Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 40 of 113
Found at i:11500746 original size:6 final size:7
Alignment explanation
Indices: 11500714--11500752 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
11500704 AGGGTGTTCC
*
11500714 TTTTTTA
1 TTTTTAA
*
11500721 TTTTTTA
1 TTTTTAA
11500728 TTTTTATA
1 TTTTTA-A
11500736 TTTTTAA
1 TTTTTAA
11500743 TTTTTAA
1 TTTTTAA
11500750 TTT
1 TTT
11500753 CCTTTTGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTAA
Found at i:11502236 original size:27 final size:26
Alignment explanation
Indices: 11502182--11502241 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
11502172 TATTTGATAC
*
11502182 ATAAGATTATGATAGGATATGATAAA
1 ATAATATTATGATAGGATATGATAAA
* *
11502208 ATGATATTATGAATAGGAT-TAGATTAA
1 ATAATATTATG-ATAGGATAT-GATAAA
11502235 ATAATAT
1 ATAATAT
11502242 CATCATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (26 bp):
ATAATATTATGATAGGATATGATAAA
Found at i:11503137 original size:2 final size:2
Alignment explanation
Indices: 11503130--11503169 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
11503120 GATCCAATAG
*
11503130 TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11503170 AAACTCTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11503254 original size:29 final size:30
Alignment explanation
Indices: 11503221--11503280 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
11503211 TATTGTCTTC
* *
11503221 ATTTTAACTTTTACAATAAAATAGA-TAAA
1 ATTTTAACTTTTACAACAAAAGAGATTAAA
11503250 ATTTTAACTTTTACAACAAAAGAGATTAAA
1 ATTTTAACTTTTACAACAAAAGAGATTAAA
11503280 A
1 A
11503281 GGTTTGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTTAACTTTTACAACAAAAGAGATTAAA
Found at i:11504453 original size:17 final size:17
Alignment explanation
Indices: 11504428--11504464 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
11504418 TTGCATGATA
11504428 ATTTATTTGCCTAATAT
1 ATTTATTTGCCTAATAT
* *
11504445 ATTTGTTTGCCTAATCT
1 ATTTATTTGCCTAATAT
11504462 ATT
1 ATT
11504465 AAGATCTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTTATTTGCCTAATAT
Found at i:11504591 original size:17 final size:18
Alignment explanation
Indices: 11504548--11504591 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
11504538 ATTTGAATTT
*
11504548 CAAATTTAAATAAAATCA
1 CAAATTTAAAAAAAATCA
*
11504566 CAATCTTTAAAAAAAATCA
1 CAA-ATTTAAAAAAAATCA
11504585 -AAATTTA
1 CAAATTTA
11504592 TGGTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 13 0.59
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (18 bp):
CAAATTTAAAAAAAATCA
Found at i:11504822 original size:22 final size:23
Alignment explanation
Indices: 11504786--11504831 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
11504776 ATAATAGAAT
11504786 TAATTAAATTGATAAAAATTAAA
1 TAATTAAATTGATAAAAATTAAA
* *
11504809 TAATT-AATTTATAAAACTTAAA
1 TAATTAAATTGATAAAAATTAAA
11504831 T
1 T
11504832 TCAATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATTAAATTGATAAAAATTAAA
Found at i:11510733 original size:16 final size:15
Alignment explanation
Indices: 11510710--11510781 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
11510700 AAATTAAAAA
11510710 ATAATAAATATTATT
1 ATAATAAATATTATT
*
11510725 ATAATTAAAAATT-TT
1 ATAA-TAAATATTATT
11510740 AATAAATAAATA-TATT
1 -AT-AATAAATATTATT
*
11510756 A-AATAAATTTTATT
1 ATAATAAATATTATT
* *
11510770 AAAATTAATATT
1 ATAATAAATATT
11510782 TAAATTCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 7 0.15
14 5 0.11
15 16 0.35
16 16 0.35
17 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATTATT
Found at i:11510769 original size:14 final size:14
Alignment explanation
Indices: 11510733--11510772 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
11510723 TTATAATTAA
*
11510733 AAATTTTAATAAAT
1 AAATTTTATTAAAT
*
11510747 AAA-TATATTAAAT
1 AAATTTTATTAAAT
11510760 AAATTTTATTAAA
1 AAATTTTATTAAA
11510773 ATTAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTTTATTAAAT
Found at i:11510792 original size:28 final size:27
Alignment explanation
Indices: 11510733--11510786 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
11510723 TTATAATTAA
11510733 AAATTTTAATAAATAAATATATTAAAT
1 AAATTTTAATAAATAAATATATTAAAT
* *
11510760 AAATTTTATTAAAATTAATAT-TTAAAT
1 AAATTTTAAT-AAATAAATATATTAAAT
11510787 TCAATTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATTTTAATAAATAAATATATTAAAT
Found at i:11513607 original size:46 final size:46
Alignment explanation
Indices: 11513540--11513634 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
11513530 TGACAACTAT
* *
11513540 TGTTCTGGTTCTATTAGAATGTTGCATGTGCATTACTTGAAGTGTG
1 TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
*
11513586 TGTTCTGGTTCTATTATAATGTTGCATATGCATTACTTAAAGTGTG
1 TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
11513632 TGT
1 TGT
11513635 CATTCTGTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.45
Consensus pattern (46 bp):
TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
Found at i:11513751 original size:25 final size:25
Alignment explanation
Indices: 11513717--11513767 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11513707 TATGAATACT
11513717 TAATTGTAAATTAGGGTTTCTTGTG
1 TAATTGTAAATTAGGGTTTCTTGTG
11513742 TAATTGTAAATTAGGGTTTCTTGTG
1 TAATTGTAAATTAGGGTTTCTTGTG
11513767 T
1 T
11513768 TCTTTTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.49
Consensus pattern (25 bp):
TAATTGTAAATTAGGGTTTCTTGTG
Found at i:11517127 original size:22 final size:22
Alignment explanation
Indices: 11517081--11517141 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
11517071 AAATTCGACT
**
11517081 TTAATTAAATTAATCGATTGAA
1 TTAATTAAATTAATAAATTGAA
11517103 TTAATTAAATTTAATAAATTG-A
1 TTAATTAAA-TTAATAAATTGAA
11517125 TTAGTTATTAAATTAAT
1 TTA---ATTAAATTAAT
11517142 TTTAGTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 13 0.39
23 9 0.27
24 5 0.15
25 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (22 bp):
TTAATTAAATTAATAAATTGAA
Found at i:11517364 original size:27 final size:26
Alignment explanation
Indices: 11517301--11517364 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
11517291 GGATGATTTT
*
11517301 ATTTAATTTATTTT-AAATATAAAAA
1 ATTTAATATATTTTAAAATATAAAAA
11517326 ATTTAA-A-A-TTTAAAATATAATTAAA
1 ATTTAATATATTTTAAAATATAA--AAA
11517351 A-TTAATATATTTTA
1 ATTTAATATATTTTA
11517365 TTATTTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
22 3 0.09
23 9 0.28
24 4 0.12
25 11 0.34
26 1 0.03
27 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAATATATTTTAAAATATAAAAA
Found at i:11518013 original size:26 final size:26
Alignment explanation
Indices: 11517991--11518042 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
11517981 ATGAAAATTT
*
11517991 TAAATTATTTAATATTTATAAAATTAA
1 TAAATTA-TTAAAATTTATAAAATTAA
*
11518018 TAAATTATTAAAATTTATTAAATTA
1 TAAATTATTAAAATTTATAAAATTA
11518043 TATTTATGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATTATTAAAATTTATAAAATTAA
Found at i:11518041 original size:18 final size:17
Alignment explanation
Indices: 11518009--11518043 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11517999 TTAATATTTA
11518009 TAAAATTAATAAATTAT
1 TAAAATTAATAAATTAT
*
11518026 TAAAATTTATTAAATTAT
1 TAAAA-TTAATAAATTAT
11518044 ATTTATGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTAATAAATTAT
Found at i:11520048 original size:16 final size:17
Alignment explanation
Indices: 11520015--11520048 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11520005 AGAAAGGTCA
11520015 ACTTAAAATGACTTTTT
1 ACTTAAAATGACTTTTT
11520032 ACTTAAAATGA-TTTTT
1 ACTTAAAATGACTTTTT
11520048 A
1 A
11520049 AAATTAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (17 bp):
ACTTAAAATGACTTTTT
Found at i:11520507 original size:29 final size:30
Alignment explanation
Indices: 11520465--11520544 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
11520455 ATAAAAAAAC
*
11520465 TTAATTATGGTGAAAATAAATATTT-AAGAT
1 TTAATT-TGATGAAAATAAATATTTAAAGAT
**
11520495 TTAATTTGATGAAAATTGATATTTAAAGAT
1 TTAATTTGATGAAAATAAATATTTAAAGAT
* *
11520525 TCAA-TTGAATGAAAAAAAAT
1 TTAATTTG-ATGAAAATAAAT
11520545 TAAGAACTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 18 0.44
30 23 0.56
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (30 bp):
TTAATTTGATGAAAATAAATATTTAAAGAT
Found at i:11523528 original size:18 final size:17
Alignment explanation
Indices: 11523488--11523530 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
11523478 AAATTTTAGT
*
11523488 TTAAATATATTTAAAAA
1 TTAAAAATATTTAAAAA
*
11523505 TATAAAAATATTTATATAA
1 T-TAAAAATATTTA-AAAA
11523524 TTAAAAA
1 TTAAAAA
11523531 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:11523863 original size:7 final size:7
Alignment explanation
Indices: 11523847--11523877 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11523837 AGGGTGTTCC
*
11523847 TTTTTTA
1 TTTTTAA
11523854 TTTTTAA
1 TTTTTAA
11523861 TTTTTAA
1 TTTTTAA
11523868 TTTTTAA
1 TTTTTAA
11523875 TTT
1 TTT
11523878 CCTTTTGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:11525366 original size:27 final size:26
Alignment explanation
Indices: 11525312--11525371 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
11525302 TATTTGATAC
*
11525312 ATAAGATTATGATAGGATATGATAAA
1 ATAATATTATGATAGGATATGATAAA
* *
11525338 ATGATATTATGAATAGGAT-TAGATTAA
1 ATAATATTATG-ATAGGATAT-GATAAA
11525365 ATAATAT
1 ATAATAT
11525372 CATCATATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (26 bp):
ATAATATTATGATAGGATATGATAAA
Found at i:11526391 original size:29 final size:29
Alignment explanation
Indices: 11526342--11526400 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
11526332 TATTGTTGTT
* * *
11526342 ATTTTAACTTTTACAATAAAATATATAAA
1 ATTTTAACTTTTACAACAAAAGAGATAAA
*
11526371 ATTTTAACTTTTAGAACAAAAGAGATAAA
1 ATTTTAACTTTTACAACAAAAGAGATAAA
11526400 A
1 A
11526401 AGGTTTGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTAACTTTTACAACAAAAGAGATAAA
Found at i:11527689 original size:17 final size:18
Alignment explanation
