGTAA-CTACTGTAAG
1 TTATGTATTATGTAAGTTA-TGTAAG
* *
50130471 TAATGTAAGTTATGTAAGTAATGTA
1 TTATGT-A-TTATGTAAGTTATGTA
50130496 TAATGTAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 2 0.05
25 26 0.62
26 1 0.02
27 12 0.29
28 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.44
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:50130471 original size:34 final size:33
Alignment explanation
Indices: 50130423--50130542 Score: 113
Period size: 34 Copynumber: 3.6 Consensus size: 33
50130413 ATATATTTTT
* *
50130423 ATGTATTA-TGTAAGTTATGTAAGTTATGTATT
1 ATGTAATACTGTAAGTTATGTAAGTTATGTATA
*
50130455 ATGTAACTACTGTAAGTAATGTAAGTTATGTAAGTA
1 ATGTAA-TACTGTAAGTTATGTAAGTTATGT-A-TA
* *
50130491 ATGT-ATAATGTAAGTTAAG-AAGGTTATGTATA
1 ATGTAATACTGTAAGTTATGTAA-GTTATGTATA
50130523 ATGTAAGT-CATGTAAGTTAT
1 ATGTAA-TAC-TGTAAGTTAT
50130543 TTATGTAAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
32 11 0.15
33 6 0.08
34 48 0.67
35 2 0.03
36 5 0.07
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41
Consensus pattern (33 bp):
ATGTAATACTGTAAGTTATGTAAGTTATGTATA
Found at i:50130519 original size:25 final size:25
Alignment explanation
Indices: 50130471--50130554 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 25
50130461 CTACTGTAAG
*
50130471 TAATGTAAGTTATGTAAGTAATGTA
1 TAATGTAAGTTAAGTAAGTAATGTA
*
50130496 TAATGTAAGTTAAG-AAGGTTATGTA
1 TAATGTAAGTTAAGTAA-GTAATGTA
* * *
50130521 TAATGTAAGTCATGTAAGTTAT-T-
1 TAATGTAAGTTAAGTAAGTAATGTA
50130544 T-ATGTAAGTTA
1 TAATGTAAGTTA
50130555 TGTAGGCTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.17
23 1 0.02
24 3 0.06
25 37 0.71
26 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.40
Consensus pattern (25 bp):
TAATGTAAGTTAAGTAAGTAATGTA
Found at i:50130550 original size:13 final size:13
Alignment explanation
Indices: 50130532--50130583 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
50130522 AATGTAAGTC
50130532 ATGTAAGTTATTT
1 ATGTAAGTTATTT
*
50130545 ATGTAAGTTATGT
1 ATGTAAGTTATTT
*
50130558 AGGCTAAG-TA-TT
1 ATG-TAAGTTATTT
*
50130570 ATGCAAGTTATTT
1 ATGTAAGTTATTT
50130583 A
1 A
50130584 AGTAGTGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.10
12 5 0.16
13 19 0.61
14 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (13 bp):
ATGTAAGTTATTT
Found at i:50130558 original size:9 final size:9
Alignment explanation
Indices: 50130428--50130542 Score: 93
Period size: 9 Copynumber: 13.4 Consensus size: 9
50130418 TTTTTATGTA
50130428 TTATGTAAG
1 TTATGTAAG
50130437 TTATGTAAG
1 TTATGTAAG
50130446 TTATGT-A-
1 TTATGTAAG
50130453 TTATGTAA-
1 TTATGTAAG
*
50130461 CTACTGTAAG
1 TTA-TGTAAG
*
50130471 TAATGTAAG
1 TTATGTAAG
50130480 TTATGTAAG
1 TTATGTAAG
*
50130489 TAATGT-A-
1 TTATGTAAG
*
50130496 TAATGTAAG
1 TTATGTAAG
*
50130505 TTAAG-AAGG
1 TTATGTAA-G
50130514 TTATGT-A-
1 TTATGTAAG
*
50130521 TAATGTAAG
1 TTATGTAAG
*
50130530 TCATGTAAG
1 TTATGTAAG
50130539 TTAT
1 TTAT
50130543 TTATGTAAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
7 17 0.20
8 9 0.10
9 59 0.69
10 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41
Consensus pattern (9 bp):
TTATGTAAG
Found at i:50130650 original size:20 final size:20
Alignment explanation
Indices: 50130600--50130651 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50130590 GTAAGTGTTG
*
50130600 TATTATGTAAATAAGTTATT
1 TATTATGTAAGTAAGTTATT
50130620 TATTATGTAAGTAAGTTATT
1 TATTATGTAAGTAAGTTATT
50130640 TATTATGTAAGT
1 TATTATGTAAGT
50130652 TTTAAGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (20 bp):
TATTATGTAAGTAAGTTATT
Found at i:50133873 original size:7 final size:7
Alignment explanation
Indices: 50133848--50133896 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
50133838 CTAAAGCAGT
50133848 CTAAACC
1 CTAAACC
*
50133855 CCAAACC
1 CTAAACC
* *
50133862 GTAAACT
1 CTAAACC
*
50133869 CTAAACTT
1 CTAAAC-C
50133877 CTAAACC
1 CTAAACC
50133884 CTAAACC
1 CTAAACC
50133891 CTAAAC
1 CTAAAC
50133897 ACCAAAACCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 28 0.80
8 7 0.20
ACGTcount: A:0.43, C:0.37, G:0.02, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:50133904 original size:22 final size:21
Alignment explanation
Indices: 50133848--50133905 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
50133838 CTAAAGCAGT
* * *
50133848 CTAAACCCCAAACCGTAAACT
1 CTAAACCCAAAACCCTAAACC
* *
50133869 CTAAACTTCTAAACCCTAAACC
1 CTAAAC-CCAAAACCCTAAACC
50133891 CTAAACACCAAAACC
1 CTAAAC-CCAAAACC
50133906 TACATCATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.16
Consensus pattern (21 bp):
CTAAACCCAAAACCCTAAACC
Found at i:50134092 original size:7 final size:7
Alignment explanation
Indices: 50134049--50134114 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
50134039 CCAAACTCTC
50134049 AAACCCT
1 AAACCCT
**
50134056 AAACCAA
1 AAACCCT
*
50134063 AAACACT
1 AAACCCT
50134070 AAA-CCT
1 AAACCCT
* * *
50134076 ACATCGT
1 AAACCCT
50134083 AAACCCT
1 AAACCCT
50134090 AAACCCT
1 AAACCCT
*
50134097 AAACTCT
1 AAACCCT
50134104 AAACCCT
1 AAACCCT
50134111 AAAC
1 AAAC
50134115 TATAATTCAA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
6 4 0.09
7 41 0.91
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:50134115 original size:14 final size:14
Alignment explanation
Indices: 50134041--50134115 Score: 64
Period size: 14 Copynumber: 5.4 Consensus size: 14
50134031 CTTAATCACC
50134041 AAACTCTCAAACCCT
1 AAACTCT-AAACCCT
* *
50134056 AAAC-CAAAAACACT
1 AAACTC-TAAACCCT
* * *
50134070 AAAC-CTACATCGT
1 AAACTCTAAACCCT
*
50134083 AAACCCTAAACCCT
1 AAACTCTAAACCCT
50134097 AAACTCTAAACCCT
1 AAACTCTAAACCCT
50134111 AAACT
1 AAACT
50134116 ATAATTCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 7 0.15
14 36 0.77
15 4 0.09
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (14 bp):
AAACTCTAAACCCT
Found at i:50134177 original size:17 final size:17
Alignment explanation
Indices: 50134155--50134204 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
50134145 TATCCTATTT
50134155 CCTACATTATATAATAA
1 CCTACATTATATAATAA
50134172 CCTACATTATATAATAA
1 CCTACATTATATAATAA
*
50134189 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
50134205 TCTAGCGGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:50134407 original size:113 final size:111
Alignment explanation
Indices: 50134226--50134576 Score: 384
Period size: 113 Copynumber: 3.1 Consensus size: 111
50134216 TTCCCACAAC
* * * *
50134226 GCGCCGCTAATAATATGTTTTACCGGCGTTTTACCATAAGCGCCAC-AACTGGTAGTATACATCA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-T-GTAGTATACATCA
50134290 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
63 AGACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
* * * * *
50134339 GCGCCGCTAATACTATGCTTTGGCGGCGTTTTCAAATAAGTGCCACTAATCGTAATGTACCTCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAAT-GTAGTATACATCAA
* * * * *
50134404 GACCAAA-CTCTGCGTTTTGGTTAA-GAAATATTGCGGCGCTTTTCACTAC
64 GACCAAAGCGCTGCGTTTTGGTTAATG---TTTTGCGGCGCTTTACAATAA
* * * *
50134453 TCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCCACTACTGCTAGTATACATCAA
1 GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATG-TAGTATACATCAA
* * * *
50134518 GACCAAAGCGCTGCGTTTTGGTTAATATTTTACGGCGTTTTCCAATAA
64 GACCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
*
50134566 GCGCCACTAAT
1 GCGCCGCTAAT
50134577 CCTAATATAC
Statistics
Matches: 195, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
111 1 0.01
112 16 0.08
113 84 0.43
114 78 0.40
115 16 0.08
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
GCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGTAGTATACATCAAGA
CCAAAGCGCTGCGTTTTGGTTAATGTTTTGCGGCGCTTTACAATAA
Found at i:50134679 original size:188 final size:188
Alignment explanation
Indices: 50134362--50134758 Score: 668
Period size: 188 Copynumber: 2.1 Consensus size: 188
50134352 TATGCTTTGG
* * * * *
50134362 CGGCGTTTTCAAATAAGTGCCACTAATCGTAATGTACCTCAAGACCAAACTCTGCGTTTTGGTTA
1 CGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTA
50134427 AGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAA
66 AGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAA
50134492 GCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTA
131 GCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTA
50134550 CGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTA
1 CGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTA
* * * *
50134615 AGAAATCTTGTGGCGCTTTTCACTACTCGCTGCTAATACTATTCTTTAGTAGCGTTTTAATATAA
66 AGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAA
* *
50134680 GCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTG
131 GCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTA
* * *
50134738 CGACGCTTTACAATAAGCGCC
1 CGGCGTTTTCCAATAAGCGCC
50134759 GCTACTACTA
Statistics
Matches: 195, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 195 1.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (188 bp):
CGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTA
AGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAA
GCGCCACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTA
Found at i:50134819 original size:113 final size:114
Alignment explanation
Indices: 50134546--50134959 Score: 444
Period size: 114 Copynumber: 3.6 Consensus size: 114
50134536 TGGTTAATAT
* **
50134546 TTTA-CGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 TTTAGCGGCGTTTT-AATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACTCTGCGTTT
* * * * * *
50134609 TGGTTAAGAAATCTTGTGGCGCTTTTCACTACTCGCTGCTAATACTATTC
65 TGGTTAAGAAATATTGCGACGCTTTTCAATACTCGCCGCTAATACTATAC
** * ** * *
50134659 TTTAGTAGCGTTTTAATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTT
1 TTTAGCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-CTCTGCGTTT
* * * ** * *
50134724 TGGTT-A-ATATTTTGCGACGCTTTACAATAAGCGCCGCTACTACTATGC
65 TGGTTAAGAAATATTGCGACGCTTTTCAATACTCGCCGCTAATACTATAC
* * *
50134772 GTTAGCGGCGTTTTTAA-ATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTT
1 TTTAGCGGCG-TTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACTCTGCGTTT
*
50134836 TGGTTAAGAAATATTGCGACGCTTTTCAGTACTCGCCGCTAATACTATAC
65 TGGTTAAGAAATATTGCGACGCTTTTCAATACTCGCCGCTAATACTATAC
* ** * *
50134886 TTTAGCGGCGTTTGAATATAAGCGCCACTAAGGCTACTATTCATCAAGACCAAAGCAT-TGCGTT
1 TTTAGCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAA-C-TCTGCGTT
*
50134950 TTGGATAAGA
64 TTGGTTAAGA
50134960 GCTTTTGCGG
Statistics
Matches: 244, Mismatches: 48, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
112 14 0.06
113 80 0.33
114 119 0.49
115 30 0.12
116 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (114 bp):
TTTAGCGGCGTTTTAATATAAGCGCCACTAATCCTAATATACATCAAGACCAAACTCTGCGTTTT
GGTTAAGAAATATTGCGACGCTTTTCAATACTCGCCGCTAATACTATAC
Found at i:50143045 original size:21 final size:20
Alignment explanation
Indices: 50143003--50143045 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
50142993 GTAAATTAAG
*
50143003 TTTTATTTTTATAAAAGTAT
1 TTTTATTTTTATAAAAGAAT
50143023 TTTTATTTTTTATATAAA-AAT
1 TTTTA-TTTTTATA-AAAGAAT
50143044 TT
1 TT
50143046 AATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 12 0.60
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTATTTTTATAAAAGAAT
Found at i:50147234 original size:30 final size:31
Alignment explanation
Indices: 50147186--50147259 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
50147176 TGATTTGACG
* *
50147186 CAAT-TATACATATGAAACTTTGATTGTGGTT
1 CAATGTATACATA-GAAACTTTAATTGTGATT
*
50147217 CAATGTATACATA-AAACTTTAATTTTGATT
1 CAATGTATACATAGAAACTTTAATTGTGATT
*
50147247 CAATTGTACACAT
1 CAA-TGTATACAT
50147260 TTAAAGGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 17 0.46
31 12 0.32
32 8 0.22
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (31 bp):
CAATGTATACATAGAAACTTTAATTGTGATT
Found at i:50153622 original size:37 final size:37
Alignment explanation
Indices: 50153561--50153706 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
50153551 TACGTATGAT
* *
50153561 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
50153596 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
50153633 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
50153670 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
50153707 TAAAGCTATC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 91 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:50153749 original size:52 final size:52
Alignment explanation
Indices: 50153670--50153788 Score: 193
Period size: 52 Copynumber: 2.2 Consensus size: 52
50153660 TAAGTGTAGC
* * *
50153670 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCACT-TGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
50153723 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
50153775 CACTTTGTCACTTG
1 CACTTT-TCACTTG
50153789 ATCAGAAGTA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 45 0.73
53 17 0.27
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
Found at i:50158604 original size:19 final size:18
Alignment explanation
Indices: 50158567--50158621 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
50158557 ATAGTATGAC
*
50158567 AAAATTTAATTACTTTTT
1 AAAATTTAAATACTTTTT
*
50158585 AAAATTTAAAATATTTTTT
1 AAAATTT-AAATACTTTTT
* *
50158604 AATAATTTTAATAATTTT
1 AA-AATTTAAATACTTTT
50158622 GAAATTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 7 0.23
19 19 0.61
20 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AAAATTTAAATACTTTTT
Found at i:50161879 original size:12 final size:12
Alignment explanation
Indices: 50161862--50161886 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50161852 CGATCAGTCC
50161862 ACGTGCAGTTTG
1 ACGTGCAGTTTG
50161874 ACGTGCAGTTTG
1 ACGTGCAGTTTG
50161886 A
1 A
50161887 AGCATAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (12 bp):
ACGTGCAGTTTG
Found at i:50167944 original size:25 final size:27
Alignment explanation
Indices: 50167906--50167976 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 27
50167896 GATTTTTTAA
* *
50167906 AAAAATTTAGAATTTTTTTAAA-A-AT
1 AAAATTTTAAAATTTTTTTAAATATAT
* *
50167931 AAAATTTTAAAATTTTTATAAATATTT
1 AAAATTTTAAAATTTTTTTAAATATAT
* *
50167958 TAAATTTTAAATTTTTTTT
1 AAAATTTTAAAATTTTTTT
