Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, 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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 31
Found at i:6301355 original size:29 final size:29
Alignment explanation
Indices: 6301322--6301379 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
6301312 TGACAAAATG
6301322 CACAAAC-AGAGAAGAAATAAGTTAGTATA
1 CACAAACAAGAGAA-AAATAAGTTAGTATA
6301351 CACAAACAAAAGAGAAAAATAAGTTAGTA
1 CACAAAC--AAGAGAAAAATAAGTTAGTA
6301380 CATGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
31 13 0.50
32 6 0.23
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.16
Consensus pattern (29 bp):
CACAAACAAGAGAAAAATAAGTTAGTATA
Found at i:6302448 original size:16 final size:16
Alignment explanation
Indices: 6302424--6302474 Score: 84
Period size: 16 Copynumber: 3.1 Consensus size: 16
6302414 TGCAAAACAA
*
6302424 TTTTAAGAAAAATCAT
1 TTTTTAGAAAAATCAT
6302440 TTTTTAGAAAAATCAT
1 TTTTTAGAAAAATCAT
6302456 TTTTTATGAAAAATCAT
1 TTTTTA-GAAAAATCAT
6302473 TT
1 TT
6302475 CTTAAGACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTTTAGAAAAATCAT
Found at i:6302451 original size:17 final size:17
Alignment explanation
Indices: 6302424--6302474 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
6302414 TGCAAAACAA
*
6302424 TTTTAAGAAAAATCATT
1 TTTTATGAAAAATCATT
6302441 TTTTA-GAAAAATCATT
1 TTTTATGAAAAATCATT
6302457 TTTTATGAAAAATCATT
1 TTTTATGAAAAATCATT
6302474 T
1 T
6302475 CTTAAGACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.48
17 17 0.52
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTTATGAAAAATCATT
Found at i:6303242 original size:28 final size:28
Alignment explanation
Indices: 6303211--6303269 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
6303201 TGGTAATAAC
* * *
6303211 AAATTAAAGGGCTAAAACAGCAAAATAG
1 AAATTAAAAGACTAAAACAGCAAAACAG
**
6303239 AAATTAAAAGACTAAAATGGCAAAACAG
1 AAATTAAAAGACTAAAACAGCAAAACAG
6303267 AAA
1 AAA
6303270 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.14
Consensus pattern (28 bp):
AAATTAAAAGACTAAAACAGCAAAACAG
Found at i:6305094 original size:3 final size:3
Alignment explanation
Indices: 6305081--6305142 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
6305071 AGAATATGTA
** *
6305081 AAT AA- AAT AAT AAT AAT AAT TCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
6305125 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
6305143 AAAAGATCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6314211 original size:64 final size:65
Alignment explanation
Indices: 6314098--6314240 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 65
6314088 TGTACTAAGA
*
6314098 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCA-TGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATTGACTG
* ** * *
6314162 GTGCATCGATGCATCAAATGCATTCTATGTTT-AATTTAATTCATG-GTGCATCGATGCATTGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-AGTCA-GAGTGCATCGATGCATTGAC
6314225 TG
64 TG
6314227 GTGCATCGATGCAT
1 GTGCATCGATGCAT
6314241 GGATTGGTGC
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
63 3 0.04
64 47 0.67
65 20 0.29
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATTGACTG
Found at i:6314260 original size:20 final size:20
Alignment explanation
Indices: 6314205--6314253 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
6314195 ATTTAATTCA
*
6314205 TGGTGCATCGATGCATTGAT
1 TGGTGCATCGATGCATGGAT
6314225 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
6314245 TGGTGCATC
1 TGGTGCATC
6314254 AGTGCATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.33
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:6316902 original size:20 final size:20
Alignment explanation
Indices: 6316879--6316927 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
6316869 TCAAGGATGC
6316879 ATCGATGCACTGTTAGGTGT
1 ATCGATGCACTGTTAGGTGT
6316899 ATCGATGCACTGTTAGGTGT
1 ATCGATGCACTGTTAGGTGT
6316919 ATCGATGCA
1 ATCGATGCA
6316928 TGAAGCACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (20 bp):
ATCGATGCACTGTTAGGTGT
Found at i:6316902 original size:40 final size:42
Alignment explanation
Indices: 6316815--6316907 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 42
6316805 GGCCTTGTGC
*
6316815 ATCGATGCACATTCAAGGCGTGCATCAGTGCATCTTTATGGTGT