Indices: 11527646--11527689 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
11527636 ATTTGAATTT
*
11527646 CAAATTTAAATAAAATCA
1 CAAATTTAAAAAAAATCA
*
11527664 CAATCTTTAAAAAAAATCA
1 CAA-ATTTAAAAAAAATCA
11527683 -AAATTTA
1 CAAATTTA
11527690 TGGTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 13 0.59
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (18 bp):
CAAATTTAAAAAAAATCA
Found at i:11528889 original size:31 final size:30
Alignment explanation
Indices: 11528844--11528928 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
11528834 TTGAGATATA
11528844 AAATATTTATTTTCATTTAATTGAGTTTTT
1 AAATATTTATTTTCATTTAATTGAGTTTTT
* * * * *
11528874 GAATAATTTACTTTCATTAAATTAATTTTTT
1 AAAT-ATTTATTTTCATTTAATTGAGTTTTT
*
11528905 AAATATTTATTTTTATTTAATTGA
1 AAATATTTATTTTCATTTAATTGA
11528929 ACTTTCAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 19 0.43
31 25 0.57
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.58
Consensus pattern (30 bp):
AAATATTTATTTTCATTTAATTGAGTTTTT
Found at i:11529256 original size:20 final size:22
Alignment explanation
Indices: 11529228--11529268 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
11529218 TATCTTTTAG
*
11529228 ATATGATATTT-TA-TATATTT
1 ATATCATATTTATATTATATTT
11529248 ATATCATATTTATATTATATT
1 ATATCATATTTATATTATATT
11529269 AATTATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATATCATATTTATATTATATTT
Found at i:11536229 original size:46 final size:46
Alignment explanation
Indices: 11536162--11536254 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
11536152 TGACAACTAT
* *
11536162 TGTTCTGGTTCTATTAGAATGTTGCATGTGCATTACTTGAAGTGTG
1 TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
*
11536208 TGTTCTGGTTCTATTATAATGTTGCATATGCATTACTTAAAGTGTG
1 TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
11536254 T
1 T
11536255 CATTCTGTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.22, C:0.11, G:0.23, T:0.45
Consensus pattern (46 bp):
TGTTCTGGTTCTATTAGAATGTTGCATATGCATTACTTAAAGTGTG
Found at i:11542129 original size:2 final size:2
Alignment explanation
Indices: 11542124--11542158 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11542114 TTTTTTTTTA
11542124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11542159 CACACACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11542689 original size:52 final size:52
Alignment explanation
Indices: 11542627--11542730 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
11542617 AACTCTTTGA
*
11542627 CATAGTTTACAACTTCTACAAGTACCTGTCAAAGTTGAGACTAGGAGCAATT
1 CATAGTTTACAACTTCTACAAGTACCTGACAAAGTTGAGACTAGGAGCAATT
* * * *
11542679 CATAGTTTACAACTTCTACACGTACCTGACATAGTTGAGAGTTGGAGCAATT
1 CATAGTTTACAACTTCTACAAGTACCTGACAAAGTTGAGACTAGGAGCAATT
11542731 TCTTAAGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (52 bp):
CATAGTTTACAACTTCTACAAGTACCTGACAAAGTTGAGACTAGGAGCAATT
Found at i:11552180 original size:22 final size:22
Alignment explanation
Indices: 11552155--11552199 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11552145 GAATTCTTTT
11552155 TAGCTGCTCATAATGCTTGGAA
1 TAGCTGCTCATAATGCTTGGAA
*
11552177 TAGCTGCTTATAATGCTTGGAA
1 TAGCTGCTCATAATGCTTGGAA
11552199 T
1 T
11552200 CGTTCTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (22 bp):
TAGCTGCTCATAATGCTTGGAA
Found at i:11554198 original size:16 final size:16
Alignment explanation
Indices: 11554164--11554197 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11554154 AAGTATTTTG
*
11554164 AAATTATTTATTATTA
1 AAATTATTTAATATTA
11554180 AAATTA-TTAATATTA
1 AAATTATTTAATATTA
11554195 AAA
1 AAA
11554198 AACAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTATTTAATATTA
Found at i:11554307 original size:26 final size:28
Alignment explanation
Indices: 11554278--11554357 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 28
11554268 TTTATTCTTT
*
11554278 ATAGTATTTATTAATATATTATA-T-TA
1 ATAGTATTTATTAATATAATATATTATA
*
11554304 ATAGTATATTATTTATTAATAATATATTATA
1 ATAGTAT-TTA-TTAAT-ATAATATATTATA
* *
11554335 ATATTATTTACTAATATAATATA
1 ATAGTATTTATTAATATAATATA
11554358 CTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 7 0.16
27 3 0.07
28 12 0.27
29 10 0.23
30 4 0.09
31 8 0.18
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (28 bp):
ATAGTATTTATTAATATAATATATTATA
Found at i:11554320 original size:18 final size:19
Alignment explanation
Indices: 11554294--11554340 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
11554284 TTTATTAATA
*
11554294 TATTATATTAATAGTATAT
1 TATTATATTAATAATATAT
11554313 TATT-TATTAATAATATAT
1 TATTATATTAATAATATAT
*
11554331 TATAATATTA
1 TATTATATTA
11554341 TTTACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTATATTAATAATATAT
Found at i:11554320 original size:31 final size:28
Alignment explanation
Indices: 11554277--11554357 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 28
11554267 TTTTATTCTT
*
11554277 TATAGTATTTATTAATATATTATATTAATA
1 TATATTATTTATTAATATA-TATATT-ATA
11554307 GTATATTATTTATTAATA-ATATATTATA
1 -TATATTATTTATTAATATATATATTATA
*
11554335 -ATATTATTTACTAATATAATATA
1 TATATTATTTATTAATAT-ATATA
11554358 CTATTTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
26 15 0.33
28 8 0.17
29 6 0.13
30 1 0.02
31 16 0.35
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
TATATTATTTATTAATATATATATTATA
Found at i:11554334 original size:23 final size:23
Alignment explanation
Indices: 11554308--11554383 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
11554298 ATATTAATAG
11554308 TATATTATTTATTAATAATATAT
1 TATATTATTTATTAATAATATAT
* * *
11554331 TATAATA-TTATTTACTAATATAA
1 TATATTATTTA-TTAATAATATAT
*
11554354 TATACTATTTATTAAT-ATAATAT
1 TATATTATTTATTAATAAT-ATAT
11554377 TAT-TTAT
1 TATATTAT
11554384 AAAAAATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
22 8 0.19
23 32 0.74
24 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTATTTATTAATAATATAT
Found at i:11554383 original size:18 final size:18
Alignment explanation
Indices: 11554331--11554383 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 18
11554321 AATAATATAT
*
11554331 TATAATATTATTTACTAA
1 TATAATATTATTTATTAA
11554349 TATAATATACTATTTATTAA
1 TATAATAT--TATTTATTAA
11554369 TATAATATTATTTAT
1 TATAATATTATTTAT
11554384 AAAAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.47
20 17 0.53
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATATTATTTATTAA
Found at i:11555419 original size:21 final size:19
Alignment explanation
Indices: 11555375--11555431 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
11555365 AGTACATTAG
* *
11555375 ATTTA-TTTATTTTAGTATT
1 ATTTATTTTATTTAAATA-T
11555394 ATTTATTTTGATATTAAATAT
1 ATTTATTTT-AT-TTAAATAT
11555415 ATTTATTTTATTTAAAT
1 ATTTATTTTATTTAAAT
11555432 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 11 0.33
20 5 0.15
21 12 0.36
22 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
ATTTATTTTATTTAAATAT
Found at i:11557891 original size:150 final size:150
Alignment explanation
Indices: 11557581--11557884 Score: 572
Period size: 150 Copynumber: 2.0 Consensus size: 150
11557571 TTTGAAAAAT
*
11557581 TGTTAAATAAAGGAACAAACTATGGCTAAGAGCATAATCTGCACTACTGCTTAGAATGAAATGCA
1 TGTTAAATAAAGGAACAAACTATGGCTAAGAGCATAATCTGCACTACTGCATAGAATGAAATGCA
* *
11557646 AGAGGCTGTACTAAAGGCATGCCAATGTTAAAGATTTTACAGTATTTACTGGGTATTGTCAATCA
66 AGAGGCTGTACTAAAGGCATGCCAATGTTAAAGATTTTACAGTATTTACTAGGCATTGTCAATCA
11557711 ACTCTTTGAACCTAACAATG
131 ACTCTTTGAACCTAACAATG
11557731 TGTTAAATAAAGGAACAAACTATGGCTAAGAGCATAATCTGCACTACTGCATAGAATGAAATGCA
1 TGTTAAATAAAGGAACAAACTATGGCTAAGAGCATAATCTGCACTACTGCATAGAATGAAATGCA
*
11557796 AGAGGCTGTACTAAAGGCATGCTAATGTTAAAGATTTTACAGTATTTACTAGGCATTGTCAATCA
66 AGAGGCTGTACTAAAGGCATGCCAATGTTAAAGATTTTACAGTATTTACTAGGCATTGTCAATCA
11557861 ACTCTTTGAACCTAACAATG
131 ACTCTTTGAACCTAACAATG
11557881 TGTT
1 TGTT
11557885 CTATAAATAT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (150 bp):
TGTTAAATAAAGGAACAAACTATGGCTAAGAGCATAATCTGCACTACTGCATAGAATGAAATGCA
AGAGGCTGTACTAAAGGCATGCCAATGTTAAAGATTTTACAGTATTTACTAGGCATTGTCAATCA
ACTCTTTGAACCTAACAATG
Found at i:11575400 original size:37 final size:37
Alignment explanation
Indices: 11575359--11575446 Score: 88
Period size: 37 Copynumber: 2.4 Consensus size: 37
11575349 TTTAATTTTG
* * **
11575359 TATTTATATATATTATATTAATAAAATTATTATATAA
1 TATTTATATATAATATATTAATAAAATAAAAATATAA
* ** *
11575396 TATTT-TAATTTAATATATTAATTTAATAAAAATATTA
1 TATTTAT-ATATAATATATTAATAAAATAAAAATATAA
11575433 TATTTATATATAAT
1 TATTTATATATAAT
11575447 TAAGATATAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
36 1 0.03
37 38 0.95
38 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATTTATATATAATATATTAATAAAATAAAAATATAA
Found at i:11575409 original size:13 final size:13
Alignment explanation
Indices: 11575372--11575423 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
11575362 TTATATATAT
**
11575372 TATATTAATAAAA
1 TATATTAATTTAA
*
11575385 T-TATT-ATATAA
1 TATATTAATTTAA
*
11575396 TATTTTAATTTAA
1 TATATTAATTTAA
11575409 TATATTAATTTAA
1 TATATTAATTTAA
11575422 TA
1 TA
11575424 AAAATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 7 0.21
13 20 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTAATTTAA
Found at i:11575447 original size:42 final size:42
Alignment explanation
Indices: 11575360--11575488 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 42
11575350 TTAATTTTGT
* *
11575360 ATTTATATATATT-ATATTAATAAAATTATTATATAATATTTTA
1 ATTTA-ATATATTAAT-TTAATAAAAATATTATATAATATTATA
*
11575403 ATTTAATATATTAATTTAATAAAAATATTATAT-TTATATATA
1 ATTTAATATATTAATTTAATAAAAATATTATATAATAT-TATA
*
11575445 A-TTAAGATA-TAATTTATATTAAAAAATATT-TAATAAATATTATA
1 ATTTAATATATTAATTTA-A-T-AAAAATATTAT-AT-AATATTATA
11575489 TTAAAATTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
40 7 0.10
41 11 0.15
42 30 0.41
43 18 0.25
44 4 0.05
45 3 0.04
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (42 bp):
ATTTAATATATTAATTTAATAAAAATATTATATAATATTATA
Found at i:11579407 original size:23 final size:23
Alignment explanation
Indices: 11579381--11579426 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