50167977 TGTAATTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 19 0.51
26 1 0.03
27 17 0.46
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AAAATTTTAAAATTTTTTTAAATATAT
Found at i:50167962 original size:19 final size:19
Alignment explanation
Indices: 50167929--50167965 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
50167919 TTTTTTAAAA
50167929 ATAAAATTTTAAAATTTTT
1 ATAAAATTTTAAAATTTTT
50167948 ATAAATATTTT-AAATTTT
1 ATAAA-ATTTTAAAATTTT
50167966 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAAAATTTTAAAATTTTT
Found at i:50168787 original size:18 final size:20
Alignment explanation
Indices: 50168747--50168788 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
50168737 TCTCTCAACA
*
50168747 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAT
50168767 AAAATT-CAAAAT-ATTTAT
1 AAAATTACAAAATAATTTAT
50168785 AAAA
1 AAAA
50168789 AAATTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAT
Found at i:50168789 original size:19 final size:20
Alignment explanation
Indices: 50168746--50168789 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
50168736 GTCTCTCAAC
50168746 AAAAATTACAAAATAATTTT
1 AAAAATTACAAAATAATTTT
*
50168766 TAAAATT-CAAAAT-ATTTAT
1 AAAAATTACAAAATAATTT-T
50168785 AAAAA
1 AAAAA
50168790 AATTCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 11 0.52
20 6 0.29
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTACAAAATAATTTT
Found at i:50168790 original size:20 final size:20
Alignment explanation
Indices: 50168746--50168805 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
50168736 GTCTCTCAAC
50168746 AAAAATTACAAAATAATTT-T-
1 AAAAATT-CAAAAT-ATTTATA
*
50168766 TAAAATTCAAAATATTTATAA
1 AAAAATTCAAAATATTTAT-A
*
50168787 AAAAATTCCAAA-ATTTATA
1 AAAAATTCAAAATATTTATA
50168806 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 12 0.35
21 10 0.29
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTCAAAATATTTATA
Found at i:50168793 original size:21 final size:20
Alignment explanation
Indices: 50168767--50168805 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
50168757 AATAATTTTT
50168767 AAAATTCAAAATATTTATAAA
1 AAAATTCAAAA-ATTTATAAA
*
50168788 AAAATTCCAAAATTTATA
1 AAAATTCAAAAATTTATA
50168806 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTCAAAAATTTATAAA
Found at i:50171068 original size:23 final size:24
Alignment explanation
Indices: 50171025--50171073 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
50171015 AAATATATAA
* *
50171025 ATAATATTTTATTAAGTAAA-TAT
1 ATAATATTTAATAAAGTAAATTAT
50171048 ATAATATTTAATAAA-TGAAATTAT
1 ATAATATTTAATAAAGT-AAATTAT
50171072 AT
1 AT
50171074 TTATAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 16 0.73
24 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
ATAATATTTAATAAAGTAAATTAT
Found at i:50174286 original size:25 final size:26
Alignment explanation
Indices: 50174218--50174287 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
50174208 TTCCGTTACC
*
50174218 AATTAAATATTC-TATAA-AATAAATA
1 AATTAAAT-TTCAAATAATAATAAATA
* *
50174243 AATCAAATTCCTAAA-AATAAT-AATA
1 AATTAAATTTC-AAATAATAATAAATA
50174268 AATTAAATTTCAAATAATAA
1 AATTAAATTTCAAATAATAA
50174288 AAGCGAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
24 5 0.14
25 27 0.75
26 4 0.11
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (26 bp):
AATTAAATTTCAAATAATAATAAATA
Found at i:50178875 original size:9 final size:9
Alignment explanation
Indices: 50178861--50178893 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
50178851 TGTTTTTTTT
50178861 AAAAAAATA
1 AAAAAAATA
50178870 AAAAAAATA
1 AAAAAAATA
50178879 CAAAAAAATA
1 -AAAAAAATA
50178889 AAAAA
1 AAAAA
50178894 TTACATTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAAAATA
Found at i:50178876 original size:10 final size:10
Alignment explanation
Indices: 50178861--50178893 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
50178851 TGTTTTTTTT
50178861 AAAAAAAT-A
1 AAAAAAATAA
*
50178870 AAAAAAATAC
1 AAAAAAATAA
50178880 AAAAAAATAA
1 AAAAAAATAA
50178890 AAAA
1 AAAA
50178894 TTACATTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:50178960 original size:30 final size:29
Alignment explanation
Indices: 50178890--50179014 Score: 110
Period size: 29 Copynumber: 4.2 Consensus size: 29
50178880 AAAAAAATAA
* *
50178890 AAAATTACATTCTGACCGCTAAAATTTT-T
1 AAAATTACATTTTGACCCCT-AAATTTTCT
* * * *
50178919 GAAATTGCATTTTAACCCCTAAGTTTTCCT
1 AAAATTACATTTTGACCCCTAAATTTT-CT
*
50178949 AAAATTACATTTTGACCCATAAAATTTT-T
1 AAAATTACATTTTGACCCCT-AAATTTTCT
* * *
50178978 TAAATTACATTTTGACCTCTGAATTTTCTT
1 AAAATTACATTTTGACCCCTAAATTTTC-T
50179008 AAAATTA
1 AAAATTA
50179015 TGTTTTGGCC
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
28 12 0.16
29 33 0.44
30 24 0.32
31 6 0.08
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAATTTTCT
Found at i:50179021 original size:59 final size:59
Alignment explanation
Indices: 50178890--50179014 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 59
50178880 AAAAAAATAA
* *
50178890 AAAATTACATTCTGACCGC-TAAAATTTTTGAAATTGCATTTTAACCCCTAAGTTTTCCT
1 AAAATTACATTTTGACC-CATAAAATTTTTGAAATTACATTTTAACCCCTAAGTTTTCCT
* * * *
50178949 AAAATTACATTTTGACCCATAAAATTTTTTAAATTACATTTTGACCTCTGAA-TTTTCTT
1 AAAATTACATTTTGACCCATAAAATTTTTGAAATTACATTTTAACCCCT-AAGTTTTCCT
50179008 AAAATTA
1 AAAATTA
50179015 TGTTTTGGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.02
59 55 0.95
60 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (59 bp):
AAAATTACATTTTGACCCATAAAATTTTTGAAATTACATTTTAACCCCTAAGTTTTCCT
Found at i:50179692 original size:10 final size:10
Alignment explanation
Indices: 50179674--50179748 Score: 77
Period size: 11 Copynumber: 7.6 Consensus size: 10
50179664 GAGGCAGGCC
50179674 AGAAAAAAAGG
1 AGAAAAAAA-G
50179685 AGAAAAAAAG
1 AGAAAAAAAG
50179695 AGAAAAAAAAG
1 AG-AAAAAAAG
*
50179706 AGAAAAAAAA
1 AGAAAAAAAG
*
50179716 AG-GAAAAAG
1 AGAAAAAAAG
50179725 -G-AAAAAAG
1 AGAAAAAAAG
50179733 A-AAAAAAAG
1 AGAAAAAAAG
50179742 AAGAAAA
1 -AGAAAA
50179749 GTTCAATTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.13
9 12 0.22
10 13 0.24
11 23 0.42
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:50179699 original size:21 final size:21
Alignment explanation
Indices: 50179674--50179748 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
50179664 GAGGCAGGCC
50179674 AGAAAAAAAGGAGAAAAAAAG
1 AGAAAAAAAGGAGAAAAAAAG
* *
50179695 AGAAAAAAAAGAGAAAAAAAA
1 AGAAAAAAAGGAGAAAAAAAG
*
50179716 AG-GAAAAA-G-G-AAAAAAG
1 AGAAAAAAAGGAGAAAAAAAG
*
50179733 A-AAAAAAAGAAGAAAA
1 AGAAAAAAAGGAGAAAA
50179749 GTTCAATTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 12 0.27
18 1 0.02
19 2 0.05
20 8 0.18
21 21 0.48
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAGGAGAAAAAAAG
Found at i:50179927 original size:21 final size:21
Alignment explanation
Indices: 50179903--50179942 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50179893 GTATTTATAT
50179903 TTTTAATTTAATTTAATTCAA
1 TTTTAATTTAATTTAATTCAA
* *
50179924 TTTTAATTTTATTTTATTC
1 TTTTAATTTAATTTAATTC
50179943 TAAATAATTT