1 ATCGATG--CATTCAAGGCATGCATCAGTGCATCTTTATGGTGT
6316859 ATCGATGCATTCAAGG-ATGCATC-GATGCA-CTGTTA-GGTGT
1 ATCGATGCATTCAAGGCATGCATCAG-TGCATCT-TTATGGTGT
6316899 ATCGATGCA
1 ATCGATGCA
6316908 CTGTTAGGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
40 17 0.37
41 13 0.28
42 9 0.20
44 7 0.15
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (42 bp):
ATCGATGCATTCAAGGCATGCATCAGTGCATCTTTATGGTGT
Found at i:6322801 original size:241 final size:239
Alignment explanation
Indices: 6322359--6322838 Score: 892
Period size: 241 Copynumber: 2.0 Consensus size: 239
6322349 ATTGGTGCAT
6322359 CGGTGCATCACTTTGATAATTGATTTTAGACTTGATTTTGGTTCAAAATACTTTATGAAAATTGT
1 CGGTGCATCACTTTGATAATTGATTTTAGACTTGATTTTGGTTCAAAATACTTTATGAAAATTGT
6322424 TTCAAAAATAGTTAGTATAAAACACAATTTTACACATTTAGTAAGGTTTGAATTTGAACTTGAAG
66 TTCAAAAATAGTTAGTATAAAACACAATTTTACACATTTAGTAAGGTTTGAATTTGAACTTGAAG
*
6322489 ACTTGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAATCATTTGTAAAA
131 ACATGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAATCATTTGTAAAA
6322554 TCTTAAAATTTATTTAAACTTAATTTGTTATATCGAAACACAAA
196 TCTTAAAATTTATTTAAACTTAATTTGTTATATCGAAACACAAA
*
6322598 CGGTGCATCACTTTGATAAATTGATTTTAGGCTTGATTTTGGTTCAAAATACTTTATG-AAATTG
1 CGGTGCATCACTTTGAT-AATTGATTTTAGACTTGATTTTGGTTCAAAATACTTTATGAAAATTG
6322662 TTTCAAAAATAGTTTAAGTATAAAACACAATTTTACACATTTAGTAAGGTTTGAATTTGAACTTG
65 TTTCAAAAATAG-TT-AGTATAAAACACAATTTTACACATTTAGTAAGGTTTGAATTTGAACTTG
6322727 AAAGACATGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAATCATTTGT
128 -AAGACATGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAATCATTTGT
6322792 -AAATCTTAAAATTTATTTAAACTTAATTTGTTATATCGAAACACAAA
192 AAAATCTTAAAATTTATTTAAACTTAATTTGTTATATCGAAACACAAA
6322839 GTATTTTCAA
Statistics
Matches: 235, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
239 35 0.15
240 41 0.17
241 96 0.41
242 63 0.27
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (239 bp):
CGGTGCATCACTTTGATAATTGATTTTAGACTTGATTTTGGTTCAAAATACTTTATGAAAATTGT
TTCAAAAATAGTTAGTATAAAACACAATTTTACACATTTAGTAAGGTTTGAATTTGAACTTGAAG
ACATGGAGTAATAATTTGATATTCGATTAATTAAATCGAATATACTTAGAAAATCATTTGTAAAA
TCTTAAAATTTATTTAAACTTAATTTGTTATATCGAAACACAAA
Found at i:6323358 original size:47 final size:47
Alignment explanation
Indices: 6323205--6323358 Score: 115
Period size: 47 Copynumber: 3.3 Consensus size: 47
6323195 AAGCATTAAT
* * * * *
6323205 TATTAAAATTTTAAAATATATTATTATATAATAATATATGT-TTTA-A
1 TATTAATATTATATAATAAATTATT-TATAATAATATATATATTTATA
** * *
6323251 TATT-ATATTATATGCTCAATTATATTATAATAATATATATATATT-TT
1 TATTAATATTATATAATAAATTAT-TTATAATAATATATATAT-TTATA
* *
6323298 TATT--TCATAATATAATAAATTATTGATAATGAATATAT-TATTTATA
1 TATTAAT-ATTATATAATAAATTATTTATAAT-AATATATATATTTATA
6323344 TATTAATATTATATA
1 TATTAATATTATATA
6323359 GTAATCTAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 17
0.72 0.14 0.15
Matches are distributed among these distances:
45 28 0.34
46 21 0.25
47 33 0.40
48 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (47 bp):
TATTAATATTATATAATAAATTATTTATAATAATATATATATTTATA
Found at i:6323401 original size:23 final size:24
Alignment explanation
Indices: 6323369--6323417 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
6323359 GTAATCTAAT
*
6323369 AATATTTTAA-TAAAAATGTTTAA
1 AATATATTAATTAAAAATGTTTAA
* *
6323392 AATATATTAATTAATAATTTTTAA
1 AATATATTAATTAAAAATGTTTAA
6323416 AA
1 AA
6323418 ATAATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
AATATATTAATTAAAAATGTTTAA
Found at i:6323575 original size:25 final size:23
Alignment explanation
Indices: 6323536--6323593 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
6323526 ATAATTATTC
*
6323536 TAATATTTTAAAAATAATAATAT
1 TAATTTTTTAAAAATAATAATAT
* *
6323559 TAAGTTTTTTAATAAATACTATTAT
1 TAA-TTTTTTAA-AAATAATAATAT
*
6323584 TTATTTTTTA
1 TAATTTTTTA
6323594 TATTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 3 0.10
24 14 0.48
25 12 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATTTTTTAAAAATAATAATAT
Found at i:6328975 original size:29 final size:29
Alignment explanation
Indices: 6328922--6328977 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
6328912 TTGAATAACA
*
6328922 AAATGAAACGTTAGGCGCTAACTGAAACG
1 AAATGAAACGTTAGGCACTAACTGAAACG
*