11579371 AAAGCACTCT
11579381 TTATGCCGGCTTAAAAATTCTTG
1 TTATGCCGGCTTAAAAATTCTTG
11579404 TTATGCCGGCTTAAAAATTCTTG
1 TTATGCCGGCTTAAAAATTCTTG
11579427 AACTGTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
TTATGCCGGCTTAAAAATTCTTG
Found at i:11582204 original size:15 final size:15
Alignment explanation
Indices: 11582186--11582218 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11582176 CATATCAAAT
*
11582186 TTATTTATTTTAGAA
1 TTATTTATTTTAAAA
11582201 TTATTTATTTTAAAA
1 TTATTTATTTTAAAA
11582216 TTA
1 TTA
11582219 AATATATTAA
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:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTTATTTTAAAA
Found at i:11582299 original size:22 final size:22
Alignment explanation
Indices: 11582273--11582316 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11582263 TTATAATTAA
11582273 AAATATATTTAAACAAA-AATTT
1 AAATATATTTAAA-AAAGAATTT
*
11582295 AAATATTTTTAAAAAAGAATTT
1 AAATATATTTAAAAAAGAATTT
11582317 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATATATTTAAAAAAGAATTT
Found at i:11582398 original size:15 final size:14
Alignment explanation
Indices: 11582364--11582400 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
11582354 AAAAAATATA
11582364 TAATTTTTGAAAAT
1 TAATTTTTGAAAAT
*
11582378 TAATTTTTGATAAT
1 TAATTTTTGAAAAT
11582392 TATATTTTT
1 TA-ATTTTT
11582401 TTCTCAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (14 bp):
TAATTTTTGAAAAT
Found at i:11589742 original size:15 final size:15
Alignment explanation
Indices: 11589722--11589754 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11589712 CATATCAAAT
*
11589722 TTATTTATTTTAGAA
1 TTATTTATTTTAAAA
11589737 TTATTTATTTTAAAA
1 TTATTTATTTTAAAA
11589752 TTA
1 TTA
11589755 AATATATTAA
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:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTTATTTTAAAA
Found at i:11589904 original size:14 final size:14
Alignment explanation
Indices: 11589885--11589921 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
11589875 AAAAAATATA
11589885 TAATTTTTGAAAAT
1 TAATTTTTGAAAAT
11589899 TAATTTTTGAAAAT
1 TAATTTTTGAAAAT
11589913 TATATTTTT
1 TA-ATTTTT
11589922 TTCTCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TAATTTTTGAAAAT
Found at i:11595262 original size:27 final size:27
Alignment explanation
Indices: 11595222--11595284 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
11595212 CATACCATAC
*
11595222 TGCACATAGAAGGTTGGGTAATGAATG
1 TGCACAAAGAAGGTTGGGTAATGAATG
*
11595249 TGCACAAAGGAGGTTGGGTAATGAATG
1 TGCACAAAGAAGGTTGGGTAATGAATG
11595276 TGCACAAAG
1 TGCACAAAG
11595285 TTGGGTGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.33, T:0.22
Consensus pattern (27 bp):
TGCACAAAGAAGGTTGGGTAATGAATG
Found at i:11596863 original size:2 final size:2
Alignment explanation
Indices: 11596826--11596852 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11596816 AATCGTATGC
11596826 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11596853 CACACTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11599802 original size:17 final size:17
Alignment explanation
Indices: 11599782--11599815 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11599772 AATACGTAGT
11599782 CTGCTCACTTTTATTGA
1 CTGCTCACTTTTATTGA
11599799 CTGCTCACTTTTATTGA
1 CTGCTCACTTTTATTGA
11599816 GTCAGTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.47
Consensus pattern (17 bp):
CTGCTCACTTTTATTGA
Found at i:11599845 original size:34 final size:34
Alignment explanation
Indices: 11599802--11599871 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
11599792 TTATTGACTG
11599802 CTCACTTTTATTGAGTCAGTAGTCGAGAGAATTT
1 CTCACTTTTATTGAGTCAGTAGTCGAGAGAATTT
** * *
11599836 CTCACTTTTATTGAGTTGGTAGTTGAGAGGATTT
1 CTCACTTTTATTGAGTCAGTAGTCGAGAGAATTT
11599870 CT
1 CT
11599872 ATCTTCAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (34 bp):
CTCACTTTTATTGAGTCAGTAGTCGAGAGAATTT
Found at i:11600228 original size:32 final size:32
Alignment explanation
Indices: 11600170--11600243 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 32
11600160 AATATAACTT
11600170 TTGAAAATTCATTTTCAAGAATTTTTTGAGTTA
1 TTGAAAA-TCATTTTCAAGAATTTTTTGAGTTA
* *
11600203 TTGAAAATCATTTTTCAATAATTTTTTGAGTTC
1 TTGAAAATCA-TTTTCAAGAATTTTTTGAGTTA
11600236 TTGAAAAT
1 TTGAAAAT
11600244 GAATTTTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (32 bp):
TTGAAAATCATTTTCAAGAATTTTTTGAGTTA
Found at i:11600391 original size:15 final size:15
Alignment explanation
Indices: 11600354--11600387 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11600344 AATTTTAATT
*
11600354 TAAATAATATTAAAA
1 TAAATAATACTAAAA
11600369 TAAATAATACTAAAA
1 TAAATAATACTAAAA
11600384 -AAAT
1 TAAAT
11600388 TAATCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATAATACTAAAA
Found at i:11603642 original size:23 final size:24
Alignment explanation
Indices: 11603588--11603642 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
11603578 TTAATTTTTG
*
11603588 AATAATTATCATAATCTTTTTAAT
1 AATAATAATCATAATCTTTTTAAT
* *
11603612 -ATATATAATGATAA-CTTTTTATT
1 AATA-ATAATCATAATCTTTTTAAT
11603635 AATAATAA
1 AATAATAA
11603643 ATACAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (24 bp):
AATAATAATCATAATCTTTTTAAT
Found at i:11603996 original size:13 final size:14
Alignment explanation
Indices: 11603978--11604012 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11603968 TAAAAAAATG
11603978 TTTAAGGTG-ATTA
1 TTTAAGGTGTATTA
*
11603991 TTTAAGGAGTATTA
1 TTTAAGGTGTATTA
11604005 TTTAAGGT
1 TTTAAGGT
11604013 ATTTTTCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TTTAAGGTGTATTA
Found at i:11612024 original size:10 final size:10
Alignment explanation
Indices: 11612005--11612041 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
11611995 CTATTCACCC
*
11612005 TTTTTGCTTT
1 TTTTTTCTTT
11612015 TTTTTTC--T
1 TTTTTTCTTT
11612023 TTTTTTCTTT
1 TTTTTTCTTT
11612033 TTTTTTCTT
1 TTTTTTCTT
11612042 AAATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:11612032 original size:18 final size:18
Alignment explanation
Indices: 11612005--11612041 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
11611995 CTATTCACCC
11612005 TTTTTGCTTTTTTTTTCT
1 TTTTTGCTTTTTTTTTCT
*
11612023 TTTTTTCTTTTTTTTTCT
1 TTTTTGCTTTTTTTTTCT
11612041 T
1 T
11612042 AAATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTCT
Found at i:11613251 original size:32 final size:35
Alignment explanation
Indices: 11613210--11613275 Score: 93
Period size: 32 Copynumber: 2.0 Consensus size: 35
11613200 TACTTATCTT
11613210 TAAAATTATT-TAATAAATA-CTTTTAAA-ATTTA
1 TAAAATTATTATAATAAATATCTTTTAAAGATTTA
* *
11613242 TAAAATTATTATTATAAATATTTTTTAAAGATTT
1 TAAAATTATTATAATAAATATCTTTTAAAGATTT
11613276 TTTTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.34
33 8 0.28
34 7 0.24
35 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (35 bp):
TAAAATTATTATAATAAATATCTTTTAAAGATTTA
Found at i:11615353 original size:54 final size:55
Alignment explanation
Indices: 11615258--11615362 Score: 158
Period size: 54 Copynumber: 1.9 Consensus size: 55
11615248 GAAATTAATC
*
11615258 CCATTACAAATGATCATAATACCCTTTTTAATTACTTGACAATTGAATTACATGT
1 CCATTACAAATGATCATAATACCCTTTTTAATTACTTGACAATTAAATTACATGT
* * * *
11615313 CCATTACAAATGATCATGAT-GCTTTTTTAGTTACTTGACAATTAAATTAC
1 CCATTACAAATGATCATAATACCCTTTTTAATTACTTGACAATTAAATTAC
11615363 GTGTATCCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 26 0.58
55 19 0.42
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (55 bp):
CCATTACAAATGATCATAATACCCTTTTTAATTACTTGACAATTAAATTACATGT
Found at i:11616840 original size:34 final size:32
Alignment explanation
Indices: 11616782--11616853 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 32
11616772 ACATTTTTCA
*
11616782 AAAAAATAAAATATATTAATTTTTATTATTAAAT
1 AAAAAATAAAATATATTAATTTTTA-TA-AAAAT
* *
11616816 AAAAAATTAAATAT-TTTATATTTTATAAAAAT
1 AAAAAATAAAATATATTAAT-TTTTATAAAAAT
11616848 AAAAAA
1 AAAAAA
11616854 ATTTTGTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 10 0.29
33 6 0.18
34 18 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
AAAAAATAAAATATATTAATTTTTATAAAAAT
Found at i:11620414 original size:3 final size:3
Alignment explanation
Indices: 11620406--11620444 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
11620396 TAATACATGC
11620406 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
11620445 TGTTTCTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11622762 original size:255 final size:254
Alignment explanation
Indices: 11622311--11622776 Score: 593
Period size: 255 Copynumber: 1.8 Consensus size: 254
11622301 AGAGAGAGGG
* * *
11622311 TATATTAGAAGTTGGAAAGAAATCCAGGCATTTTGGGTATATTTGGTTCACAAGACGAGGGAGGA
1 TATATTAGAAGTTGGAAAGAAATCCAGACATTTAGGGTATATTTGGTACACAAGACGAGGGAGGA
* * *
11622376 AAGGACTAGGAAATGAGGAGGATAGAGTTAGATGATGTTATCTTATTCTCTGTTTGTTGTGTGCA
66 AAGGACTAGGAAATGAGGAGGATAGAATTAGATGATGTTATCTTATTCTCTATTTGTCGTGTGCA
* * * * * **
11622441 TGATTGAGAGTATGATAGGATAATTTTTATCTTATCCTACGTTTAGTGTGTGAAACATTGAGTGT
131 TGATTCAGAGTATGATAGGATAATTTTTATCCTATCCTACGATTAATGCGTGAAACATCCAGTGT
*
11622506 ACAACAGGATGATCCAGGTCAAAATTAGCTTTCCCTGTAAAGGTAAGAGATGGAGGGTA
196 ACAACAAGATGATCCAGGTCAAAATTAGCTTTCCCTGTAAAGGTAAGAGATGGAGGGTA
* * * *
11622565 TATATTGGAAGTTGGAGAGAAATCCAGACATTTAGGGTGTCTTTGGTACACAAGACCGAGAGAGA
1 TATATTAGAAGTTGGAAAGAAATCCAGACATTTAGGGTATATTTGGTACACAAGA-CGAG-G-GA
* * *
11622630 GGCAAGGATTA-GATTATTGA-GAGGATAGAATTAGATGATGTTATCTTA-TC-CTATATT-TCG
63 GGAAAGGACTAGGA--AATGAGGAGGATAGAATTAGATGATGTTATCTTATTCTCTAT-TTGTCG
* * * * *
11622690 TGTGCTTGATTCAGAGTATTG-TAGGATAATTTTTATCCTATGCTATGATTAATGCGTGCAATAT
125 TGTGCATGATTCAGAGTA-TGATAGGATAATTTTTATCCTATCCTACGATTAATGCGTGAAACAT
11622754 CCAGTGTACAACAAGATGATCCA
189 CCAGTGTACAACAAGATGATCCA
11622777 ATTATGTCGG
Statistics
Matches: 179, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
254 48 0.27
255 80 0.45
256 9 0.05
257 38 0.21
258 4 0.02
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (254 bp):