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:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAATTTAATTTAATTCAA
Found at i:50180337 original size:35 final size:34
Alignment explanation
Indices: 50180298--50180604 Score: 221
Period size: 35 Copynumber: 8.7 Consensus size: 34
50180288 AAAAAAATCC
*
50180298 TCGTGTTTTCAAAATTTCCGGTGTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTCC-GTGTTTCAAAAATTT
* *
50180333 TCGTGTTTTC-AAAATTCCAATGATTCAAAAAATTT
1 TCGTGTTTTCAAAAATTCC-GTGTTTC-AAAAATTT
50180368 TCGTGTTTTCTAAAAATTCCTGTGTTTCAAAAAAAATTT
1 TCGTGTTTTC-AAAAATTCC-GTGTTTC---AAAAATTT
* * * *
50180407 TCGTGTTTACAAAAATTTTCATATTCTC-AAAATTT
1 TCGTGTTTTCAAAAA-TTCCGTGTT-TCAAAAATTT
* * *
50180442 TCGTGTTTTTAACAATTCTCGTGTTTCACAAATTT
1 TCGTGTTTTCAAAAATTC-CGTGTTTCAAAAATTT
* * * *
50180477 TCGTGTTTTAAAAAAAT--GT-TTTAAAAAAATT
1 TCGTGTTTTCAAAAATTCCGTGTTTCAAAAATTT
* ** *
50180508 TCTTGTGTTTCAAAAATTGTAGTGTTTCAAAAATCT
1 TCGTGT-TTTCAAAAATT-CCGTGTTTCAAAAATTT
* * *
50180544 TCGTGTTTTCAAAAATTTTCGGGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAA-TTCCGTG-TTTCAAAAATTT
* *
50180580 TCGTG-ATTCAAAAACTTTCGTGTTT
1 TCGTGTTTTCAAAAA-TTCCGTGTTT
50180605 TTTTTAAAAA
Statistics
Matches: 218, Mismatches: 38, Indels: 33
0.75 0.13 0.11
Matches are distributed among these distances:
31 14 0.06
32 11 0.05
34 19 0.09
35 99 0.45
36 31 0.14
37 13 0.06
38 8 0.04
39 23 0.11
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (34 bp):
TCGTGTTTTCAAAAATTCCGTGTTTCAAAAATTT
Found at i:50180412 original size:20 final size:20
Alignment explanation
Indices: 50180359--50180421 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
50180349 CCAATGATTC
50180359 AAAAAATTTTCGTGTTTTC--
1 AAAAAATTTTCGTG-TTTCAA
* *
50180378 TAAAAA-TTCCTGTGTTTCAA
1 AAAAAATTTTC-GTGTTTCAA
50180398 AAAAAATTTTCGTGTTTACAA
1 AAAAAATTTTCGTGTTT-CAA
50180419 AAA
1 AAA
50180422 TTTTCATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
20 11 0.31
21 9 0.26
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAAAATTTTCGTGTTTCAA
Found at i:50180437 original size:39 final size:39
Alignment explanation
Indices: 50180359--50180438 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
50180349 CCAATGATTC
* * * *
50180359 AAAAAATTTTCGTGTTTTCTAAAAATTCCTGTGTTTCAA
1 AAAAAATTTTCGTGTTTACTAAAAATTCATATGTCTCAA
50180398 AAAAAATTTTCGTGTTTAC-AAAAATTTTCATAT-TCTCAA
1 AAAAAATTTTCGTGTTTACTAAAAA--TTCATATGTCTCAA
50180437 AA
1 AA
50180439 TTTTCGTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 5 0.14
39 25 0.71
40 5 0.14
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (39 bp):
AAAAAATTTTCGTGTTTACTAAAAATTCATATGTCTCAA
Found at i:50180505 original size:14 final size:13
Alignment explanation
Indices: 50180480--50180506 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50180470 CAAATTTTCG
50180480 TGTTTTAAAAAAA
1 TGTTTTAAAAAAA
50180493 TGTTTTAAAAAAA
1 TGTTTTAAAAAAA
50180506 T
1 T
50180507 TTCTTGTGTT
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:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TGTTTTAAAAAAA
Found at i:50180532 original size:17 final size:16
Alignment explanation
Indices: 50180298--50180604 Score: 154
Period size: 18 Copynumber: 17.5 Consensus size: 16
50180288 AAAAAAATCC
50180298 TCGTGTTTTC-AAAATT
1 TCGTG-TTTCAAAAATT
50180314 TCCGGTGTTTCAAAAATTT
1 T-C-GTGTTTCAAAAA-TT
50180333 TCGTGTTTTC-AAAATT
1 TCGTG-TTTCAAAAATT
* * *
50180349 CCAATGATTCAAAAAATTT
1 TC-GTGTTTC-AAAAA-TT
50180368 TCGTGTTTTCTAAAAATT
1 TCGTG-TTTC-AAAAATT
*
50180386 CCTGTGTTTCAAAAAAAATTT
1 TC-GTGTTTC---AAAAA-TT
50180407 TCGTGTTTACAAAAATTT
1 TCGTGTTT-CAAAAA-TT
* * *
50180425 TCATATTCTCAAAATTT
1 TCGTGTT-TCAAAAATT
* *
50180442 TCGTGTTTTTAACAATT
1 TCGTG-TTTCAAAAATT
*
50180459 CTCGTGTTTCACAAATTT
1 -TCGTGTTTCA-AAAATT
* **
50180477 TCGTGTTTTAAAAAAA
1 TCGTGTTTCAAAAATT
*
50180493 T-GT-TTTAAAAAAATT
1 TCGTGTTT-CAAAAATT
50180508 TCTTGTGTTTCAAAAATT
1 TC--GTGTTTCAAAAATT
*
50180526 GTAGTGTTTCAAAAATCT
1 -TCGTGTTTCAAAAAT-T
50180544 TCGTGTTTTCAAAAATTT
1 TCGTG-TTTCAAAAA-TT
*
50180562 TCGGGTTTTCAAAAATT
1 TCGTG-TTTCAAAAATT
*
50180579 CTCGTGATTCAAAAACTT
1 -TCGTGTTTCAAAAA-TT
50180597 TCGTGTTT
1 TCGTGTTT
50180605 TTTTTAAAAA
Statistics
Matches: 226, Mismatches: 35, Indels: 59
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.01
15 8 0.04
16 11 0.05
17 72 0.32
18 94 0.42
19 23 0.10
20 11 0.05
21 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (16 bp):
TCGTGTTTCAAAAATT
Found at i:50187383 original size:17 final size:18
Alignment explanation
Indices: 50187361--50187396 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
50187351 ATTTTGTTAG
*
50187361 AAAATATCTTA-TTTAAT
1 AAAATATATTATTTTAAT
50187378 AAAATATATTATTTTAAT
1 AAAATATATTATTTTAAT
50187396 A
1 A
50187397 GAATTACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATATTATTTTAAT
Found at i:50191270 original size:19 final size:20
Alignment explanation
Indices: 50191232--50191272 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
50191222 AAATTTTTTC
50191232 AGGAGGAAAAAACTAAAATTT
1 AGGAGGAAAAAACT-AAATTT
*
50191253 AGGAGGAAAAATCT-AATTT
1 AGGAGGAAAAAACTAAATTT
50191272 A
1 A
50191273 TCATTCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (20 bp):
AGGAGGAAAAAACTAAATTT
Found at i:50196026 original size:17 final size:18
Alignment explanation
Indices: 50196004--50196039 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
50195994 ATTTTGTTAG
*
50196004 AAAATATCTTA-TTTAAT
1 AAAATATATTATTTTAAT
50196021 AAAATATATTATTTTAAT
1 AAAATATATTATTTTAAT
50196039 A
1 A
50196040 GAATTACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATATTATTTTAAT
Found at i:50200545 original size:18 final size:18
Alignment explanation
Indices: 50200522--50200559 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
50200512 GTAAGAAAGT
50200522 ATGTAT-AATAAAATTAAA
1 ATGTATAAAT-AAATTAAA
50200540 ATGTATAAATAAATTAAA
1 ATGTATAAATAAATTAAA
50200558 AT
1 AT
50200560 AAATTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATGTATAAATAAATTAAA
Found at i:50203966 original size:19 final size:20
Alignment explanation
Indices: 50203929--50203968 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
50203919 TATAATATTT
50203929 TATTTAAAAATAAAAAATAAA
1 TATTTAAAAAT-AAAAATAAA
50203950 TATTTAAAAAT-AAAATAAA
1 TATTTAAAAATAAAAATAAA
50203969 CTTTAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TATTTAAAAATAAAAATAAA
Found at i:50204285 original size:15 final size:15
Alignment explanation
Indices: 50204265--50204295 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
50204255 TATTATAAAA
50204265 ATAGTATACTTATTC
1 ATAGTATACTTATTC
50204280 ATAGTATACTTATTC
1 ATAGTATACTTATTC
50204295 A
1 A
50204296 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAGTATACTTATTC
Found at i:50205982 original size:11 final size:11
Alignment explanation
Indices: 50205966--50205996 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
50205956 AAGTATGGGT
50205966 AGGTATGGGAA
1 AGGTATGGGAA
*
50205977 AGGTATGGGCA
1 AGGTATGGGAA
50205988 AGGTATGGG
1 AGGTATGGG
50205997 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:50210067 original size:18 final size:18