6328951 AAAT-AAACGTTAGGTACTACACTGAAA
1 AAATGAAACGTTAGGCACTA-ACTGAAA
6328978 AAAAAATCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
AAATGAAACGTTAGGCACTAACTGAAACG
Found at i:6330218 original size:21 final size:19
Alignment explanation
Indices: 6330169--6330206 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6330159 TTGTTTAAAC
6330169 ATTTA-AAAT-CATAAAATA
1 ATTTATAAATACA-AAAATA
6330187 ATTTATAAATACAAAAATA
1 ATTTATAAATACAAAAATA
6330206 A
1 A
6330207 ATTTTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 11 0.61
20 2 0.11
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTTATAAATACAAAAATA
Found at i:6330833 original size:32 final size:31
Alignment explanation
Indices: 6330796--6330882 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 31
6330786 AGGGCCCGAA
* *
6330796 GCCTACCCAAGAAGGTTACTC-AGGGCCACAAG
1 GCCTACCCAAGAAAGAT-CTCGA-GGCCACAAG
* *
6330828 GCCTACCCAA-AAAGATCTCGAGGCCGCAGG
1 GCCTACCCAAGAAAGATCTCGAGGCCACAAG
6330858 GCCTACCCAAGAAAGATCTCG-GGCC
1 GCCTACCCAAGAAAGATCTCGAGGCC
6330883 TGGAGCCTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.49
31 15 0.31
32 10 0.20
ACGTcount: A:0.30, C:0.33, G:0.25, T:0.11
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCGAGGCCACAAG
Found at i:6338769 original size:85 final size:85
Alignment explanation
Indices: 6338585--6338770 Score: 270
Period size: 85 Copynumber: 2.2 Consensus size: 85
6338575 TGTAAGTCAT
*
6338585 ACAAATGTGTGTCATCTTCATTTATGACGGGAGCTTCAATGACACGCAATGTAAGTCATACATGC
1 ACAAATGTGTGTCATCTTCATTTATGACGGGAGCTTCAATGACACGCAATGTAAGTCATAAATGC
6338650 GTGTCATAAATTTATGACAC
66 GTGTCATAAATTTATGACAC
* * *
6338670 ACAAATGTATGTCATCTTCATTTATGACGAGG-GCTTCAATGACGCGCAATG-AGCGTCATAAAT
1 ACAAATGTGTGTCATCTTCATTTATGACG-GGAGCTTCAATGACACGCAATGTA-AGTCATAAAT
*
6338733 GCGTGTCATAGATTTATGACAC
64 GCGTGTCATAAATTTATGACAC
*
6338755 A-AAATTGTGCGTCATC
1 ACAAA-TGTGTGTCATC
6338771 AAAAATTCAT
Statistics
Matches: 91, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
84 4 0.04
85 85 0.93
86 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (85 bp):
ACAAATGTGTGTCATCTTCATTTATGACGGGAGCTTCAATGACACGCAATGTAAGTCATAAATGC
GTGTCATAAATTTATGACAC
Found at i:6339727 original size:22 final size:21
Alignment explanation
Indices: 6339693--6339753 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
6339683 GGACCACTAC
6339693 GTCCCAAAGGACCACTGGATAT
1 GTCCCAAA-GACCACTGGATAT
*
6339715 GTCCCGAAAGACCTCTGGATAT
1 GTCCC-AAAGACCACTGGATAT
*
6339737 GTCCCCAAGGACCACTG
1 GT-CCCAAAGACCACTG
6339754 TAACCCTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 28 0.82
23 6 0.18
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (21 bp):
GTCCCAAAGACCACTGGATAT
Found at i:6341024 original size:2 final size:2
Alignment explanation
Indices: 6341017--6341078 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
6341007 TGTGTAGCTA
6341017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6341058 A- AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
6341079 GTATCCCTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6346255 original size:20 final size:19
Alignment explanation
Indices: 6346226--6346267 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
6346216 TTTAGTTCAC
6346226 GAAATATAAGATTACCAGTG
1 GAAATATAAGATTACCAG-G
*
6346246 GAAATGTAAGATTACCAGG
1 GAAATATAAGATTACCAGG
6346265 GAA
1 GAA
6346268 TATGATTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (19 bp):
GAAATATAAGATTACCAGG
Found at i:6356544 original size:33 final size:33
Alignment explanation
Indices: 6356502--6356596 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
6356492 GTGATTTGGA
6356502 GAAGACTCCAAGATTGTTACACGTCTTCAACGT
1 GAAGACTCCAAGATTGTTACACGTCTTCAACGT
6356535 GAAGACTCCAAGATTGTTACACGTCTTCAACGT
1 GAAGACTCCAAGATTGTTACACGTCTTCAACGT
*
6356568 GAAGACTCCAAGATT-TTCTCACGTCTTCA
1 GAAGACTCCAAGATTGTT-ACACGTCTTCA
6356597 GCTTGTATGT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (33 bp):
GAAGACTCCAAGATTGTTACACGTCTTCAACGT
Found at i:6356744 original size:14 final size:14
Alignment explanation
Indices: 6356727--6356778 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
6356717 TGCATACTAT
6356727 TAAATGCCCATGAA
1 TAAATGCCCATGAA
*
6356741 TAAATGCATGCAGTGAAA
1 TAAATGC--CCA-TG-AA
6356759 TAAATGCCCATGAA
1 TAAATGCCCATGAA