TATATTAGAAGTTGGAAAGAAATCCAGACATTTAGGGTATATTTGGTACACAAGACGAGGGAGGA
AAGGACTAGGAAATGAGGAGGATAGAATTAGATGATGTTATCTTATTCTCTATTTGTCGTGTGCA
TGATTCAGAGTATGATAGGATAATTTTTATCCTATCCTACGATTAATGCGTGAAACATCCAGTGT
ACAACAAGATGATCCAGGTCAAAATTAGCTTTCCCTGTAAAGGTAAGAGATGGAGGGTA
Found at i:11623567 original size:81 final size:83
Alignment explanation
Indices: 11623436--11623596 Score: 265
Period size: 81 Copynumber: 2.0 Consensus size: 83
11623426 TAATCATAAT
* *
11623436 AACAAATTTTAAATATTTTTATAGTGGTTTAAATTAATATACGCCTTATCCAGAAAGAAGAGTGA
1 AACAAAATTTAAATATTTTTATAGTGGTTTAAATGAATATACGCCTTATCCAGAAAGAAGAGTGA
*
11623501 AAATATCAGTGAAGCATA
66 AAATATCAGTAAAGCATA
11623519 AACAAAATTTAAATA-TTTT-TAGTGGTTTAAATGAATATAC-CCTTTATCCAGAAAGAAGAGTG
1 AACAAAATTTAAATATTTTTATAGTGGTTTAAATGAATATACGCC-TTATCCAGAAAGAAGAGTG
11623581 AAAATATCAGTAAAGC
65 AAAATATCAGTAAAGC
11623597 CTAACTATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
80 2 0.03
81 54 0.73
82 4 0.05
83 14 0.19
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (83 bp):
AACAAAATTTAAATATTTTTATAGTGGTTTAAATGAATATACGCCTTATCCAGAAAGAAGAGTGA
AAATATCAGTAAAGCATA
Found at i:11625817 original size:373 final size:369
Alignment explanation
Indices: 11624761--11625867 Score: 1348
Period size: 370 Copynumber: 3.0 Consensus size: 369
11624751 ACAAGGGCCT
* * * **
11624761 TACAGTTTCACTAATGGATTAAATCCATAGAACTAGGCATGATAAGAGGGTATGGACTATGGACA
1 TACAGTTTCACTAATGTATTAAATCCATGGAACTATGCATGCCAA-AGGGTATGGACTATGGACA
* *
11624826 TAAGGTAAAGGAGAGGGATTTCATGATCCTGGTG-T-TC-TCTCATCCAATCATATGATTCACTC
65 TAAGGTAAAGGAGAGGGATTTCATGATCCTGGTGTTCTCTTCTCATCGAATCAAATGA-TCACT-
*
11624888 TCTCAAAAGAATTCCTAGAAAACTTGTTATAAAAGTGAATGAAATTAAAAAGGCCAAAAACAGAT
128 TCTCAAAAGAATTCCTA-AAAACTTGTTATAAAAGTGAATGAAATTAAGAAGGCCAAAAACAGAT
* ** * *
11624953 GTAAAGCTAAGATAAAATGCCATAAAATCTAATCTGAAATGAAGGCAATTTGTGTATGGAAATCG
192 GAAAAGCTAAGGGAAAATGCCATAAAATCTAATCTGAAATGAAGGCAATTCGTGTATAGAAATCG
* * * *
11625018 GAGAGTTGACTAATTTACCCTAGTGGTGGGATAGGTTCAAGGCTACAAAATATAATATACACATT
257 GAGACTTGACTAATTTACCCTAGTGGTGGGGTAGGTTCAAGGCTGC-AAATATAATATACATATT
* * *
11625083 TATTATCTAAGAATTTTTGGCAAA-CAAACTCCACAGTTCTATGGGCTC
321 TATTATCTAAGAATTATTGGCAAAGAAAACTACACAGTTCTATGGGCTC
* * * * * * *
11625131 TA-AGGTTTAACTAATCTATTAAAACCACGGAGCTATGCATGCTGAAAGGTTATGGACTATGGAC
1 TACA-GTTTCACTAATGTATTAAATCCATGGAACTATGCATGC-CAAAGGGTATGGACTATGGAC
* * * * *
11625195 ATGAGATAAAGGAGAGGGATTTCATGATCCTGGTGTTCTCTCCTCCT-GCAGT-AATATGATCCA
64 ATAAGGTAAAGGAGAGGGATTTCATGATCCTGGTGTTCTCTTCTCATCG-AATCAA-ATGAT-CA
* * *
11625258 C-TCTCAAAACG-GTTCCTAAAGAACTAGTTATACAAGTGAATGAAATTAAGAAGGCCAAAAACA
126 CTTCTCAAAA-GAATTCCTAAA-AACTTGTTATAAAAGTGAATGAAATTAAGAAGGCCAAAAACA
* *
11625321 GAAGAAAAGCTAAGGGAAAATGCCATAAAATCTAATCTGAACA--AAGG-AGAGTCGTGTATAGA
189 GATGAAAAGCTAAGGGAAAATGCCATAAAATCTAATCTGAA-ATGAAGGCA-ATTCGTGTATAGA
* ** * * * *
11625383 AATCAGAGACTTGA-TAAATTTACCCTAGTGGTGCAAG-AGGTACAATGCAGCAAAAATAATATA
252 AATCGGAGACTTGACT-AATTTACCCTAGTGGTG-GGGTAGGTTCAAGGCTGCAAATATAATATA
* * * ** *
11625446 CGTATTTATTACCTAAGAATTGTTGGCAAAGAAAACTATGCTGTTCTATGGGCTC
315 CATATTTATTATCTAAGAATTATTGGCAAAGAAAACTACACAGTTCTATGGGCTC
*
11625501 TACAATTTCACTAATGTATTAAATCCATGGAACTATGCATGCCAAATGGGTATGGACTATGGACA
1 TACAGTTTCACTAATGTATTAAATCCATGGAACTATGCATGCCAAA-GGGTATGGACTATGGACA
11625566 TAAGGTAAAGGAGAGGGATTTCATGAT-CTCGGTGTTCTCTTCTCATCGAATCAAATGACTCACT
65 TAAGGTAAAGGAGAGGGATTTCATGATCCT-GGTGTTCTCTTCTCATCGAATCAAATGA-TCACT
*
11625630 TCTCAAAAGAATTCCT-AAAACTTGTTATAAAAGTAAGTGAATGAACTTAAGAAGGCCAAAAACA
128 TCTCAAAAGAATTCCTAAAAACTTGTTAT--AA--AAGTGAATGAAATTAAGAAGGCCAAAAACA
* * * * *
11625694 TATGAAAAACTAAGGGAAAATGCCATAAAATTTAATCTGAAATGAAGGCCATTCATGTATAGAAA
189 GATGAAAAGCTAAGGGAAAATGCCATAAAATCTAATCTGAAATGAAGGCAATTCGTGTATAGAAA
*
11625759 T-GGAAACTTGACTAATTTACCCTAGTGGTGGGGTAGGTTCAAGGCTGCAAATATAATATACATA
254 TCGGAGACTTGACTAATTTACCCTAGTGGTGGGGTAGGTTCAAGGCTGCAAATATAATATACATA
**
11625823 TTTATTATCTAAGAATTATTGGCAAAGAAAACGCCACAGTTCTAT
319 TTTATTATCTAAGAATTATTGGCAAAGAAAACTACACAGTTCTAT
11625868 TTGGTTACCT
Statistics
Matches: 617, Mismatches: 88, Indels: 61
0.81 0.11 0.08
Matches are distributed among these distances:
369 54 0.09
370 257 0.42
371 112 0.18
372 8 0.01
373 167 0.27
374 19 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (369 bp):
TACAGTTTCACTAATGTATTAAATCCATGGAACTATGCATGCCAAAGGGTATGGACTATGGACAT
AAGGTAAAGGAGAGGGATTTCATGATCCTGGTGTTCTCTTCTCATCGAATCAAATGATCACTTCT
CAAAAGAATTCCTAAAAACTTGTTATAAAAGTGAATGAAATTAAGAAGGCCAAAAACAGATGAAA
AGCTAAGGGAAAATGCCATAAAATCTAATCTGAAATGAAGGCAATTCGTGTATAGAAATCGGAGA
CTTGACTAATTTACCCTAGTGGTGGGGTAGGTTCAAGGCTGCAAATATAATATACATATTTATTA
TCTAAGAATTATTGGCAAAGAAAACTACACAGTTCTATGGGCTC
Found at i:11629273 original size:22 final size:23
Alignment explanation
Indices: 11629247--11629289 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11629237 TGTATATTTA
*
11629247 TATTTGTAT-CTCTAGAATTAAG
1 TATTTGTATGCCCTAGAATTAAG
11629269 TATTTGTATGCCCTAGAATTA
1 TATTTGTATGCCCTAGAATTA
11629290 GGAAAGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
TATTTGTATGCCCTAGAATTAAG
Found at i:11629679 original size:18 final size:18
Alignment explanation
Indices: 11629656--11629690 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11629646 ATGTTCTTTG
11629656 GGTAAAGTTTCTAGTTCA
1 GGTAAAGTTTCTAGTTCA
*
11629674 GGTAAAGTTTCTGGTTC
1 GGTAAAGTTTCTAGTTC
11629691 TCATGGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (18 bp):
GGTAAAGTTTCTAGTTCA
Found at i:11633158 original size:22 final size:22
Alignment explanation
Indices: 11633132--11633175 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11633122 TGTATATTTA
*
11633132 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
11633154 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
11633176 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:11636216 original size:15 final size:16
Alignment explanation
Indices: 11636188--11636218 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11636178 TATCACTATC
11636188 AAATTAATTTCTAATT
1 AAATTAATTTCTAATT
11636204 AAATTAA-TTCTAATT
1 AAATTAATTTCTAATT
11636219 CAAGTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTAATTTCTAATT
Found at i:11645378 original size:161 final size:164
Alignment explanation
Indices: 11645186--11645497 Score: 375
Period size: 168 Copynumber: 1.9 Consensus size: 164
11645176 ATTTATTCTA
**
11645186 AAAAGATAAAATATTTTATATTTATATTTATTTCATAAAAACTTCAAAAAA-AAAAT-T-T-T-A
1 AAAAGATAAAATATTAAATATTTATATTTATTTCATAAAAACTTCAAAAAATAAAATATATGTAA
** * **
11645246 TATTTATATTTATTTTGTAAAACCCTAAAATAATTAATTATTAACGAGTATATTTATTGCTCATA
66 TA-TTATATTTATTTCATAAAAACCTAAAATAATTAATTATTAACGAACATATTTATTGCTCATA
11645311 ATCTAACTT-TAGATATATAATTATTTTGTCAATTT
130 ATCTAA-TTATAGATATATAATTATTTTGTCAATTT
* ** *
11645346 AAAAGAATAAAGTATTAAATATTTATATTTATTTTGTGAAAACTTCAAAAAATAAAATAAAATAT
1 AAAAG-ATAAAATATTAAATATTTATATTTATTTCATAAAAACTTCAAAAAATAAAAT---ATAT
* * * * *
11645411 GTAATATTCTATTTATTTCATAAAAACTTAAAATACTTAATTATTAATGAACATATTTATTGTTC
62 GTAATATTATATTTATTTCATAAAAACCTAAAATAATTAATTATTAACGAACATATTTATTGCTC
*
11645476 ATAATCTAATTATATATATATA
127 ATAATCTAATTATAGATATATA
11645498 TATGTTGATT
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
160 5 0.04
161 40 0.32
162 5 0.04
166 1 0.01
167 3 0.02
168 68 0.54
169 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (164 bp):
AAAAGATAAAATATTAAATATTTATATTTATTTCATAAAAACTTCAAAAAATAAAATATATGTAA
TATTATATTTATTTCATAAAAACCTAAAATAATTAATTATTAACGAACATATTTATTGCTCATAA
TCTAATTATAGATATATAATTATTTTGTCAATTT
Found at i:11648894 original size:27 final size:27
Alignment explanation
Indices: 11648864--11648927 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
11648854 GTCCCTACAA
11648864 ATCACAATGAACCTTCATAAATAAGTC
1 ATCACAATGAACCTTCATAAATAAGTC
* *
11648891 ATCATAATAAACCTTCATAAATAAGTC
1 ATCACAATGAACCTTCATAAATAAGTC
*
11648918 ATCCCAATGA
1 ATCACAATGA
11648928 TCATTAATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (27 bp):
ATCACAATGAACCTTCATAAATAAGTC
Found at i:11648897 original size:14 final size:14
Alignment explanation
Indices: 11648878--11648920 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11648868 CAATGAACCT
11648878 TCATAAATAAGTCA
1 TCATAAATAAGTCA
** *
11648892 TCAT-AATAAACCT
1 TCATAAATAAGTCA
11648905 TCATAAATAAGTCA
1 TCATAAATAAGTCA
11648919 TC
1 TC
11648921 CCAATGATCA
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (14 bp):
TCATAAATAAGTCA
Found at i:11652415 original size:18 final size:18
Alignment explanation
Indices: 11652392--11652437 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
11652382 ATGTGTTTTT
11652392 TCATCATTATTAGCATCA
1 TCATCATTATTAGCATCA
* * **
11652410 TCATCATCATTATCATTG
1 TCATCATTATTAGCATCA
11652428 TCATCATTAT
1 TCATCATTAT
11652438 CCTTCTTGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.43
Consensus pattern (18 bp):
TCATCATTATTAGCATCA
Found at i:11652458 original size:3 final size:3
Alignment explanation
Indices: 11652450--11652474 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11652440 TTCTTGTCGA
11652450 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
11652475 TTATTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:11654751 original size:21 final size:21
Alignment explanation
Indices: 11654725--11654768 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
11654715 GTCCCATACA
11654725 ATGAGGATATGATAAGTTTTC
1 ATGAGGATATGATAAGTTTTC
11654746 ATGAGGATATGATAAGTTTTC
1 ATGAGGATATGATAAGTTTTC
11654767 AT
1 AT
11654769 AAGTGCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.39
Consensus pattern (21 bp):
ATGAGGATATGATAAGTTTTC
Found at i:11656997 original size:18 final size:19
Alignment explanation
Indices: 11656971--11657013 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
11656961 AAATCTCAAC
* *
11656971 AAAACTTTCACAA-ATAAA
1 AAAAATTTCACAACAAAAA
*
11656989 AAAAATTTCTCAACAAAAA
1 AAAAATTTCACAACAAAAA
11657008 AAAAAT
1 AAAAAT
11657014 CCCTAACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATTTCACAACAAAAA
Found at i:11657149 original size:60 final size:58
Alignment explanation
Indices: 11657079--11657278 Score: 206
Period size: 59 Copynumber: 3.4 Consensus size: 58
11657069 AATACTCAAC
* * **
11657079 AAAAAA-TTCAACAGATATATAATCAACAAATTTCAACAAACAT-ATAACCAAAACCCA
1 AAAAAATTTCAACAAATATATAACCAACAAAACTCAACAAA-ATGATAACCAAAACCCA
* * * *
11657136 AAAAAATTTTTCAACAAATATAAAACCAATAAAACTCAACAAATTGGTAACCAAAACCCA
1 AAAAAA--TTTCAACAAATATATAACCAACAAAACTCAACAAAATGATAACCAAAACCCA
* * * * * *
11657196 AATAAATTTCAACAAATAAATAACCAACAAAAACTCAACACATTGGTAACCAAAATCCA
1 AAAAAATTTCAACAAATATATAACCAAC-AAAACTCAACAAAATGATAACCAAAACCCA
* *
11657255 AACAAATTTCAACAAATTTATAAC
1 AAAAAATTTCAACAAATATATAAC
11657279 AAAAAATTAA
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
57 6 0.05
58 19 0.16
59 50 0.41
60 46 0.38
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.20
Consensus pattern (58 bp):
AAAAAATTTCAACAAATATATAACCAACAAAACTCAACAAAATGATAACCAAAACCCA
Found at i:11657201 original size:33 final size:32
Alignment explanation
Indices: 11657157--11657272 Score: 86
Period size: 33 Copynumber: 3.8 Consensus size: 32
11657147 CAACAAATAT
11657157 AAAACC-AATAAAACTCAACAAATTGGTAACC
1 AAAACCAAATAAAACTCAACAAATTGGTAACC
**
11657188 AAAACCCAAATAAATTTCAACAAA----TAA--
1 AAAA-CCAAATAAAACTCAACAAATTGGTAACC
* *
11657215 ATAACCAACA-AAAACTCAACACATTGGTAACC
1 AAAACCAA-ATAAAACTCAACAAATTGGTAACC
* **
11657247 AAAATCCAAACAAATTTCAACAAATT
1 AAAA-CCAAATAAAACTCAACAAATT
11657273 TATAACAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
26 14 0.22
27 4 0.06
29 3 0.05
30 3 0.05
31 4 0.06
32 6 0.09
33 30 0.47
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.18
Consensus pattern (32 bp):
AAAACCAAATAAAACTCAACAAATTGGTAACC
Found at i:11657246 original size:59 final size:58
Alignment explanation
Indices: 11657123--11657284 Score: 211
Period size: 59 Copynumber: 2.8 Consensus size: 58
11657113 AACAAACATA
*
11657123 TAACCAAAACCCAAAAAAATTTTTCAACAAATATAAAACCAATAAAACTCAACAAATTGG
1 TAACCAAAACCCAAAAAAA--TTTCAACAAATATAAAACCAAAAAAACTCAACAAATTGG
* *
11657183 TAACCAAAACCCAAATAAATTTCAACAAATA-AATAACCAACAAAAACTCAACACATTGG
1 TAACCAAAACCCAAAAAAATTTCAACAAATATAA-AACCAA-AAAAACTCAACAAATTGG
* * * *
11657242 TAACCAAAATCCAAACAAATTTCAACAAATTTATAA-CAAAAAA
1 TAACCAAAACCCAAAAAAATTTCAACAAATATAAAACCAAAAAA
11657285 TTAAACCCTA
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
57 6 0.07
58 21 0.23
59 46 0.50
60 19 0.21
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.19
Consensus pattern (58 bp):
TAACCAAAACCCAAAAAAATTTCAACAAATATAAAACCAAAAAAACTCAACAAATTGG
Found at i:11660086 original size:15 final size:16
Alignment explanation
Indices: 11660056--11660092 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
11660046 ATTCCAAAAG
11660056 TAAAA-AAATAATATA
1 TAAAATAAATAATATA
11660071 TAAAATAAATAA-ATA
1 TAAAATAAATAATATA
11660086 TAAAATA
1 TAAAATA
11660093 GAAACAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATAAATAATATA
Found at i:11660235 original size:154 final size:154
Alignment explanation
Indices: 11660077--11660356 Score: 542
Period size: 154 Copynumber: 1.8 Consensus size: 154
11660067 TATATAAAAT
*
11660077 AAATAAATATAAAATAGAAACAAAAAGTAAAATGAGAGTGGAAAAAGAAAACAATTCAAATTTCA
1 AAATAAATATAAAATAGAAACAAAAAGTAAAATGAGAGTGGAAAAAGAAAACAACTCAAATTTCA
11660142 AATGGGTTGGACTTATCTAGATCGTTGAAAAATTTAACCAAAAATTCAATGTACTTAAGAATATA
66 AATGGGTTGGACTTATCTAGATCGTTGAAAAATTTAACCAAAAATTCAATGTACTTAAGAATATA
11660207 AAATGAGAGTGGAAAACAATTCAA
131 AAATGAGAGTGGAAAACAATTCAA
11660231 AAATAAATATAAAATAGAAACAAAAAGTAAAATGAGAGTGGAAAAAGAAAACAACTCAAATTTCA
1 AAATAAATATAAAATAGAAACAAAAAGTAAAATGAGAGTGGAAAAAGAAAACAACTCAAATTTCA
*
11660296 AATGGGTTGGACTTATCTAGATCGTTGAAAAATTTAACCAAAAATTTAATGTACTTAAGAA
66 AATGGGTTGGACTTATCTAGATCGTTGAAAAATTTAACCAAAAATTCAATGTACTTAAGAA
11660357 AAGAGAAAAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 124 1.00
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.24
Consensus pattern (154 bp):
AAATAAATATAAAATAGAAACAAAAAGTAAAATGAGAGTGGAAAAAGAAAACAACTCAAATTTCA
AATGGGTTGGACTTATCTAGATCGTTGAAAAATTTAACCAAAAATTCAATGTACTTAAGAATATA
AAATGAGAGTGGAAAACAATTCAA
Found at i:11660994 original size:44 final size:44
Alignment explanation
Indices: 11660930--11661703 Score: 226
Period size: 44 Copynumber: 17.9 Consensus size: 44
11660920 TTTAAAGGGT
* *
11660930 CAACTTTTAAAAAATTTAAAAGGCTCTTCTCATCAGAGGCTTAA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTAA
* * * * *
11660974 TAACTTTTGAAAAATATAAAAAGCT-TATCTAAAT-AAAAGCTTAA
1 CAACTTTTGAAAAATATAAAAGGCTCT-TCT-CATCAGAGGCTTAA
* * * * * * *
11661018 CAA-TTTTGAAAAATCTAAAAAGCTTTTCTAAACATAGGTTTAA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTAA
* * * * *
11661061 CAACTTTAGAAAAATTTAAAAGGCT-TCTCTTATAAGAAG-TTAAA
1 CAACTTTTGAAAAATATAAAAGGCTCT-TCTCATCAGAGGCTT-AA
* * * * * *
11661105 CAAC-TTTGAAAAATTTAAAAAGTTCCTCTTATCAGAGGCTATGA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCT-TAA
* *** * * * ***
11661149 -AAC-TTT-AAAAATAAAAAAAATTC-TCTTA-CTGGGTGCTCGT
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAG-GCTTAA
* * * *
11661189 CAACTTTTGAAAAAT-TATAAAGACTCATCTCATCAGAAGTTTAA
1 CAACTTTTGAAAAATATA-AAAGGCTCTTCTCATCAGAGGCTTAA
** * * *
11661233 CAACTTTCAAAAAATATAAAAGACTCTTCTCATTAGAGGCTCAA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTAA
* *
11661277 CAACTTTTGAAAAATATAATAGGCT-TATCTCATC--A--CTGAA
1 CAACTTTTGAAAAATATAAAAGGCTCT-TCTCATCAGAGGCTTAA
** ** *
11661317 CAA-TTTTGAAAAATATAAAATACTAATCTTATCA-ATGG-TTATGA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGA-GGCTTA--A
* * * *
11661361 -AAC-TTT-AAATATTTGAAAA-GCT-TCTCTAATCAGAGGCTATGA
1 CAACTTTTGAAAAATAT-AAAAGGCTCT-TCTCATCAGAGGCT-TAA
* * **
11661403 -AAC-TTTGAAAATTTATAAAAGACTCTTCTCATCAGA-TATTCAA
1 CAACTTTTGAAAA-ATATAAAAGGCTCTTCTCATCAGAGGCTT-AA
** *
11661446 CAA-TTTT-AGAAAATCATAAAAGATTCTTCTCAT-ATGAGACTTAA
1 CAACTTTTGA-AAAAT-ATAAAAGGCTCTTCTCATCA-GAGGCTTAA
* * * * * * *
11661490 CAACTTTGGAAAATTATTAAAGGCTGTTTTCATTAAAGGCTTAA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTAA
* ** * * * *
11661534 TAAC-TTTGAAAAATCATAAAAACCTCATATCATTAGACG-TTATGA
1 CAACTTTTGAAAAAT-ATAAAAGGCTCTTCTCATCAGAGGCTTA--A
* * * * *
11661579 -AAC-TTT-AAAAATTTAAAAGGTTCATCTAATCAGATG-TTATA
1 CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTA-A
* * * * * *
11661620 AAAC-TTT-AAATATTTCAAAATGGCTCATCTCATAAGAGGCTCAA
1 CAACTTTTGAAAAATAT-AAAA-GGCTCTTCTCATCAGAGGCTTAA
* *
11661664 CAA-TTTTGAAAAATATAAAAGGTTCATT-TCATTAGAGGCT
1 CAACTTTTGAAAAATATAAAAGGCTC-TTCTCATCAGAGGCT
11661704 ATTAAACTTT
Statistics
Matches: 550, Mismatches: 124, Indels: 113
0.70 0.16 0.14
Matches are distributed among these distances:
39 24 0.04
40 12 0.02
41 12 0.02
42 80 0.15
43 142 0.26
44 252 0.46
45 27 0.05
46 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (44 bp):
CAACTTTTGAAAAATATAAAAGGCTCTTCTCATCAGAGGCTTAA
Found at i:11661037 original size:43 final size:44
Alignment explanation
Indices: 11660968--11661126 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 44
11660958 CTCATCAGAG
* *
11660968 GCTTAATAACTTTTGAAAAATATAAAAAGCTTATCTAAATAAAA
1 GCTTAACAACTTTTGAAAAATTTAAAAAGCTTATCTAAATAAAA
* * * * *
11661012 GCTTAACAA-TTTTGAAAAATCTAAAAAGCTTTTCTAAACATAG
1 GCTTAACAACTTTTGAAAAATTTAAAAAGCTTATCTAAATAAAA
* * * * *
11661055 GTTTAACAACTTTAGAAAAATTTAAAAGGCTTCTCT-TATAAGAA
1 GCTTAACAACTTTTGAAAAATTTAAAAAGCTTATCTAAATAA-AA
11661099 G-TTAAACAAC-TTTGAAAAATTTAAAAAG
1 GCTT-AACAACTTTTGAAAAATTTAAAAAG
11661127 TTCCTCTTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
43 57 0.60
44 38 0.40
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (44 bp):
GCTTAACAACTTTTGAAAAATTTAAAAAGCTTATCTAAATAAAA
Found at i:11661155 original size:87 final size:87
Alignment explanation
Indices: 11660930--11661144 Score: 220
Period size: 87 Copynumber: 2.5 Consensus size: 87
11660920 TTTAAAGGGT
* * * * * *
11660930 CAACTTTTAAAAAATTTAAAAGGCTCTTCTCATCAGAGGCTTAATAACTTTTGAAAAATATAAAA
1 CAAC-TTTGAAAAATTTAAAAAGTTCTTCTAATCAGAGGCTTAACAACTTTAGAAAAATATAAAA
11660995 AGCTTATCTAAATAAAAGCTTAA
65 AGCTTATCTAAATAAAAGCTTAA
* * * * * *
11661018 CAATTTTGAAAAATCTAAAAAGCTT-TTCTAAACATAGGTTTAACAACTTTAGAAAAATTTAAAA
1 CAACTTTGAAAAATTTAAAAAG-TTCTTCTAATCAGAGGCTTAACAACTTTAGAAAAATATAAAA
* * *
11661082 GGCTTCTCT-TATAAGAAG-TTAAA
65 AGCTTATCTAAATAA-AAGCTT-AA
* *
11661105 CAACTTTGAAAAATTTAAAAAGTTCCTCTTATCAGAGGCT
1 CAACTTTGAAAAATTTAAAAAGTTCTTCTAATCAGAGGCT
11661145 ATGAAACTTT
Statistics
Matches: 101, Mismatches: 22, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
86 8 0.08
87 89 0.88
88 4 0.04
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (87 bp):
CAACTTTGAAAAATTTAAAAAGTTCTTCTAATCAGAGGCTTAACAACTTTAGAAAAATATAAAAA
GCTTATCTAAATAAAAGCTTAA
Found at i:11662978 original size:18 final size:18
Alignment explanation
Indices: 11662927--11662983 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
11662917 TTTTGATTTG
11662927 ATTTGATTTA-ATTTTTAT
1 ATTT-ATTTATATTTTTAT
*
11662945 GTTT-TTTATA---TTAT
1 ATTTATTTATATTTTTAT
11662959 ATTTATTTATATTTTTAT
1 ATTTATTTATATTTTTAT
11662977 ATTTATT
1 ATTTATT
11662984 ATTTTAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 7 0.22
15 6 0.19
16 4 0.12
17 1 0.03
18 14 0.44
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTATTTATATTTTTAT
Found at i:11662989 original size:8 final size:9
Alignment explanation
Indices: 11662953--11662989 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
11662943 ATGTTTTTTA
11662953 TATTATATT
1 TATTATATT
11662962 TATTTATATT
1 TA-TTATATT
11662972 T-TTATATT
1 TATTATATT
11662980 TATTAT-TT
1 TATTATATT
11662988 TA
1 TA
11662990 AAGGGTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 12 0.46
9 6 0.23
10 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TATTATATT
Found at i:11663161 original size:25 final size:27
Alignment explanation
Indices: 11663107--11663161 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
11663097 TTTTACATTA
*
11663107 ATTGCATGATAGTTTCTATATTATATT
1 ATTGCATGATAGTCTCTATATTATATT
*
11663134 ATTGCATGATAG-CT-TATGTTATATT
1 ATTGCATGATAGTCTCTATATTATATT