Alignment explanation
Indices: 50210044--50210136 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
50210034 CCCAACTACT
*
50210044 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
50210062 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
50210080 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
50210098 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
50210116 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
50210134 GTA
1 GTA
50210137 AACGGTCGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:50210698 original size:11 final size:11
Alignment explanation
Indices: 50210682--50210712 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
50210672 AAGTATGGGT
50210682 AGGTATGGGAA
1 AGGTATGGGAA
*
50210693 AGGTATGGGCA
1 AGGTATGGGAA
50210704 AGGTATGGG
1 AGGTATGGG
50210713 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:50212889 original size:21 final size:21
Alignment explanation
Indices: 50212851--50212895 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
50212841 GTGAATTCTA
*
50212851 TTAAATTCTATTCTTATCCTAT
1 TTAAATTCTATTCATATCC-AT
*
50212873 TTAATTTCTATT-ATATCCAT
1 TTAAATTCTATTCATATCCAT
50212893 TTA
1 TTA
50212896 TTTAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 11 0.52
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTCTATTCATATCCAT
Found at i:50216981 original size:22 final size:22
Alignment explanation
Indices: 50216938--50216980 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
50216928 TTAAAAATTA
*
50216938 CAAATAAATTTTTATACTTTTT
1 CAAATAAATTTTAATACTTTTT
50216960 CAAATAAA-TTTAATACTTTTT
1 CAAATAAATTTTAATACTTTTT
50216981 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (22 bp):
CAAATAAATTTTAATACTTTTT
Found at i:50216990 original size:17 final size:17
Alignment explanation
Indices: 50216968--50217000 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
50216958 TTCAAATAAA
50216968 TTTAATACTTT-TTTATT
1 TTTAATA-TTTGTTTATT
50216985 TTTAATATTTGTTTAT
1 TTTAATATTTGTTTAT
50217001 AATTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTAATATTTGTTTATT
Found at i:50220241 original size:72 final size:72
Alignment explanation
Indices: 50220119--50220273 Score: 222
Period size: 72 Copynumber: 2.2 Consensus size: 72
50220109 AACGTGGTTC
* * *
50220119 CAACATCTCACATCACTCCGAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCTGA
1 CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
50220184 A-GAGATG
66 AGGA-ATG
* * * * *
50220191 CAACACCTCACATCCCTTCAAAGTCTTGAAATTGATGATTGCCCAGAGCTGTCGTTTCTGCCCGA
1 CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
50220256 AGGAATG
66 AGGAATG
50220263 CAACACCTCAC
1 CAACACCTCAC
50220274 TGCACTCAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 72 0.97
73 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (72 bp):
CAACACCTCACATCACTCCAAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
AGGAATG
Found at i:50220297 original size:72 final size:72
Alignment explanation
Indices: 50220119--50220297 Score: 204
Period size: 72 Copynumber: 2.5 Consensus size: 72
50220109 AACGTGGTTC
* * * * *
50220119 CAACATCTCACATCACTCCGAAGTCTTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCTGA
1 CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
50220184 AGAGATG
66 AGAGATG
* * * * *
50220191 CAACACCTCACATCCCTTCAAAGTCTTGAAATTGATGATTGCCCAGAGCTGTCGTTTCTGCCCGA
1 CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
50220256 AG-GAATG
66 AGAG-ATG
50220263 CAACACCTCAC-TGCAC-TCAAAAG-ATTAAAGATTGA
1 CAACACCTCACAT-CACTTC-AAAGTATTAAA-ATTGA
50220298 AGGGTGTCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
71 8 0.09
72 84 0.91
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (72 bp):
CAACACCTCACATCACTTCAAAGTATTAAAATTGATGATTGCCCAAAGCTGTCGTTTCTACCCGA
AGAGATG
Found at i:50221616 original size:9 final size:10
Alignment explanation
Indices: 50221596--50221661 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
50221586 TTTTTATTTT
50221596 AAAAATTAAA
1 AAAAATTAAA
50221606 AAAAATTAAA
1 AAAAATTAAA
*
50221616 AAAAGTATTTTAA
1 AAAA--A-TTAAA
* **
50221629 AAATATTTTA
1 AAAAATTAAA
**
50221639 AAATTTTAAA
1 AAAAATTAAA
50221649 AAAAATTAAA
1 AAAAATTAAA
50221659 AAA
1 AAA
50221662 GTATGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 36 0.80
11 1 0.02
12 1 0.02
13 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:50221630 original size:12 final size:11
Alignment explanation
Indices: 50221615--50221683 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
50221605 AAAAAATTAA
50221615 AAAAAGTATTTT
1 AAAAA-TATTTT
50221627 AAAAATATTTT
1 AAAAATATTTT
50221638 --AAA-ATTTT
1 AAAAATATTTT
* * *
50221646 AAAAAAAATTA
1 AAAAATATTTT
* *
50221657 AAAAAGTATGTA
1 AAAAA-TATTTT
50221669 AAAAATATTTT
1 AAAAATATTTT
50221680 AAAA
1 AAAA
50221684 TTAAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 3 0.07
11 22 0.48
12 13 0.28
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:50221636 original size:42 final size:41
Alignment explanation
Indices: 50221590--50221692 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 41
50221580 GGCCCATTTT
* *
50221590 TATTTTAAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTAAAAAAAATT-AAAAAAGTATGTAAAAAA
*
50221632 TATTTTAAAATTTTAAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAA-ATTAAAAAAAATTAAAAAAGTATGTAAAAAA
50221674 TATTTT-AAAATTAAAAAAA
1 TATTTTAAAAATTAAAAAAA
50221693 TAAATATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 9 0.16
41 3 0.05
42 32 0.57
43 12 0.21
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (41 bp):
TATTTTAAAAATTAAAAAAAATTAAAAAAGTATGTAAAAAA
Found at i:50221660 original size:19 final size:19
Alignment explanation
Indices: 50221622--50221660 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
50221612 TAAAAAAAGT
* * *
50221622 ATTTTAAAAATATTTTAAA
1 ATTTTAAAAAAAATTAAAA
50221641 ATTTTAAAAAAAATTAAAA
1 ATTTTAAAAAAAATTAAAA
50221660 A
1 A
50221661 AGTATGTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAAAATTAAAA
Found at i:50225349 original size:25 final size:26
Alignment explanation
Indices: 50225301--50225349 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
50225291 TAGTTTCTTC
* *
50225301 TTTTATATTATATATACAATATTTTA
1 TTTTATATTATATATAAAAAATTTTA
*
50225327 TTTT-TATTTTATATAAAAAATTT
1 TTTTATATTATATATAAAAAATTT
50225350 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTTTATATTATATATAAAAAATTTTA
Found at i:50228690 original size:16 final size:15
Alignment explanation
Indices: 50228661--50228704 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
50228651 AAATTAGAGA
50228661 ATTCTATTAAATTTT
1 ATTCTATTAAATTTT
* *
50228676 ATTCTTATTATATTTA
1 ATTC-TATTAAATTTT
50228692 ATTTCTATTAAAT
1 A-TTCTATTAAAT
50228705 CCATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 17 0.71
17 3 0.12
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTCTATTAAATTTT
Found at i:50230357 original size:19 final size:19
Alignment explanation
Indices: 50230333--50230403 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