*
6356773 TGAATG
1 TAAATG
6356779 AATGAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.45
15 2 0.06
16 4 0.13
17 2 0.06
18 9 0.29
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (14 bp):
TAAATGCCCATGAA
Found at i:6359957 original size:14 final size:14
Alignment explanation
Indices: 6359938--6359966 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6359928 GACTAGACGA
6359938 CTGCCATACGTCTT
1 CTGCCATACGTCTT
6359952 CTGCCATACGTCTT
1 CTGCCATACGTCTT
6359966 C
1 C
6359967 AGCAGGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.38, G:0.14, T:0.34
Consensus pattern (14 bp):
CTGCCATACGTCTT
Found at i:6360025 original size:14 final size:14
Alignment explanation
Indices: 6360008--6360059 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
6359998 TGCATACTAT
6360008 TAAATGCCCATGAA
1 TAAATGCCCATGAA
*
6360022 TAAATGCATGCAGTGAAA
1 TAAATGC--CCA-TG-AA
6360040 TAAATGCCCATGAA
1 TAAATGCCCATGAA
*
6360054 TGAATG
1 TAAATG
6360060 AATGAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 14 0.45
15 2 0.06
16 4 0.13
17 2 0.06
18 9 0.29
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (14 bp):
TAAATGCCCATGAA
Found at i:6361014 original size:12 final size:12
Alignment explanation
Indices: 6360994--6361025 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6360984 AGGTATATAA
*
6360994 TATTAATTGATT
1 TATTTATTGATT
6361006 TATTTATTGATT
1 TATTTATTGATT
6361018 TATTTATT
1 TATTTATT
6361026 TATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
TATTTATTGATT
Found at i:6362675 original size:19 final size:19
Alignment explanation
Indices: 6362652--6362707 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
6362642 AACCATCACT
*
6362652 ATTAAATTATTATTAAATC
1 ATTAAATAATTATTAAATC
* *
6362671 CTTAAATAATTATTAATTC
1 ATTAAATAATTATTAAATC
*
6362690 ATTAAATCATTATTAAAT
1 ATTAAATAATTATTAAAT
6362708 TGTTAAATCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAATAATTATTAAATC
Found at i:6362713 original size:8 final size:8
Alignment explanation
Indices: 6362702--6362740 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
6362692 TAAATCATTA
*
6362702 TTAAATTG
1 TTAAATCG
6362710 TTAAATCG
1 TTAAATCG
6362718 TTAAATCG
1 TTAAATCG
* *
6362726 TTAAACCA
1 TTAAATCG
6362734 TTAAATC
1 TTAAATC
6362741 ATTACATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (8 bp):
TTAAATCG
Found at i:6362713 original size:19 final size:19
Alignment explanation
Indices: 6362651--6362716 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
6362641 AAACCATCAC
*
6362651 TATTAAATTATTATTAAAT
1 TATTAAATCATTATTAAAT
** *
6362670 CCTTAAATAATTATT-AAT
1 TATTAAATCATTATTAAAT
6362688 TCATTAAATCATTATTAAAT
1 T-ATTAAATCATTATTAAAT
*
6362708 TGTTAAATC
1 TATTAAATC
6362717 GTTAAATCGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 3 0.08
19 31 0.82
20 4 0.11
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTAAATCATTATTAAAT
Found at i:6367252 original size:2 final size:2
Alignment explanation
Indices: 6367247--6367296 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
6367237 ATTGTATGTG
6367247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6367289 AT AT AT AT
1 AT AT AT AT
6367297 GATTTGTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6370047 original size:3 final size:3
Alignment explanation
Indices: 6370039--6370095 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
6370029 ATTTTAATAG
6370039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6370087 AAT AAT AAT
1 AAT AAT AAT
6370096 CTTTGAGCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6375090 original size:14 final size:15
Alignment explanation
Indices: 6375071--6375106 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
6375061 AAGTTTATTT
6375071 TGTTTTTTATTTT-A
1 TGTTTTTTATTTTCA
6375085 TGTTTTTTATTTTCA
1 TGTTTTTTATTTTCA
6375100 T-TTTTTT
1 TGTTTTTT
6375107 CTAGATAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 19 0.90
15 2 0.10
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (15 bp):
TGTTTTTTATTTTCA
Found at i:6381514 original size:55 final size:51
Alignment explanation
Indices: 6381448--6381668 Score: 165
Period size: 55 Copynumber: 4.1 Consensus size: 51
6381438 TCCTTGATAG
**
6381448 GATGTTTTCAAATGAACTTTTAAAAGAAGTTAAGCCTAATTTTTAGGGGTTTCTT