11663159 ATT
1 ATT
11663162 ATTGCATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 13 0.50
26 1 0.04
27 12 0.46
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (27 bp):
ATTGCATGATAGTCTCTATATTATATT
Found at i:11663246 original size:15 final size:14
Alignment explanation
Indices: 11663219--11663245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11663209 TTTTCAAATT
11663219 AAAAAAATGTTTTA
1 AAAAAAATGTTTTA
11663233 AAAAAAATGTTTT
1 AAAAAAATGTTTT
11663246 TCAATCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
AAAAAAATGTTTTA
Found at i:11678979 original size:193 final size:192
Alignment explanation
Indices: 11678649--11679224 Score: 704
Period size: 193 Copynumber: 3.0 Consensus size: 192
11678639 TTCCTAGGGG
* * * * *
11678649 AGATTGTTGGTAGATCGAAAGTTGGTTGCTTCCATCAAC-TCTATGTGTTCAAATGTCGGTATTA
1 AGATTGTTGGCAGATCGAAGGTTGATTGCATCCATCAACTTC-ATGTGCTCAAATGTCGGTATTA
* * * * *
11678713 AAATATTCGACTTGAATGCAGTGAATATATAATAATATGCAGAAACGGAACACTCAAGTAGGTGA
65 AAATATTCGACTTGGATGCAGTGAGTATATAATAATATACAGAAATGAAACACTCAAGTAGGTGA
* * * *
11678778 TATGTTGAGTCAACCTAAAGTGTACGTTTGAGGAAGCATTGAGACAACCTAGGTAGCTAGAGGA
130 TGTGTTGAGTCAACCTAGAGTGTAAGTTTGAGG-AGCATTGAGACAACCTAGGCAGCTAGAGGA
* * *
11678842 AGATTGTTGGCAAATCGAAGGTTGATTGCATCCATCAACTTCATGTGCTCAAATGTTGATATTAA
1 AGATTGTTGGCAGATCGAAGGTTGATTGCATCCATCAACTTCATGTGCTCAAATGTCGGTATTAA
*
11678907 AATATTCGACTTGGATGCAGTCAGTATATAATAATATACAGAAATGAAACACTCAAGTAGGTGAT
66 AATATTCGACTTGGATGCAGTGAGTATATAATAATATACAGAAATGAAACACTCAAGTAGGTGAT
* * * * * * *
11678972 GTGTTGAGTCAATCTAGAGTATAAGTTTGAGGGAGCATTGAGACAACCTAAGCAACCAGGGGG
131 GTGTTGAGTCAACCTAGAGTGTAAGTTTGA-GGAGCATTGAGACAACCTAGGCAGCTAGAGGA
* ** * * ** *
11679035 AGATTGTTGGCAGATCGAAGGTTAACCGCGTCCATCAACTCCATGTGCTTGAATGTCGGTACTAA
1 AGATTGTTGGCAGATCGAAGGTTGATTGCATCCATCAACTTCATGTGCTCAAATGTCGGTATTAA
* * * * * * *
11679100 AATATTCGACTTTGATGCAATGAGTATTATAATAATAGACAAAAATGAAACACCCAATTGGGTGA
66 AATATTCGACTTGGATGCAGTGAGTA-TATAATAATATACAGAAATGAAACACTCAAGTAGGTGA
* * * *
11679165 TGTGTTGAGTCAACATGGAGTGTAAGCTTGATGGAGCATTGAGACAACTTAGGCAGCTAG
130 TGTGTTGAGTCAACCTAGAGTGTAAGTTTGA-GGAGCATTGAGACAACCTAGGCAGCTAG
11679225 GTTGAGTACT
Statistics
Matches: 326, Mismatches: 54, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
193 239 0.73
194 87 0.27
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (192 bp):
AGATTGTTGGCAGATCGAAGGTTGATTGCATCCATCAACTTCATGTGCTCAAATGTCGGTATTAA
AATATTCGACTTGGATGCAGTGAGTATATAATAATATACAGAAATGAAACACTCAAGTAGGTGAT
GTGTTGAGTCAACCTAGAGTGTAAGTTTGAGGAGCATTGAGACAACCTAGGCAGCTAGAGGA
Found at i:11683058 original size:16 final size:17
Alignment explanation
Indices: 11683027--11683059 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11683017 AGACTTAATT
*
11683027 TTTTAAATATTAAAATA
1 TTTTAAATAGTAAAATA
11683044 TTTTAAA-AGTAAAATA
1 TTTTAAATAGTAAAATA
11683060 CTAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTTAAATAGTAAAATA
Found at i:11683086 original size:41 final size:39
Alignment explanation
Indices: 11683022--11683099 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 39
11683012 ATTAAAGACT
*
11683022 TAATTTTTTAAATATTAAAATATTTTAAAAGTAAAATAC
1 TAATATTTTAAATATTAAAATATTTTAAAAGTAAAATAC
* *
11683061 TAATATTTTAATATTATTAATATATTTTAAAATTAAAAT
1 TAATATTTTAA-A-TATTAAAATATTTTAAAAGTAAAAT
11683100 TATATAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.29
40 1 0.03
41 23 0.68
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (39 bp):
TAATATTTTAAATATTAAAATATTTTAAAAGTAAAATAC
Found at i:11683096 original size:25 final size:25
Alignment explanation
Indices: 11683068--11683125 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
11683058 TACTAATATT
*
11683068 TTAATATTAT-T-AATATATTTTAAAA
1 TTAATATTATATAAAAATATTTT--AA
*
11683093 TTAAAATTATATAAAAATATTTTAA
1 TTAATATTATATAAAAATATTTTAA
11683118 TTAATATT
1 TTAATATT
11683126 TTTATATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 18 0.64
26 1 0.04
27 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATATTATATAAAAATATTTTAA
Found at i:11683103 original size:19 final size:19
Alignment explanation
Indices: 11683041--11683104 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
11683031 AAATATTAAA
*
11683041 ATATTTTAAAAGTAAAATACT
1 ATATTTTAAAATTAAAAT--T
* *
11683062 AATATTTTAATATTATTAA-T
1 -ATATTTTAAAATTA-AAATT
11683082 ATATTTTAAAATTAAAATT
1 ATATTTTAAAATTAAAATT
11683101 ATAT
1 ATAT
11683105 AAAAATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.06
19 18 0.51
20 1 0.03
22 12 0.34
23 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
ATATTTTAAAATTAAAATT
Found at i:11685050 original size:32 final size:31
Alignment explanation
Indices: 11684949--11685057 Score: 121
Period size: 35 Copynumber: 3.4 Consensus size: 31
11684939 GCCACAAATA
* *
11684949 TAAATGCTTTTA-TATTCATGTTTTGGATTT
1 TAAATGCTTTTAGTAATCATGTTTTAGATTT
* *
11684979 TAAATGCTTTTGGTAATCATGCTTTTTTATTATTT
1 TAAATGCTTTTAGTAATCATG---TTTTA-GATTT
11685014 TAAATGCTTTTAGTAATCATGTTTTAGATTT
1 TAAATGCTTTTAGTAATCATGTTTTAGATTT
*
11685045 ATAAATACTTTTA
1 -TAAATGCTTTTA
11685058 ACCATAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
30 11 0.17
31 11 0.17
32 16 0.24
34 4 0.06
35 24 0.36
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (31 bp):
TAAATGCTTTTAGTAATCATGTTTTAGATTT
Found at i:11687472 original size:21 final size:21
Alignment explanation
Indices: 11687426--11687466 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11687416 CTTTCTATTC
*
11687426 CTCAAATTGGTGATGTTGATA
1 CTCAAATTGGTAATGTTGATA
*
11687447 CTCAAGTTGGTAATGTTGAT
1 CTCAAATTGGTAATGTTGAT
11687467 GTTCAAAATA
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:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (21 bp):
CTCAAATTGGTAATGTTGATA
Found at i:11691422 original size:287 final size:287
Alignment explanation
Indices: 11690913--11691431 Score: 672
Period size: 287 Copynumber: 1.8 Consensus size: 287
11690903 TTAAAGAGCA
* * * * * *
11690913 AAAATATAAATTTGTAGTTATTGTTCTGTTTTAACAGTTTAGATAGTTTTAATACATGATATTAA
1 AAAATACAAATTTATAGTTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAA
* * **
11690978 ATTTGTCTAAATGATTGAACTTGGTTTCCACAATTGATATGTATGAAAAAGTTATTGTTTATGTT
66 ATTTGTCTAAATGATTGAACTTGATTTCCACAATTGATATATATGAAAAAGTTACCGTTTATGTT
* * * *
11691043 TTTTTAAGACTTTGTTGTACGTTAAAGGATAAAAATATAATTTTACAATTATATTTAGGTTTTAA
131 TATTTAAGACTTTGTTGTACGTTAAAGGACAAAAATACAAATTTACAATTATATTTA-GTTTTAA
* *
11691108 TAATTTAGATAGCTTAAATATATGATATTAAACTTGTCCGACTGATTAAACTTGGTTTCTATCTA
195 CAATTTAGATAGCTTAAATACATGATATTAAACTTGTCCGACTGATTAAACTTGGTTTCTATCTA
11691173 TTTAGCACTTTTGTGCCATTAAAAGGTC
260 TTTAGCACTTTTGTGCCATTAAAAGGTC
* *
11691201 AAAATACAAATTTATATTTATTATTCTATTTTAACATTTTAGATAGCTTCAATACATGAT-TTAA
1 AAAATACAAATTTATAGTTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAA
* * * *
11691265 ACTTAT-TC-GAATGATTGAACTTGATTTTCATAGTTGATATATATGAAAAAGTTACCGTTTATG
66 A-TT-TGTCTAAATGATTGAACTTGATTTCCACAATTGATATATATGAAAAAGTTACCGTTTATG
* * *
11691328 TTTATTTAAGACTTCTTTTGT-CGTTAAAAGG-CCAAAATACAAATTTACATTTATTATTCTA-T
129 TTTATTTAAGACTT-TGTTGTACGTT-AAAGGACAAAAATACAAATTTACAATTA-TATT-TAGT
* * * *
11691390 TTTAACAGTTTAGGTAGTTTTAATACATGATATTAAACTTGT
190 TTTAACAATTTAGATAGCTTAAATACATGATATTAAACTTGT
11691432 TTAAGGGGTT
Statistics
Matches: 196, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
287 123 0.63
288 70 0.36
289 3 0.02
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (287 bp):
AAAATACAAATTTATAGTTATTATTCTATTTTAACAGTTTAGATAGCTTCAATACATGATATTAA
ATTTGTCTAAATGATTGAACTTGATTTCCACAATTGATATATATGAAAAAGTTACCGTTTATGTT
TATTTAAGACTTTGTTGTACGTTAAAGGACAAAAATACAAATTTACAATTATATTTAGTTTTAAC
AATTTAGATAGCTTAAATACATGATATTAAACTTGTCCGACTGATTAAACTTGGTTTCTATCTAT
TTAGCACTTTTGTGCCATTAAAAGGTC
Found at i:11691518 original size:161 final size:160
Alignment explanation
Indices: 11691173--11692233 Score: 862
Period size: 162 Copynumber: 6.6 Consensus size: 160
11691163 TTTCTATCTA
* *
11691173 TTTAGCAC-TTTTGTGCCATTAAAAGGTC-AAAATACAAATTTATATTTATTATTCTATTTTAAC
1 TTTAGCACTTTTTGTGTCATTAAAAGG-CAAAAATACAAATTTACATTTATTATTCTATTTTAAC
* * *
11691236 ATTTTAGATAGCTTCAATACATGAT-TTAAACTTATTCGAATGATTGAACTTGATTTTCATAGTT
65 AATTTAGATAGCTTCAATACATGATATTAAACTTGTT-GAATGATTGAACTTGGTTTTCATAGTT
* * *
11691300 GATATATATGAAAAAGTTACCGTTTATGTTTA
129 GATATGTATGAAAAAGTTATCGTTTATGTTTG
* *
11691332 TTTAAG-ACTTCTTT-TGTCGTTAAAAGGCCAAAATACAAATTTACATTTATTATTCTATTTTAA
1 TTT-AGCACTT-TTTGTGTCATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTATTTTAA
* * * * * * * *
11691395 CAGTTTAGGTAGTTTTAATACATGATATTAAACTTGTTTAAGGGGTTGAACTTGGTTTTCATGGT
64 CAATTTAGATAGCTTCAATACATGATATTAAACTTGTTGAA-TGATTGAACTTGGTTTTCATAGT
* *
11691460 TGATATGTATGAAAAAGTTATTGTTTATGTCTG
128 TGATATGTATGAAAAAGTTATCGTTTATGTTTG
* * * *
11691493 TTTAGGACTTTTTGTGTCATTAAAAGGCAAAAATGCAAATTTGCATTTATTATTATATTTTAACA
1 TTTAGCACTTTTTGTGTCATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTATTTTAACA
*
11691558 ATTTAGATAGCTTCAAAACATGATATTAAACTTGTCTGAATGATTGAACTTGGTTTTC-TCAGTT
66 ATTTAGATAGCTTCAATACATGATATTAAACTTGT-TGAATGATTGAACTTGGTTTTCAT-AGTT
* * * * * *
11691622 AATATGTGTAAAAAAGTTATTGTTTATCTTTA
129 GATATGTATGAAAAAGTTATCGTTTATGTTTG
* * * * * ** *
11691654 TTAAGCACTTTTTTATGTCGA-TAAAAGGAAAAAATATAATTTTGTAGTTA-TATT-TATGTTTT
1 TTTAGCAC-TTTTTGTGTC-ATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTA--TTTT
* *
11691716 AACAATTTAGATAGCTTCAATACATGATATTAAACTTATTTGAATGATTGAACTTGGTTTGCAT-
62 AACAATTTAGATAGCTTCAATACATGATATTAAACTT-GTTGAATGATTGAACTTGGTTTTCATA
* *
11691780 GATTGATGTGTGTGAAAAAGTTATCGTTTATGTTTG
126 G-TTGATATGTATGAAAAAGTTATCGTTTATGTTTG
* * * * *
11691816 TTTAGCACTTTTATAATG-C--TAAAATGCAAAAATGCAAATTTATATTTTTTATTCTA--TT--
1 TTTAGCACTTTT-T-GTGTCATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTATTTTAA
* * * * *
11691874 ---TTTAGATATCTTCAATACATGATATTAAA-TTAGTTCGAATTATTGAACATAGTTTTCATAA
64 CAATTTAGATAGCTTCAATACATGATATTAAACTT-GTT-GAATGATTGAACTTGGTTTTCATAG
* * *
11691935 TTGATATGTGTGAAAGAGTTA-CTGTTTATGTTTT
127 TTGATATGTATGAAAAAGTTATC-GTTTATGTTTG
* * * * * * * * *