50230323 TAAATATATT
50230333 TATTTTTTAAATTTTAAAA
1 TATTTTTTAAATTTTAAAA
**
50230352 TATTTTTTACATACTTTTTTAA
1 TATTTTTTA-A-A-TTTTAAAA
50230374 T-TTTTTTAAATTTTAAAA
1 TATTTTTTAAATTTTAAAA
*
50230392 TATTTTTAAAAT
1 TATTTTTTAAAT
50230404 ACTTTTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.16
19 19 0.44
20 2 0.05
21 8 0.19
22 7 0.16
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTTAAATTTTAAAA
Found at i:50230379 original size:10 final size:10
Alignment explanation
Indices: 50230335--50230431 Score: 53
Period size: 9 Copynumber: 9.7 Consensus size: 10
50230325 AATATATTTA
50230335 TTTTTTAAA-
1 TTTTTTAAAT
*
50230344 -TTTTAAAAT
1 TTTTTTAAAT
*
50230353 ATTTTTTACATAC
1 -TTTTTTA-A-AT
50230366 TTTTTT-AAT
1 TTTTTTAAAT
50230375 TTTTTTAAA-
1 TTTTTTAAAT
*
50230384 -TTTTAAAAT
1 TTTTTTAAAT
*
50230393 ATTTTTAAAAT
1 -TTTTTTAAAT
*
50230404 ACTTTTTTTAAT
1 --TTTTTTAAAT
50230416 TTTTTT-AAT
1 TTTTTTAAAT
50230425 TTTTTTA
1 TTTTTTA
50230432 TTTTAAAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 21
0.70 0.08 0.21
Matches are distributed among these distances:
8 14 0.20
9 16 0.23
10 9 0.13
11 14 0.20
12 15 0.22
13 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:50230398 original size:11 final size:11
Alignment explanation
Indices: 50230384--50230514 Score: 69
Period size: 11 Copynumber: 11.9 Consensus size: 11
50230374 TTTTTTTAAA
50230384 TTTTAAAATAT
1 TTTTAAAATAT
50230395 TTTTAAAATACT
1 TTTTAAAATA-T
** *
50230407 TTTTTTAATTT
1 TTTTAAAATAT
** *
50230418 TTTTAATTTTTTT
1 TTTTAA--AATAT
50230431 ATTTTAAAATAT
1 -TTTTAAAATAT
50230443 TTTTAAAATACT
1 TTTTAAAATA-T
*
50230455 TTTT----TAA
1 TTTTAAAATAT
50230462 TTTTAAAATAT
1 TTTTAAAATAT
50230473 TTTTAAAATACTT
1 TTTTAAAATA--T
**
50230486 TTTTTTAAT-T
1 TTTTAAAATAT
50230496 TTTT-AAA-AT
1 TTTTAAAATAT
50230505 TTTTAAAATA
1 TTTTAAAATA
50230515 AAAATGGGCC
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
7 4 0.04
8 2 0.02
9 7 0.08
10 8 0.09
11 38 0.42
12 15 0.16
13 11 0.12
14 6 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:50230430 original size:9 final size:9
Alignment explanation
Indices: 50230406--50230435 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
50230396 TTTAAAATAC
50230406 TTTTTTTAA
1 TTTTTTTAA
50230415 TTTTTTTAA
1 TTTTTTTAA
50230424 TTTTTTT-A
1 TTTTTTTAA
50230432 TTTT
1 TTTT
50230436 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:50230438 original size:48 final size:49
Alignment explanation
Indices: 50230344--50230465 Score: 178
Period size: 48 Copynumber: 2.5 Consensus size: 49
50230334 ATTTTTTAAA
* *
50230344 TTTTAAAATA-TTTTTTACATACTTTTTTAATTTTTTTAAATTTTAAAATAT
1 TTTTAAAATACTTTTTT-TA-ATTTTTTTAATTTTTTT-AATTTTAAAATAT
50230395 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTT-ATTTTAAAATAT
1 TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAATTTTAAAATAT
50230443 TTTTAAAATAC-TTTTTTAATTTT
1 TTTTAAAATACTTTTTTTAATTTT
50230466 AAAATATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
47 12 0.18
48 23 0.34
50 16 0.24
51 11 0.16
52 6 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (49 bp):
TTTTAAAATACTTTTTTTAATTTTTTTAATTTTTTTAATTTTAAAATAT
Found at i:50230475 original size:48 final size:49
Alignment explanation
Indices: 50230372--50230476 Score: 151
Period size: 48 Copynumber: 2.1 Consensus size: 49
50230362 ATACTTTTTT
***
50230372 AATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTT
1 AATTTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAA
50230422 AATTTTTTT-ATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTAAA
1 AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAA
50230469 ATATTTTT
1 A-ATTTTT
50230477 AAAATACTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
47 13 0.25
48 29 0.57
50 9 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (49 bp):
AATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAA
Found at i:50230495 original size:32 final size:31
Alignment explanation
Indices: 50230424--50230514 Score: 134
Period size: 30 Copynumber: 3.0 Consensus size: 31
50230414 ATTTTTTTAA
50230424 TTTTTTT-ATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
50230454 -TTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
*
50230484 TTTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 -TTTTTTTAA-TTTTAAAATATTTTTAAAATA
50230515 AAAATGGGCC
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
29 6 0.11
30 23 0.41
32 20 0.36
33 7 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:50233113 original size:5 final size:5
Alignment explanation
Indices: 50233103--50233148 Score: 69
Period size: 5 Copynumber: 9.4 Consensus size: 5
50233093 AAATTTGATT
50233103 AATTA AATTA AATTA AATTA AATTA AATTA AATATA AA--A AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AAT-TA AATTA AATTA AA
50233149 AGTGGAGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
5 31 0.82
6 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATTA
Found at i:50239945 original size:31 final size:32
Alignment explanation
Indices: 50239886--50239950 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
50239876 AGCAAATTAC
50239886 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
50239918 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
50239949 AA
1 AA
50239951 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:50244503 original size:20 final size:20
Alignment explanation
Indices: 50244478--50244580 Score: 62
Period size: 21 Copynumber: 4.7 Consensus size: 20
50244468 TACGCAACTT
*
50244478 TTTTTTTTGCTTTTTTTTTG
1 TTTTTTTTGCTTTTTTTCTG
* * *
50244498 TTTTTTTTGCGCTTTTTACTC
1 TTTTTTTTGC-TTTTTTTCTG
* *
50244519 TTTTTTTGCGCTTTTTTGCTTTTTTG
1 TTTTTTT-TGC---TTT--TTTTCTG
*
50244545 TTTTTTTTGCTGTTTTTGCTG
1 TTTTTTTTGCT-TTTTTTCTG
50244566 TTTTTTTTTGCTTTT
1 -TTTTTTTTGCTTTT
50244581 ATTTAAAGAA
Statistics
Matches: 62, Mismatches: 13, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
20 10 0.16
21 21 0.34
22 14 0.23
23 2 0.03
24 2 0.03
25 2 0.03
26 11 0.18
ACGTcount: A:0.01, C:0.11, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTTTTTTGCTTTTTTTCTG
Found at i:50244580 original size:9 final size:9
Alignment explanation
Indices: 50244479--50244571 Score: 64
Period size: 9 Copynumber: 9.8 Consensus size: 9
50244469 ACGCAACTTT
50244479 TTTTTTTGC
1 TTTTTTTGC
*
50244488 TTTTTTTTTGT
1 --TTTTTTTGC
50244499 TTTTTTTGCGC
1 TTTTTTT--GC
*
50244510 TTTTTACT-C
1 TTTTT-TTGC
50244519 TTTTTTTGC
1 TTTTTTTGC
*
50244528 GCTTTTTTGC
1 -TTTTTTTGC
*
50244538 -TTTTTTGT
1 TTTTTTTGC
50244546 TTTTTTTGC
1 TTTTTTTGC
*
50244555 TGTTTTTGC
1 TTTTTTTGC
50244564 TGTTTTTT
1 T-TTTTTT
50244572 TTTGCTTTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
8 8 0.12
9 30 0.45
10 13 0.20
11 14 0.21
12 1 0.02
ACGTcount: A:0.01, C:0.11, G:0.13, T:0.75
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:50245185 original size:31 final size:32
Alignment explanation
Indices: 50245129--50245191 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
50245119 AAATTACAAG
50245129 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