1 GATGTTTTCAAATG-A-TTTT--AAGAAACTAAGCCTAATTTTTAGGGGTTTCTT
* * * * *
6381503 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTCTCAGAGGTTTCTT
1 GATGTTTTCAAATGA-TTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTT
* ** * *
6381555 GATGATGATTTCCAATGAATTTTCAAAAAGAAGTTCAA-CCTAATTTTTAAGGGTTTTTT
1 GATG-T--TTTCAAATG-ATTTT----AAGAAACT-AAGCCTAATTTTTAGGGGTTTCTT
* * * *
6381614 AATGTTTTTAAATGATTTTTAGAAACTAAGCCTAATTTTTAGGGGTTTATT
1 GATGTTTTCAAATGATTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTT
6381665 GATG
1 GATG
6381669 ATAACTGAAA
Statistics
Matches: 129, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
50 2 0.02
51 27 0.21
52 29 0.22
53 1 0.01
54 5 0.04
55 31 0.24
56 8 0.06
58 1 0.01
59 23 0.18
60 2 0.02
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.42
Consensus pattern (51 bp):
GATGTTTTCAAATGATTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTT
Found at i:6381609 original size:111 final size:109
Alignment explanation
Indices: 6381412--6381670 Score: 306
Period size: 110 Copynumber: 2.3 Consensus size: 109
6381402 GATGTTTTAA
* * * * * *
6381412 AGAAACCAAGTCTGGTTTTCAGAGGCTCCTTGATAGGATGTTTTCAAATGAACTTTTAAAAGAAG
1 AGAAACTAAGCCTGATTTTCAGAGGTTTCTTGAT--GATGATTTCAAATGAACTTTTAAAAGAAG
* *
6381477 TTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTT
64 TTAAGCCTAATTTTTAAGGGTTTCTTAATGTTTTCAAATGA-TTTTT
* *
6381524 AGAAACTAAGCCTGATTCTCAGAGGTTTCTTGATGATGATTTCCAATGAA-TTTTCAAAAAGAAG
1 AGAAACTAAGCCTGATTTTCAGAGGTTTCTTGATGATGATTTCAAATGAACTTTT--AAAAGAAG
* *
6381588 TTCAA-CCTAATTTTTAAGGGTTTTTTAATGTTTTTAAATGATTTTT
64 TT-AAGCCTAATTTTTAAGGGTTTCTTAATGTTTTCAAATGATTTTT
* * * *
6381634 AGAAACTAAGCCTAATTTTTAGGGGTTTATTGATGAT
1 AGAAACTAAGCCTGATTTTCAGAGGTTTCTTGATGAT
6381671 AACTGAAAAT
Statistics
Matches: 127, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
109 4 0.03
110 51 0.40
111 42 0.33
112 30 0.24
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (109 bp):
AGAAACTAAGCCTGATTTTCAGAGGTTTCTTGATGATGATTTCAAATGAACTTTTAAAAGAAGTT
AAGCCTAATTTTTAAGGGTTTCTTAATGTTTTCAAATGATTTTT
Found at i:6381966 original size:39 final size:39
Alignment explanation
Indices: 6381877--6382470 Score: 912
Period size: 39 Copynumber: 15.4 Consensus size: 39
6381867 AGGGGTCAAC
* *
6381877 ATCTCGCTTGAGGTAGTTTCACTCAAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6381915 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6381954 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6381992 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
6382030 ATCTCTCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
6382069 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6382107 ATCTCGCTTGAGATAGTTTCACTCGAAACGGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6382146 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
6382185 TTCTCACTTGAGATAGTTTCAATCGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
6382224 ATCTCGCTTGAGATAGTTTCACTTGAAACAAAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
6382262 ATCTCACTTGAGATAGTTTCACTCGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
6382301 ATCTCGCTTGAGGTAGTTTCACTTGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
6382340 ATCTCCCTTGAGATAGTTTCACTTGAAACAAAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
*
6382380 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6382419 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
6382457 ATCTCACTTGAGAT
1 ATCTCGCTTGAGAT
6382471 TATTTTTCTT
Statistics
Matches: 512, Mismatches: 39, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
38 193 0.38
39 283 0.55
40 36 0.07
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:6382004 original size:77 final size:78
Alignment explanation
Indices: 6381877--6382470 Score: 882
Period size: 77 Copynumber: 7.7 Consensus size: 78
6381867 AGGGGTCAAC
* *
6381877 ATCTCGCTTGAGGTAGTTTCACTC-AAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCACTCA
1 ATCTCGCTTGAGATAGTTTCACTCGAAAA-AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
6381940 AAACAGAAGATTTT
65 AAACAGAAGATTTT
6381954 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGA-TTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
6382018 AATAGAAGA-TTT
66 AACAGAAGATTTT
*