11691969 TTTAGGACTTTGTTGTATCGTT-AAAGAGTAAAAATATAATTTTGCAGTTA-TATTTATATTTTA
1 TTTAGCACTTT-TTGTGTCATTAAAAG-GCAAAAATACAAATTTACATTTATTA-TTCTATTTTA
* * * ** * *
11692032 ATAGTTTAGATAGCTTAAATATGTGATATTAAACTTGTTTAAATGATTGAACTTAGTTTTCATGA
63 ACAATTTAGATAGCTTCAATACATGATATTAAACTTG-TTGAATGATTGAACTTGGTTTTCAT-A
* * *
11692097 TTTAATATGTATGAATAAGTTA-CGATTTATGTTTG
126 GTTGATATGTATGAAAAAGTTATCG-TTTATGTTTG
* * ** * * ** ** * * * *
11692132 TTTAAG-ACATTTAGTAACGTCAAAAGGCAAAAATGTAAATTTGTAATTATTGTTATGTTTTAAC
1 TTT-AGCACTTTTTGTGTCATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTATTTTAAC
* * *
11692196 AGTTTAGATAGC-TCATATTGCATGATATTAAATTTGTT
65 AATTTAGATAGCTTCA-A-TACATGATATTAAACTTGTT
11692234 CAAATGTTTA
Statistics
Matches: 738, Mismatches: 118, Indels: 89
0.78 0.12 0.09
Matches are distributed among these distances:
152 7 0.01
153 88 0.12
154 6 0.01
155 20 0.03
157 2 0.00
158 2 0.00
159 6 0.01
160 100 0.14
161 209 0.28
162 232 0.31
163 64 0.09
164 2 0.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (160 bp):
TTTAGCACTTTTTGTGTCATTAAAAGGCAAAAATACAAATTTACATTTATTATTCTATTTTAACA
ATTTAGATAGCTTCAATACATGATATTAAACTTGTTGAATGATTGAACTTGGTTTTCATAGTTGA
TATGTATGAAAAAGTTATCGTTTATGTTTG
Found at i:11692022 original size:315 final size:316
Alignment explanation
Indices: 11691173--11692227 Score: 993
Period size: 315 Copynumber: 3.3 Consensus size: 316
11691163 TTTCTATCTA
* * * * * *
11691173 TTTAGCAC-TTTTGTGCCATTAAAAGGTC-AAAATACAAATTTATATTTATTATTCTATTTTAAC
1 TTTAGCACTTTTTATGTCA-TAAAAGG-CAAAAATGCAAATTT-CA-TTATTATTATATTCTAAC
*
11691236 ATTTTAGATAGCTTCAATACATGAT-TTAAACTTA-TTCGAATGATTGAACTTGATTTTCATAGT
62 ATTTTAGATAGCTTCAATACATGATATTAAACTTAGTTCGAATGATTGAACTAG-TTTTCATAGT
* * * * **
11691299 TGATATATATGAAAAAGTTACCGTTTATGTTTATTTAAGACTTCTTTTGTCGTTAAAAGGCCAAA
126 TGATATGTGTGAAAAAGTTACTGTTTATGTTTATTTAGGACTT-TTTTGTCGTTAAAAGGAAAAA
* * * * * * *
11691364 ATACAAATTTACATTTATTATTCTA-TTTTAACAGTTTAGGTAGTTTTAATACATGATATTAAAC
190 ATATAATTTTGCAGTTA-TATT-TATTTTTAACAGTTTAGATAGCTTAAATACATGATATTAAAC
* * * * *
11691428 TTGTTTAAGGGGTTGAACTTGGTTTTCATGGTTGATATGTATGAAAAAGTTATTGTTTATGTCTG
253 TTGTTTAA-TGATTGAACTTGGTTTTCATGATTGATATGTATGAAAAAGTTATCGTTTATGTTTG
* * *
11691493 TTTAGGACTTTTTGTGTCATTAAAAGGCAAAAATGCAAATTTGCATTTATTATTATATTTTAACA
1 TTTAGCACTTTTTATGTCA-TAAAAGGCAAAAATGCAAATTT-CA-TTATTATTATATTCTAACA
* * *
11691558 ATTTAGATAGCTTCAAAACATGATATTAAACTT-G-TCTGAATGATTGAACTTGGTTTTC-TCAG
63 TTTTAGATAGCTTCAATACATGATATTAAACTTAGTTC-GAATGATTGAAC-TAGTTTTCAT-AG
* * * * * * *
11691620 TTAATATGTGTAAAAAAGTTATTGTTTATCTTTATTAAGCACTTTTTTATGTCGATAAAAGGAAA
125 TTGATATGTGTGAAAAAGTTACTGTTTATGTTTATTTAGGAC-TTTTT-TGTCGTTAAAAGGAAA
* * *
11691685 AAATATAATTTTGTAGTTATATTTATGTTTTAACAATTTAGATAGCTTCAATACATGATATTAAA
188 AAATATAATTTTGCAGTTATATTTAT-TTTTAACAGTTTAGATAGCTTAAATACATGATATTAAA
* * * *
11691750 CTTATTTGAATGATTGAACTTGGTTTGCATGATTGATGTGTGTGAAAAAGTTATCGTTTATGTTT
252 CTTGTTT-AATGATTGAACTTGGTTTTCATGATTGATATGTATGAAAAAGTTATCGTTTATGTTT
11691815 G
316 G
* * *
11691816 TTTAGCACTTTTATAATG-C-TAAAATGCAAAAATGCAAATTT-A-TATT-TTTTATTCT-A-TT
1 TTTAGCACTTTT-T-ATGTCATAAAAGGCAAAAATGCAAATTTCATTATTATTATATTCTAACAT
* * *
11691874 TTTAGATATCTTCAATACATGATATTAAA-TTAGTTCGAATTATTGAACATAGTTTTCATAATTG
64 TTTAGATAGCTTCAATACATGATATTAAACTTAGTTCGAATGATTGAAC-TAGTTTTCATAGTTG
* * * *
11691938 ATATGTGTGAAAGAGTTACTGTTTATGTTTTTTTAGGACTTTGTTGTATCGTT-AAAGAGTAAAA
128 ATATGTGTGAAAAAGTTACTGTTTATGTTTATTTAGGACTTT-TT-TGTCGTTAAAAG-GAAAAA
* **
11692002 ATATAATTTTGCAGTTATATTTATATTTTAATAGTTTAGATAGCTTAAATATGTGATATTAAACT
190 ATATAATTTTGCAGTTATATTTAT-TTTTAACAGTTTAGATAGCTTAAATACATGATATTAAACT
* * *
11692067 TGTTTAAATGATTGAACTTAGTTTTCATGATTTAATATGTATGAATAAGTTA-CGATTTATGTTT
254 TGTTT-AATGATTGAACTTGGTTTTCATGA-TTGATATGTATGAAAAAGTTATCG-TTTATGTTT
11692131 G
316 G
* * * * * * *
11692132 TTTAAG-AC-ATTTA-GTAACGTCAAAAGGCAAAAATGTAAATTTGTAATTATTGTTATGTTTTA
1 TTT-AGCACTTTTTATGT--CAT-AAAAGGCAAAAATGCAAA-TT-TCATTATTATTATATTCTA
* *
11692194 ACAGTTTAGATAGC-TCATATTGCATGATATTAAA
60 ACATTTTAGATAGCTTCA-A-TACATGATATTAAA
11692228 TTTGTTCAAA
Statistics
Matches: 609, Mismatches: 90, Indels: 67
0.80 0.12 0.09
Matches are distributed among these distances:
312 1 0.00
313 1 0.00
314 10 0.02
315 182 0.30
316 37 0.06
317 25 0.04
318 6 0.01
319 1 0.00
320 10 0.02
321 80 0.13
322 93 0.15
323 134 0.22
324 14 0.02
325 15 0.02
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (316 bp):
TTTAGCACTTTTTATGTCATAAAAGGCAAAAATGCAAATTTCATTATTATTATATTCTAACATTT
TAGATAGCTTCAATACATGATATTAAACTTAGTTCGAATGATTGAACTAGTTTTCATAGTTGATA
TGTGTGAAAAAGTTACTGTTTATGTTTATTTAGGACTTTTTTGTCGTTAAAAGGAAAAAATATAA
TTTTGCAGTTATATTTATTTTTAACAGTTTAGATAGCTTAAATACATGATATTAAACTTGTTTAA
TGATTGAACTTGGTTTTCATGATTGATATGTATGAAAAAGTTATCGTTTATGTTTG
Found at i:11693896 original size:3 final size:3
Alignment explanation
Indices: 11693888--11693938 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
11693878 GTTTAAACAC
*
11693888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11693936 AAT
1 AAT
11693939 TTAAACTTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11694880 original size:14 final size:15
Alignment explanation
Indices: 11694856--11694885 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11694846 TATAGGCTTT
11694856 ATTTTTATTATATAA
1 ATTTTTATTATATAA
11694871 ATTTTT-TTATATAA
1 ATTTTTATTATATAA
11694885 A
1 A
11694886 ATCAATTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTATTATATAA
Found at i:11698009 original size:2 final size:2
Alignment explanation
Indices: 11698002--11698029 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11697992 ACATAGCAAC
11698002 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
11698030 TCTAACTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11699815 original size:11 final size:11
Alignment explanation
Indices: 11699799--11699823 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11699789 TGATAGTGAT
11699799 CGTATGTAAAC
1 CGTATGTAAAC
11699810 CGTATGTAAAC
1 CGTATGTAAAC
11699821 CGT
1 CGT
11699824 TGATTTGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (11 bp):
CGTATGTAAAC
Found at i:11704978 original size:8 final size:7
Alignment explanation
Indices: 11704961--11705011 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
11704951 ACAGGTTTTT
*
11704961 TTTTTTA
1 TTTTTGA
11704968 TTTTATGA
1 TTTT-TGA
11704976 -TTTT-A
1 TTTTTGA
11704981 TTTTTGA
1 TTTTTGA
11704988 TTTTTGA
1 TTTTTGA
11704995 TTTTTGA
1 TTTTTGA
11705002 TTTTT-A
1 TTTTTGA
11705008 TTTT
1 TTTT
11705012 AATTTTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 1 0.03
6 10 0.25
7 27 0.68
8 2 0.05
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (7 bp):
TTTTTGA
Found at i:11704984 original size:20 final size:19
Alignment explanation
Indices: 11704957--11705012 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
11704947 GGTCACAGGT
11704957 TTTTTTTTTTATTTTATGA
1 TTTTTTTTTTATTTTATGA
*
11704976 TTTTATTTTTGATTTT-TGA
1 TTTT-TTTTTTATTTTATGA
11704995 TTTTTGATTTTTATTTTA
1 TTTTT--TTTTTATTTTA
11705013 ATTTTTCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 19 0.61
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTTATTTTATGA
Found at i:11704997 original size:14 final size:13
Alignment explanation
Indices: 11704962--11705011 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
11704952 CAGGTTTTTT
11704962 TTTTTATTTTATGA
1 TTTTTATTTT-TGA
11704976 -TTTTATTTTTGA
1 TTTTTATTTTTGA
11704988 TTTTTGATTTTTGA
1 TTTTT-ATTTTTGA
11705002 TTTTTATTTT
1 TTTTTATTTT
11705012 AATTTTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.09
13 18 0.53
14 13 0.38
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTTGA
Found at i:11705016 original size:26 final size:27
Alignment explanation
Indices: 11704961--11705018 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
11704951 ACAGGTTTTT
* *
11704961 TTTTTTATTTTATGATTTTATTTTTGA
1 TTTTTGATTTTATGATTTTATTTTTAA
11704988 TTTTTGATTTT-TGATTTT-TATTTTAA
1 TTTTTGATTTTATGATTTTAT-TTTTAA
11705014 TTTTT
1 TTTTT
11705019 CTTATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 17 0.61
27 10 0.36
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (27 bp):
TTTTTGATTTTATGATTTTATTTTTAA
Found at i:11705018 original size:27 final size:27
Alignment explanation
Indices: 11704960--11705027 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
11704950 CACAGGTTTT
*
11704960 TTTTTTTATTTTATGATTTTATTTTTGA
1 TTTTTTTATTTT-TGATTTTATTTTTAA
*
11704988 -TTTTTGATTTTTGATTTT-TATTTTAA
1 TTTTTTTATTTTTGATTTTAT-TTTTAA
11705014 TTTTTCTTATTTTT
1 TTTTT-TTATTTTT
11705028 TATCTTAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 12 0.35
27 14 0.41
28 7 0.21
ACGTcount: A:0.16, C:0.01, G:0.06, T:0.76
Consensus pattern (27 bp):
TTTTTTTATTTTTGATTTTATTTTTAA
Found at i:11705178 original size:22 final size:22
Alignment explanation
Indices: 11705101--11705180 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
11705091 AAAAAGGAAA
11705101 GATTTATTATATTTATTTGCAT
1 GATTTATTATATTTATTTGCAT
* * *
11705123 GATATTTTTGTATGATTACTTGCAT
1 GAT-TTATTATAT--TTATTTGCAT
11705148 -ATTTTTATTATATTTATTTGCAT
1 GA--TTTATTATATTTATTTGCAT
11705171 GATTTATTAT
1 GATTTATTAT
11705181 GATATTTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
22 11 0.24
23 16 0.35
24 2 0.04
25 16 0.35
26 1 0.02
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (22 bp):
GATTTATTATATTTATTTGCAT
Found at i:11705185 original size:25 final size:24
Alignment explanation
Indices: 11705103--11705187 Score: 86
Period size: 25 Copynumber: 3.5 Consensus size: 24
11705093 AAAGGAAAGA
*
11705103 TTTATTATATTTATTTGCATGATAT
1 TTTATGATATTTATTTGCATGAT-T
*
11705128 TTT-TG-TATGATTACTTGCAT-ATT
1 TTTATGATAT--TTATTTGCATGATT
*
11705151 TTTATTATATTTATTTGCATGATT
1 TTTATGATATTTATTTGCATGATT
11705175 TATTATGATATTT
1 T-TTATGATATTT
11705188 TTGTTTGATA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
23 16 0.33
24 8 0.16
25 25 0.51
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTATGATATTTATTTGCATGATT
Found at i:11705209 original size:24 final size:23