50245161 AGTAATTGAATCCTAAT-AAAACTCTTTAAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAA
50245192 TTATCTAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.45
32 17 0.55
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (32 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAAA
Found at i:50245287 original size:3 final size:3
Alignment explanation
Indices: 50245279--50245324 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
50245269 GCATTAAGTA
50245279 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
50245325 TACATAAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:50253588 original size:21 final size:21
Alignment explanation
Indices: 50253562--50253602 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50253552 ATCTGCTCAA
* *
50253562 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
50253583 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
50253603 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:50264442 original size:14 final size:14
Alignment explanation
Indices: 50264425--50264455 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
50264415 TTAATTTAGA
50264425 AAATTTAATTAATT
1 AAATTTAATTAATT
*
50264439 AAATTTATTTAATT
1 AAATTTAATTAATT
50264453 AAA
1 AAA
50264456 ACAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:50265164 original size:20 final size:19
Alignment explanation
Indices: 50265116--50265170 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
50265106 ATGTTGTTGT
* *
50265116 TTTTTTAACT-TTGTTATA
1 TTTTTTAAATATTTTTATA
50265134 TTTTTTAAAATATTTTTATAA
1 TTTTTT-AAATATTTTTAT-A
50265155 TTTTTTAAATGATTTT
1 TTTTTTAAAT-ATTTT
50265171 GTGACGTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 3 0.10
20 10 0.32
21 12 0.39
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTTTAAATATTTTTATA
Found at i:50271725 original size:24 final size:25
Alignment explanation
Indices: 50271678--50271737 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
50271668 GAACAATTGC
* **
50271678 CAAGTTCAAACCCTAATATGGGAAT
1 CAAGTTCAAGCCCTAATACAGGAAT
50271703 CAAGTTCAAGCCC-AATACAGGAAT
1 CAAGTTCAAGCCCTAATACAGGAAT
50271727 CAAGTTCAAGC
1 CAAGTTCAAGC
50271738 ATTAACTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 20 0.62
25 12 0.38
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (25 bp):
CAAGTTCAAGCCCTAATACAGGAAT
Found at i:50272383 original size:12 final size:12
Alignment explanation
Indices: 50272366--50272390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50272356 TTGTTAAGGG
50272366 AAACAATCATAA
1 AAACAATCATAA
50272378 AAACAATCATAA
1 AAACAATCATAA
50272390 A
1 A
50272391 CTTTAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (12 bp):
AAACAATCATAA
Found at i:50283935 original size:9 final size:9
Alignment explanation
Indices: 50283912--50283973 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 9
50283902 TGATATAAAC
*
50283912 TTATTAAAA
1 TTATAAAAA
* *
50283921 TGATAAGAA
1 TTATAAAAA
50283930 TTATAAAAAA
1 TTAT-AAAAA
50283940 TTATAAAAA
1 TTATAAAAA
*
50283949 CTTATAAAGA
1 -TTATAAAAA
50283959 TTATAATAAA
1 TTATAA-AAA
50283969 TTATA
1 TTATA
50283974 TTTTTTTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
9 20 0.47
10 23 0.53
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:50283939 original size:19 final size:20
Alignment explanation
Indices: 50283897--50283956 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
50283887 TATAAATATT
* *
50283897 AAAACTGATATAAACTTAT-
1 AAAAATGATAAAAACTTATA
* *
50283916 TAAAATGATAAGAA-TTATA
1 AAAAATGATAAAAACTTATA
*
50283935 AAAAATTATAAAAACTTATA
1 AAAAATGATAAAAACTTATA
50283955 AA
1 AA
50283957 GATTATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 4 0.12
19 21 0.66
20 7 0.22
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAAATGATAAAAACTTATA
Found at i:50283961 original size:19 final size:17
Alignment explanation
Indices: 50283879--50283973 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 17
50283869 ATCTAATATC
*
50283879 ATAAATATTATAAATATT
1 ATAAA-ATTATAAAAATT
* * *
50283897 A-AAACTGATATAAACTT
1 ATAAAATTATA-AAAATT
* *
50283914 ATTAAAATGATAAGAATT
1 A-TAAAATTATAAAAATT
50283932 ATAAAAAATTATAAAAACTT
1 AT--AAAATTATAAAAA-TT
50283952 ATAAAGATTATAATAAATT
1 ATAAA-ATTATAA-AAATT
50283971 ATA
1 ATA
50283974 TTTTTTTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.07
17 9 0.15
18 9 0.15
19 31 0.52
20 7 0.12
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (17 bp):
ATAAAATTATAAAAATT
Found at i:50284075 original size:21 final size:21
Alignment explanation
Indices: 50284029--50284076 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
50284019 ATTAGAATTC
* *
50284029 TTAAAAAATAATAAAAGAATC
1 TTAAAAAATAATAAAAAAATA
* *
50284050 GTAAAAAATTATAAAAAAATA
1 TTAAAAAATAATAAAAAAATA
50284071 TTAAAA
1 TTAAAA
50284077 TTGATATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (21 bp):
TTAAAAAATAATAAAAAAATA
Found at i:50284578 original size:18 final size:19
Alignment explanation
Indices: 50284539--50284599 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
50284529 CGTCTCTTTT
*
50284539 TTTAATGATTTTTATAGA-AA
1 TTTAATAATTTTT-TA-ATAA
*
50284559 TTTAAT-ATTTTTTATTAA
1 TTTAATAATTTTTTAATAA
*
50284577 TTTTATAATTTTTTAATAA
1 TTTAATAATTTTTTAATAA
50284596 TTTA
1 TTTA
50284600 TTAGAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.26
19 20 0.57
20 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTTTTAATAA
Found at i:50284589 original size:49 final size:48
Alignment explanation
Indices: 50284536--50284640 Score: 115
Period size: 49 Copynumber: 2.1 Consensus size: 48
50284526 TTACGTCTCT
* * * *
50284536 TTTTTTAATGATTTTTATAGAAATTTA-ATATTTTTTATTAAT-TTTATAA
1 TTTTTTAATAATTTAT-TAG-AATTTATAGATGTTTTA-TAATATTTATAA
50284585 TTTTTTAATAATTTATTAGAATTTATTAGATGTTTTATAATATTTATAA
1 TTTTTTAATAATTTATTAGAATTTA-TAGATGTTTTATAATATTTATAA
*
50284634 TTCTTTA
1 TTTTTTA
50284641 TAAAAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
47 6 0.12
48 7 0.15
49 35 0.73
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (48 bp):
TTTTTTAATAATTTATTAGAATTTATAGATGTTTTATAATATTTATAA
Found at i:50284728 original size:18 final size:19
Alignment explanation
Indices: 50284707--50284742 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
50284697 CTAATATTTA
50284707 GTCATTT-TTATATTTTTT
1 GTCATTTCTTATATTTTTT
*
50284725 GTCATTTCTTTTATTTTT
1 GTCATTTCTTATATTTTT
50284743 ATGATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.72
Consensus pattern (19 bp):
GTCATTTCTTATATTTTTT
Found at i:50285792 original size:17 final size:17
Alignment explanation
Indices: 50285770--50285805 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
50285760 GTCAGCAAAG
50285770 TTAAAAAAAAGAGTAAC
1 TTAAAAAAAAGAGTAAC
*
50285787 TTAAAAAAAAGGGTAAC
1 TTAAAAAAAAGAGTAAC
50285804 TT
1 TT
50285806 CTCTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (17 bp):
TTAAAAAAAAGAGTAAC
Found at i:50290255 original size:27 final size:27
Alignment explanation
Indices: 50290214--50290316 Score: 147
Period size: 27 Copynumber: 3.8 Consensus size: 27
50290204 TAGTATTGGC