6382030 ATCTCTCTTGAGATAGTTTCACTCGAAACAA-AAGATTTTATCTCGCTTGAGATAGTTTCACTCG
1 ATCTCGCTTGAGATAGTTTCACTCGAAA-AAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCG
6382094 AAACAGAAGA-TTT
65 AAACAGAAGATTTT
** *
6382107 ATCTCGCTTGAGATAGTTTCACTCGAAACGGAAGATTTTATCTCGCTTGAGATAGTTTCACTCAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
6382172 AACAGAAGATTTT
66 AACAGAAGATTTT
* * * * * *
6382185 TTCTCACTTGAGATAGTTTCAATCGAAACATAAGATTTTATCTCGCTTGAGATAGTTTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
6382250 AACAAAAGA-TTT
66 AACAGAAGATTTT
* * * *
6382262 ATCTCACTTGAGATAGTTTCACTCGAAATAGAAGATTTTATCTCGCTTGAGGTAGTTTCACTTGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
6382327 AACAGAAGATTTT
66 AACAGAAGATTTT
* * *
6382340 ATCTCCCTTGAGATAGTTTCACTTGAAACAA-AAGATTTTTATCTCACTTGAGATAGTTTCACTC
1 ATCTCGCTTGAGATAGTTTCACTCGAAA-AAGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTC
6382404 GAAACAGAAGATTTT
64 GAAACAGAAGATTTT
* *
6382419 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGA-TTTATCTCACTTGAGAT
1 ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGAT
6382471 TATTTTTCTT
Statistics
Matches: 476, Mismatches: 32, Indels: 18
0.90 0.06 0.03
Matches are distributed among these distances:
76 34 0.07
77 264 0.55
78 107 0.22
79 71 0.15
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (78 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
AACAGAAGATTTT
Found at i:6383202 original size:13 final size:13
Alignment explanation
Indices: 6383184--6383208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6383174 TTATTTTATG
6383184 TTGTTTTTTGTTT
1 TTGTTTTTTGTTT
6383197 TTGTTTTTTGTT
1 TTGTTTTTTGTT
6383209 ATTTATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTGTTTTTTGTTT
Found at i:6384760 original size:28 final size:29
Alignment explanation
Indices: 6384687--6384761 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
6384677 ATATAATAAA
* *
6384687 ATATTATATATATATATAATTGAGTATATT
1 ATATTA-ATAAATATATTATTGAGTATATT
*
6384717 AT-TGTAAT-AATAATATTATT-ATTATATT
1 ATAT-TAATAAAT-ATATTATTGAGTATATT
6384745 ATATTAATAAATATATT
1 ATATTAATAAATATATT
6384762 TTAAATATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
28 20 0.53
29 14 0.37
30 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
ATATTAATAAATATATTATTGAGTATATT
Found at i:6389487 original size:24 final size:24
Alignment explanation
Indices: 6389455--6389526 Score: 72
Period size: 30 Copynumber: 2.8 Consensus size: 24
6389445 CCTTAAACTA
*
6389455 ATTTTATGTTTTTAGTATTTTTAT
1 ATTTAATGTTTTTAGTATTTTTAT
6389479 ATTTAATGTTTTGAGTATTAGTATTTTTAT
1 ATTTAATG--TT---T-TTAGTATTTTTAT
*
6389509 ATTTAATGTTTTGAGTAT
1 ATTTAATGTTTTTAGTAT
6389527 CTTATTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
24 13 0.32
25 1 0.03
26 2 0.05
28 2 0.05
29 1 0.03
30 21 0.52
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (24 bp):
ATTTAATGTTTTTAGTATTTTTAT
Found at i:6389490 original size:15 final size:15
Alignment explanation
Indices: 6389472--6389520 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
6389462 GTTTTTAGTA
6389472 TTTTTATATTTAATG
1 TTTTTATATTTAATG
* * *
6389487 TTTTGAGTA-TTAGTA
1 TTTTTA-TATTTAATG
6389502 TTTTTATATTTAATG
1 TTTTTATATTTAATG
6389517 TTTT
1 TTTT
6389521 GAGTATCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.65
Consensus pattern (15 bp):
TTTTTATATTTAATG
Found at i:6389500 original size:30 final size:30
Alignment explanation
Indices: 6389466--6389526 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
6389456 TTTTATGTTT
6389466 TTAGTATTTTTATATTTAATGTTTTGAGTA
1 TTAGTATTTTTATATTTAATGTTTTGAGTA
6389496 TTAGTATTTTTATATTTAATGTTTTGAGTA
1 TTAGTATTTTTATATTTAATGTTTTGAGTA
6389526 T
1 T
6389527 CTTATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (30 bp):
TTAGTATTTTTATATTTAATGTTTTGAGTA
Found at i:6391563 original size:48 final size:48
Alignment explanation
Indices: 6391511--6391611 Score: 184
Period size: 48 Copynumber: 2.1 Consensus size: 48
6391501 AAAATACCTT
* *
6391511 AGTTCACCATGATCCTTCATCTTGAAATTTATGTTTAAAATTCCTTTG
1 AGTTCACCATGATCATTCATCTTGAAATTTATGTTCAAAATTCCTTTG
6391559 AGTTCACCATGATCATTCATCTTGAAATTTATGTTCAAAATTCCTTTG
1 AGTTCACCATGATCATTCATCTTGAAATTTATGTTCAAAATTCCTTTG
6391607 AGTTC
1 AGTTC
6391612 CTCAATTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (48 bp):