Alignment explanation
Indices: 11705151--11705221 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
11705141 CTTGCATATT
*
11705151 TTTATTAT-AT-TTATTTGCATGA
1 TTTATTATAATATT-TTTGTATGA
* *
11705173 TTTATTATGATATTTTTGTTTGA
1 TTTATTATAATATTTTTGTATGA
11705196 TATTATTATAATATTTTTGTATGA
1 T-TTATTATAATATTTTTGTATGA
11705220 TT
1 TT
11705222 ATTTTTGCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.19
23 11 0.26
24 23 0.55
ACGTcount: A:0.27, C:0.01, G:0.10, T:0.62
Consensus pattern (23 bp):
TTTATTATAATATTTTTGTATGA
Found at i:11708417 original size:199 final size:200
Alignment explanation
Indices: 11708072--11708574 Score: 550
Period size: 199 Copynumber: 2.5 Consensus size: 200
11708062 AGAAAATTCT
* * * **
11708072 TGTTAAGCATCCAACTTAAAATTAATTGACAGTAAGTG-GATAGACCCAATCTGAATATAAGGCT
1 TGTTAAGCATCCAACCTAAAATCAATTGACAGTAAGTGAGA-AG-CCCAACCTGAATATAAGATT
* * ** * * *
11708136 ATAAGAAATTTGAAATTTATTAAATGTGGATAACCCACTTTAACAGGTCCCCATCACGTGTAGGT
64 ATAGGATATTAAAAATTTATTAGATGTGGATAACCCACTTTAACAGGACCCCATCACGTGTAGGC
* *
11708201 GAATATGGAAAAAGCCTTTCATATGACAAATTAAGAAAAGATAATAG-AAAAA-GTTCTGACTCT
129 GAACATGGAAAAAGCCTTTCATATGACAAATTAAGAAAAGATAATAGAAAAAATATTCTGACTCT
*
11708264 GATATCA
194 GATACCA
11708271 TGTTAAGCATCCAACCTAAAATCAATTGACAGTAAGTGAAGAAGCCCAACCTGAATATAAGATTA
1 TGTTAAGCATCCAACCTAAAATCAATTGACAGTAAGTG-AGAAGCCCAACCTGAATATAAGATTA
* * * *
11708336 TAGGATACTAAAAATTTATTAGATGTGGGATAACCTACTTTAACA-GACCCTATCATGTGTAGGC
65 TAGGATATTAAAAATTTATTAGATGT-GGATAACCCACTTTAACAGGACCCCATCACGTGTAGGC
* * * * *
11708400 GAACAT-GAAAGAAGCCTTTCATGTGATAAATTAGGAAAAGATAATAGAAAAAATATTTTGGCTC
129 GAACATGGAAA-AAGCCTTTCATATGACAAATTAAGAAAAGATAATAGAAAAAATATTCTGACTC
11708464 TGATACCA
193 TGATACCA
* ** * * * ** * * *
11708472 TATTAAGCATCCAA-CTCACTACCAATAGGCAGTAAGTGGAGTGGCTCAACTTGAATTTAAGATT
1 TGTTAAGCATCCAACCT-AAAATCAATTGACAGTAAGT-GAGAAGCCCAACCTGAATATAAGATT
* * *
11708536 ATAGGATATTGAAAATATATTAGATGTAAGATAACCCAC
64 ATAGGATATTAAAAATTTATTAGATGT-GGATAACCCAC
11708575 CATAACATAA
Statistics
Matches: 255, Mismatches: 41, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
198 4 0.02
199 127 0.50
200 26 0.10
201 97 0.38
202 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (200 bp):
TGTTAAGCATCCAACCTAAAATCAATTGACAGTAAGTGAGAAGCCCAACCTGAATATAAGATTAT
AGGATATTAAAAATTTATTAGATGTGGATAACCCACTTTAACAGGACCCCATCACGTGTAGGCGA
ACATGGAAAAAGCCTTTCATATGACAAATTAAGAAAAGATAATAGAAAAAATATTCTGACTCTGA
TACCA
Found at i:11708586 original size:15 final size:15
Alignment explanation
Indices: 11708566--11708597 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11708556 TAGATGTAAG
11708566 ATAACCCACCATAAC
1 ATAACCCACCATAAC
11708581 ATAACCCACCATAAC
1 ATAACCCACCATAAC
11708596 AT
1 AT
11708598 GCCATCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (15 bp):
ATAACCCACCATAAC
Found at i:11712354 original size:15 final size:15
Alignment explanation
Indices: 11712334--11712372 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11712324 TGTGAATGTT
11712334 TGAATTGGAAAATCA
1 TGAATTGGAAAATCA
*
11712349 TGAATTGAAAAATCA
1 TGAATTGGAAAATCA
*
11712364 TGACTTGGA
1 TGAATTGGA
11712373 CTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (15 bp):
TGAATTGGAAAATCA
Found at i:11713599 original size:44 final size:44
Alignment explanation
Indices: 11713548--11713754 Score: 145
Period size: 44 Copynumber: 4.6 Consensus size: 44
11713538 ATTTTGGATG
11713548 TAAACTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAATCTT
1 TAAACTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAATCTT
* **
11713592 TGAACTTTTCAAATGCA-AATCTTTGAATTTTGGAT-ATGAAT-TT
1 TAAACTTTTCAAATG-AGAATCTTTGAATTTTAAATGA-GAATCTT
* ** * *
11713635 CTAGAATTTTTTGAAT-ATGAATCTTTGGATTTT-GATGAGAATCTCT
1 -TA-AACTTTTCAAATGA-GAATCTTTGAATTTTAAATGAGAATCT-T
* * * * * *
11713681 AAAATTTTTCAAATGAAAATTTTTTAATCTTTCAAATGAGAATTTT
1 TAAACTTTTCAAATGAGAATCTTTGAAT-TTT-AAATGAGAATCTT
** * *
11713727 TAAACTTTTTGAATGTGAATTTTTGAAT
1 TAAACTTTTCAAATGAGAATCTTTGAAT
11713755 AAGAATTTTT
Statistics
Matches: 126, Mismatches: 24, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
43 4 0.03
44 60 0.48
45 30 0.24
46 23 0.18
47 9 0.07
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.45
Consensus pattern (44 bp):
TAAACTTTTCAAATGAGAATCTTTGAATTTTAAATGAGAATCTT
Found at i:11713612 original size:23 final size:22
Alignment explanation
Indices: 11713553--11713622 Score: 108
Period size: 21 Copynumber: 3.2 Consensus size: 22
11713543 GGATGTAAAC
11713553 TTTTCAAATGAGAATCTTTGAA
1 TTTTCAAATGAGAATCTTTGAA
11713575 TTTT-AAATGAGAATCTTTGAA
1 TTTTCAAATGAGAATCTTTGAA
11713596 CTTTTCAAATGCA-AATCTTTGAA
1 -TTTTCAAATG-AGAATCTTTGAA
11713619 TTTT
1 TTTT
11713623 GGATATGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 17 0.38
22 12 0.27
23 15 0.33
24 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (22 bp):
TTTTCAAATGAGAATCTTTGAA
Found at i:11713729 original size:22 final size:23
Alignment explanation
Indices: 11713687--11713734 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
11713677 CTCTAAAATT
*
11713687 TTTCAAATGAAAATTTTTTAATC
1 TTTCAAATGAAAATTTTTTAAAC
*
11713710 TTTCAAATGAGAA-TTTTTAAAC
1 TTTCAAATGAAAATTTTTTAAAC
11713732 TTT
1 TTT
11713735 TTGAATGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (23 bp):
TTTCAAATGAAAATTTTTTAAAC
Found at i:11713813 original size:24 final size:22
Alignment explanation
Indices: 11713757--11713813 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
11713747 TTTTGAATAA
*
11713757 GAATTTTTAAAATTTTAGATGT
1 GAATTTTTAAAATTTTAAATGT
* *
11713779 GAATCTCTAAAATATCTTAAATGT
1 GAATTTTTAAAAT-T-TTAAATGT
11713803 GAATTTTTAAA
1 GAATTTTTAAA
11713814 TCTTGGATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 11 0.39
23 1 0.04
24 16 0.57
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (22 bp):
GAATTTTTAAAATTTTAAATGT
Found at i:11714106 original size:22 final size:19
Alignment explanation
Indices: 11714081--11714124 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
11714071 TAAATTTTAA
11714081 AATTTTAGAAATTTCATTTGTG
1 AATTTT-GAAATTT-ATTT-TG
*
11714103 AATTTTTAAATTTATTTTG
1 AATTTTGAAATTTATTTTG
11714122 AAT
1 AAT
11714125 CATTTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 6 0.29
22 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (19 bp):
AATTTTGAAATTTATTTTG
Found at i:11714170 original size:18 final size:18
Alignment explanation
Indices: 11714149--11714281 Score: 51
Period size: 18 Copynumber: 7.4 Consensus size: 18
11714139 AGAACCTTCG
11714149 CAAATCTTGAAATCTTTA
1 CAAATCTTGAAATCTTTA
* * *
11714167 CAAAT-TTTAGAATTTTTG
1 CAAATCTTGA-AATCTTTA
* * *
11714185 CAAAACTT-AGAATTTTTC
1 CAAATCTTGA-AATCTTTA
*
11714203 CTAATCTTGAAA-CTTTA
1 CAAATCTTGAAATCTTTA
* * * *
11714220 CGAATTTTGAAACCTTTG
1 CAAATCTTGAAATCTTTA
** * *
11714238 TGAATCTT-AGAATTTTTG
1 CAAATCTTGA-AATCTTTA
*
11714256 CAAATCTTAAAAT-TCTTA
1 CAAATCTTGAAATCT-TTA
11714274 CAAATCTT
1 CAAATCTT
11714282 AGAATATTTA
Statistics
Matches: 89, Mismatches: 19, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
17 18 0.20
18 67 0.75
19 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (18 bp):
CAAATCTTGAAATCTTTA
Found at i:11714188 original size:36 final size:36
Alignment explanation
Indices: 11714133--11714302 Score: 107
Period size: 36 Copynumber: 4.8 Consensus size: 36
11714123 ATCATTTGTG
** *
11714133 AATCTTAGAACCTTCGCAAATCTTGAAATCTTTACA
1 AATCTTAGAATTTTTGCAAATCTTGAAATCTTTACA
* * * * *
11714169 AATTTTAGAATTTTTGCAAAACTT-AGAATTTTTCCT
1 AATCTTAGAATTTTTGCAAATCTTGA-AATCTTTACA
** * * * * ***
11714205 AATCTT-GAAACTTTACGAATTTTGAAACCTTTGTG
1 AATCTTAGAATTTTTGCAAATCTTGAAATCTTTACA
*
11714240 AATCTTAGAATTTTTGCAAATCTTAAAAT-TCTTACA
1 AATCTTAGAATTTTTGCAAATCTTGAAATCT-TTACA
11714276 AATCTTAGAATATTTATG--AATCTTGAA
1 AATCTTAGAAT-TTT-TGCAAATCTTGAA
11714303 CTTTTGTGAA
Statistics
Matches: 97, Mismatches: 31, Indels: 12
0.69 0.22 0.09
Matches are distributed among these distances:
35 24 0.25
36 68 0.70
37 3 0.03
38 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (36 bp):
AATCTTAGAATTTTTGCAAATCTTGAAATCTTTACA
Found at i:11714244 original size:89 final size:89
Alignment explanation
Indices: 11714151--11714352 Score: 203
Period size: 89 Copynumber: 2.3 Consensus size: 89
11714141 AACCTTCGCA
* * * * * *
11714151 AATCTT-GAAATCTTTACAAATTTTAGAATTTTTGCAAAACTTAGAATTTTTCCT-AATCTTGAA
1 AATCTTAG-AATCTTTACAAATCTTAAAATTCTTACAAAACTTAGAATATTT-ATGAATCTTG-A
*
11714214 AC-TTTACGAATTTTGAAACCTTTGTG
63 ACTTTTACGAAATTTGAAACCTTTGTG
* * *
11714240 AATCTTAGAATTTTTGCAAATCTTAAAATTCTTACAAATCTTAGAATATTTATGAATCTTGAACT
1 AATCTTAGAATCTTTACAAATCTTAAAATTCTTACAAAACTTAGAATATTTATGAATCTTGAACT
** *
11714305 TTTGTGAAATTTGAAATCTTTGTG
66 TTTACGAAATTTGAAACCTTTGTG
* * * *
11714329 AATTTTTGAATTTTTACGAATCTT
1 AATCTTAGAATCTTTACAAATCTT
11714353 GGAACTTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
88 4 0.04
89 88 0.95
90 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (89 bp):
AATCTTAGAATCTTTACAAATCTTAAAATTCTTACAAAACTTAGAATATTTATGAATCTTGAACT
TTTACGAAATTTGAAACCTTTGTG
Found at i:11714247 original size:53 final size:54
Alignment explanation
Indices: 11714116--11714325 Score: 159
Period size: 54 Copynumber: 3.9 Consensus size: 54
11714106 TTTTAAATTT
* **
11714116 ATTTTGAATCATTTGTGAATCTTAGAA-CCTTCGCAAATCTTGAAATCTTTACAA
1 ATTTTGAAACATTTGTGAATCTTAGAATTTTTC-CAAATCTTGAAATCTTTACAA
* * * * *
11714170 ATTTT-AGA-ATTTTTGCAAAACTTAGAATTTTTCCTAATCTTGAAA-CTTTACGA
1 ATTTTGAAACATTTGTG--AATCTTAGAATTTTTCCAAATCTTGAAATCTTTACAA
* * *
11714223 ATTTTGAAACCTTTGTGAATCTTAGAATTTTTGCAAATCTTAAAAT-TCTTACAA
1 ATTTTGAAACATTTGTGAATCTTAGAATTTTTCCAAATCTTGAAATCT-TTACAA
* * * *
11714277 ATCTT-AGAATATTTATGAATCTT-GAACTTTTGT-GAAAT-TTGAAATCTTT
1 ATTTTGA-AACATTTGTGAATCTTAGAA-TTTT-TCCAAATCTTGAAATCTTT
11714326 GTGAATTTTT
Statistics
Matches: 123, Mismatches: 22, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
52 6 0.05
53 50 0.41
54 58 0.47
55 9 0.07
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (54 bp):
ATTTTGAAACATTTGTGAATCTTAGAATTTTTCCAAATCTTGAAATCTTTACAA
Done.