50290214 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
* *
50290241 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
*
50290268 GCCTATCTAGG-AGGCGCCAATGGTGAT
1 GCCTATCT-GGAAGGCGCCAATGGTGGT
50290295 GCCATAT-TGGAAGGCGCCAATG
1 GCC-TATCTGGAAGGCGCCAATG
50290317 CTGTGATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
26 2 0.03
27 62 0.90
28 5 0.07
ACGTcount: A:0.20, C:0.21, G:0.36, T:0.22
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:50290936 original size:30 final size:27
Alignment explanation
Indices: 50290879--50290974 Score: 112
Period size: 27 Copynumber: 3.7 Consensus size: 27
50290869 ACGTGGGAAA
*
50290879 ATTATAATATTCATACAAAACTATAAT
1 ATTACAATATTCATACAAAACTATAAT
50290906 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAACTATAAT
* * **
50290928 ATTATAATATTCATACAAAATTACGAT
1 ATTACAATATTCATACAAAACTATAAT
50290955 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
50290975 AATTACTAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
22 15 0.25
23 5 0.08
24 1 0.02
25 1 0.02
26 4 0.07
27 34 0.57
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.33
Consensus pattern (27 bp):
ATTACAATATTCATACAAAACTATAAT
Found at i:50290956 original size:19 final size:20
Alignment explanation
Indices: 50290906--50290957 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
50290896 AAACTATAAT
50290906 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC--AAAA
*
50290928 ATTATAATATTCATAC-AAA
1 ATTACAATATTCATACAAAA
*
50290947 ATTACGATATT
1 ATTACAATATT
50290958 ACAATATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
22 15 0.56
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTACAATATTCATACAAAA
Found at i:50290957 original size:49 final size:48
Alignment explanation
Indices: 50290876--50290984 Score: 173
Period size: 49 Copynumber: 2.2 Consensus size: 48
50290866 AAGACGTGGG
*
50290876 AAAATTATAATATTCATACAAAACTATAATATTACAATATTCATACAAA
1 AAAATTATAATATTCATACAAAACTACAATATTACAATATTCATAC-AA
* *
50290925 AAAATTATAATATTCATACAAAATTACGATATTACAATATTCATACAA
1 AAAATTATAATATTCATACAAAACTACAATATTACAATATTCATACAA
50290973 AAAATTACTAAT
1 AAAATTA-TAAT
50290985 CCAAAACTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 9 0.16
49 47 0.84
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (48 bp):
AAAATTATAATATTCATACAAAACTACAATATTACAATATTCATACAA
Found at i:50291067 original size:21 final size:21
Alignment explanation
Indices: 50291038--50291092 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
50291028 TTCATACAAC
50291038 ATTACAATATTCATAAAAAAA
1 ATTACAATATTCATAAAAAAA
*
50291059 ATTATAATATTCATACAAAAAA
1 ATTACAATATTCATA-AAAAAA
* *
50291081 GTTAAAATATTC
1 ATTACAATATTC
50291093 TACAAAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTACAATATTCATAAAAAAA
Found at i:50291096 original size:21 final size:22
Alignment explanation
Indices: 50291013--50291099 Score: 85
Period size: 21 Copynumber: 4.2 Consensus size: 22
50291003 ATTTAATTAT
* *
50291013 AAAATAATTACAATATTCATAC
1 AAAAAAATTAAAATATTCATAC
* *
50291035 ---AACATTACAATATTCATA-
1 AAAAAAATTAAAATATTCATAC
*
50291053 AAAAAAATTATAATATTCATAC
1 AAAAAAATTAAAATATTCATAC
*
50291075 AAAAAAGTTAAAATATTC-TAC
1 AAAAAAATTAAAATATTCATAC
50291096 AAAA
1 AAAA
50291100 TTCTAATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
19 16 0.29
21 23 0.42
22 16 0.29
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.30
Consensus pattern (22 bp):
AAAAAAATTAAAATATTCATAC
Found at i:50291279 original size:3 final size:3
Alignment explanation
Indices: 50291267--50291310 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
50291257 TTTTTTTTCT
* *
50291267 TTC TTA TTC TTC TTC -TC TTC TTC TTC TTC TCC TTC -TC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
50291311 CCTTTCTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:50291290 original size:14 final size:14
Alignment explanation
Indices: 50291263--50291311 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
50291253 TACCTTTTTT
*
50291263 TTCTT-TCTTATTC
1 TTCTTCTCTTCTTC
50291276 TTCTTCTCTTCTTC
1 TTCTTCTCTTCTTC
50291290 TTCTTCTCCTTC-TC
1 TTCTTCT-CTTCTTC
50291304 TTCTTCTC
1 TTCTTCTC
50291312 CTTTCTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 6 0.18
14 23 0.70
15 4 0.12
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (14 bp):
TTCTTCTCTTCTTC
Found at i:50291296 original size:20 final size:20
Alignment explanation
Indices: 50291267--50291310 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
50291257 TTTTTTTTCT
*
50291267 TTCTTATTCTTCTTCTCTTC
1 TTCTTATTCTCCTTCTCTTC
*
50291287 TTCTTCTTCTCCTTCTCTTC
1 TTCTTATTCTCCTTCTCTTC
50291307 TTCT
1 TTCT
50291311 CCTTTCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTTATTCTCCTTCTCTTC
Found at i:50291312 original size:14 final size:14
Alignment explanation
Indices: 50291274--50291320 Score: 69
Period size: 14 Copynumber: 3.3 Consensus size: 14
50291264 TCTTTCTTAT
50291274 TCTTCTTCT-CTTC
1 TCTTCTTCTCCTTC
50291287 TTCTTCTTCTCCTTC
1 -TCTTCTTCTCCTTC
50291302 TCTTCTTCTCCTTTC
1 TCTTCTTCTCC-TTC
50291317 TCTT
1 TCTT
50291321 TTTTTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
TCTTCTTCTCCTTC
Found at i:50291478 original size:27 final size:27
Alignment explanation
Indices: 50291447--50291512 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
50291437 GCAGAGGACA
50291447 CCATTGGCGCCTCTCCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
* *
50291474 TCATTGGCGCCTCTGCATGAGGCTCCT
1 CCATTGGCGCCTCTCCATGAGGCTCCT
50291501 CCATTGGCGCCT
1 CCATTGGCGCCT
50291513 ACTAGATAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.11, C:0.38, G:0.24, T:0.27
Consensus pattern (27 bp):
CCATTGGCGCCTCTCCATGAGGCTCCT
Found at i:50292005 original size:27 final size:27
Alignment explanation
Indices: 50291964--50292039 Score: 120
Period size: 27 Copynumber: 2.8 Consensus size: 27
50291954 TAGTATTGGC
50291964 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGAAGGCGCCAATGGTGGT
50291991 GCCTATCTAGG-AGGCGCCAATGGTGGT
1 GCCTATCT-GGAAGGCGCCAATGGTGGT
50292018 GCCATAT-TGGAAGGCGCCAATG
1 GCC-TATCTGGAAGGCGCCAATG
50292040 CTGTGATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 2 0.04
27 39 0.85
28 5 0.11
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (27 bp):
GCCTATCTGGAAGGCGCCAATGGTGGT
Found at i:50292143 original size:18 final size:20
Alignment explanation
Indices: 50292101--50292147 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
50292091 GAAACGGAAG
50292101 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
50292121 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
50292139 AAAGAAGAA
1 AAAGAAGAA
50292148 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:50292150 original size:22 final size:23
Alignment explanation
Indices: 50292097--50292150 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
50292087 TACAGAAACG
*
50292097 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
50292121 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
50292142 GAAGAAAAA
1 GAAGAAAAA
50292151 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Done.