AGTTCACCATGATCATTCATCTTGAAATTTATGTTCAAAATTCCTTTG
Found at i:6396136 original size:22 final size:21
Alignment explanation
Indices: 6396115--6396155 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
6396105 AGTGGCTTCA
6396115 ACAAGATGATTGAGAGCTTT-
1 ACAAGATGATTGAGAGCTTTC
*
6396135 -CAATATGATTGAGAGCTTTC
1 ACAAGATGATTGAGAGCTTTC
6396155 A
1 A
6396156 TTGTCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (21 bp):
ACAAGATGATTGAGAGCTTTC
Found at i:6399336 original size:36 final size:36
Alignment explanation
Indices: 6399265--6399337 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
6399255 GTTGGAAAAT
* *
6399265 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
*
6399301 ATTTATATATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTA-AAAATTGAAAATCATAAA
6399337 A
1 A
6399338 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 23 0.70
37 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:6401464 original size:2 final size:2
Alignment explanation
Indices: 6401457--6401496 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6401447 ATTTTAAATA
6401457 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6401497 TTTTTAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6404001 original size:2 final size:2
Alignment explanation
Indices: 6403996--6404025 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6403986 TATATAGACA
6403996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6404026 TAAAATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6404164 original size:13 final size:13
Alignment explanation
Indices: 6404146--6404174 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6404136 TTTATTCTCA
6404146 TTCACTCATTTTC
1 TTCACTCATTTTC
6404159 TTCACTCATTTTC
1 TTCACTCATTTTC
6404172 TTC
1 TTC
6404175 TCTTCTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (13 bp):
TTCACTCATTTTC
Found at i:6410641 original size:35 final size:35
Alignment explanation
Indices: 6410592--6410714 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 35
6410582 GTGAATAAGA
*
6410592 AGAACAAAAAGAAGCATCGGCACTTTCGATTCAAG
1 AGAACAAAAGGAAGCATCGGCACTTTCGATTCAAG
* ** *
6410627 GGAACAAAAGGAAGCATCAACAATTTCGATTCAAG
1 AGAACAAAAGGAAGCATCGGCACTTTCGATTCAAG
* * *
6410662 AAGAACGAAAGCAAGCATCGGCACTTTCGATTTAAG
1 -AGAACAAAAGGAAGCATCGGCACTTTCGATTCAAG
* * *
6410698 TGAACGAGAGGAAGCAT
1 AGAACAAAAGGAAGCAT
6410715 AAGCATTTTC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
35 44 0.61
36 28 0.39
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (35 bp):
AGAACAAAAGGAAGCATCGGCACTTTCGATTCAAG
Found at i:6419625 original size:36 final size:36
Alignment explanation
Indices: 6419572--6419644 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
6419562 AATGCATTAA
* *
6419572 AAATTAAGCCTTTCATATATTCCTAGAAAACAATAG
1 AAATTAAGCCTTCCATATATTCATAGAAAACAATAG
*
6419608 AAATTAAGCGTTCCATATATTCATAGAAAACAATAG
1 AAATTAAGCCTTCCATATATTCATAGAAAACAATAG
6419644 A
1 A
6419645 TCATAAGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.29
Consensus pattern (36 bp):
AAATTAAGCCTTCCATATATTCATAGAAAACAATAG
Found at i:6419684 original size:2 final size:2
Alignment explanation
Indices: 6419677--6419709 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6419667 AAGTTTCTTA
6419677 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 A
6419710 AAAAGAATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6422830 original size:21 final size:22
Alignment explanation
Indices: 6422806--6422846 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6422796 GCGATTTTAG
*
6422806 GGGAGGAGGAGGA-GGAGAGGT
1 GGGACGAGGAGGAGGGAGAGGT
*
6422827 GGGACGAGGCGGAGGGAGAG
1 GGGACGAGGAGGAGGGAGAG
6422847 ACGGTGGCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.66, T:0.02
Consensus pattern (22 bp):
GGGACGAGGAGGAGGGAGAGGT
Found at i:6424339 original size:21 final size:22
Alignment explanation
Indices: 6424315--6424367 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
6424305 CCCCTAAATT
*
6424315 ATAAACTTTAAATCATAA-CTC
1 ATAAACTCTAAATCATAAGCTC
6424336 ATAAACTCTAAATCATAAGCTC
1 ATAAACTCTAAATCATAAGCTC
6424358 -TAAACTCTAA
1 ATAAACTCTAA
6424368 TTTAAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (22 bp):
ATAAACTCTAAATCATAAGCTC
Found at i:6424920 original size:30 final size:30
Alignment explanation
Indices: 6424885--6424943 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
6424875 TATATTATTT
*
6424885 CTTATT-CAACTTTATTCTTTTTTTATTTTA
1 CTTATTGCAACTTTAAT-TTTTTTTATTTTA
* *
6424915 CTTATTGTAATTTTAATTTTTTTTATTTT
1 CTTATTGCAACTTTAATTTTTTTTATTTT
6424944 GCTCGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69
Consensus pattern (30 bp):
CTTATTGCAACTTTAATTTTTTTTATTTTA
Found at i:6426988 original size:22 final size:22
Alignment explanation
Indices: 6426937--6426988 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
6426927 ACTAAGGATT
*
6426937 GATCTCTCATAAAAAAATGATC
1 GATCTCTTATAAAAAAATGATC
6426959 GATCTCTTATAAAAAAATGATC
1 GATCTCTTATAAAAAAATGATC
6426981 GATCTCTT
1 GATCTCTT
6426989 CTTTTGAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
GATCTCTTATAAAAAAATGATC
Found at i:6428486 original size:29 final size:30
Alignment explanation
Indices: 6428454--6428510 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
6428444 AAACATTCAC
*
6428454 AACAATCCTCTCAACCCGAAAA-ATCACAT
1 AACAAACCTCTCAACCCGAAAATATCACAT
* *
6428483 AACAAACCTTTCAATCCGAAAATATCAC
1 AACAAACCTCTCAACCCGAAAATATCAC
6428511 CCGACAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.46, C:0.32, G:0.04, T:0.19
Consensus pattern (30 bp):
AACAAACCTCTCAACCCGAAAATATCACAT
Found at i:6434459 original size:13 final size:13
Alignment explanation
Indices: 6434441--6434524 Score: 72
Period size: 13 Copynumber: 6.8 Consensus size: 13
6434431 ACTGTAAAAA
*
6434441 AAATAAAATAATT
1 AAATAAAATAACT
6434454 AAATAAAAT-ACT
1 AAATAAAATAACT
6434466 AAA-AAAATTAACT
1 AAATAAAA-TAACT
* *
6434479 -AATTAAATAATT
1 AAATAAAATAACT
6434491 AAATAAAAT-ACT
1 AAATAAAATAACT
*
6434503 -AATAAAAT-ATT
1 AAATAAAATAACT
*
6434514 AAATAGAATAA
1 AAATAAAATAA
6434525 AATATACCTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 14 0.24
12 21 0.36
13 23 0.40
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.29
Consensus pattern (13 bp):
AAATAAAATAACT
Found at i:6434497 original size:29 final size:29
Alignment explanation
Indices: 6434437--6434524 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
6434427 TATAACTGTA
*
6434437 AAAAAAATAAAATAATTAAATAAAATACT
1 AAAAAAATAAAATAATTAAATAAAATAAT
* * *
6434466 AAAAAAATTAACTAATTAAAT-AATTAAAT
1 AAAAAAATAAAATAATTAAATAAAAT-AAT
*
6434495 AAAATACTAATAAAAT-ATTAAATAGAATAA
1 AAAA-A--AATAAAATAATTAAATAAAATAA
6434525 AATATACCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.07
29 25 0.54
30 1 0.02
31 9 0.20
32 8 0.17
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAAAAATAAAATAATTAAATAAAATAAT
Found at i:6437706 original size:36 final size:36
Alignment explanation
Indices: 6437655--6437733 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
6437645 CGTATTCATT
6437655 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
1 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
*
6437691 GAAACATTATTGGCATTTAATAGATTATATTTTGGA
1 GAAACATTATCGGCATTTAATAGATTATATTTTGGA
6437727 GAAACAT
1 GAAACAT
6437734 CGCAATGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (36 bp):
GAAACATTATCGGCATTTAATAGATTATATTTTGGA
Found at i:6441222 original size:22 final size:22
Alignment explanation
Indices: 6441196--6441239 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6441186 TCTCTCTCTA
* *
6441196 TTTCTCTGGTTTTTTTAGATTT
1 TTTCTCTAGTTTTATTAGATTT
*
6441218 TTTCTCTAGTTTTATTATATTT
1 TTTCTCTAGTTTTATTAGATTT
6441240 CAAAATCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTTCTCTAGTTTTATTAGATTT
Found at i:6444670 original size:21 final size:21
Alignment explanation
Indices: 6444623--6444680 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
6444613 TTTTCTGGCT
*
6444623 CAAAGGATCGATCCGTTAGTA
1 CAAAGGATCGATCCCTTAGTA
*
6444644 -AAAGGATCGATCCCTTTG-A
1 CAAAGGATCGATCCCTTAGTA
6444663 CCAAAGGATCGATCCCTT
1 -CAAAGGATCGATCCCTT
6444681 GGATAACAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 16 0.48
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
CAAAGGATCGATCCCTTAGTA
Found at i:6444723 original size:20 final size:21
Alignment explanation
Indices: 6444698--6444745 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
6444688 AGTGAGTTTG
*
6444698 GGATCGACCCCTTGAC-AAAA
1 GGATCGACCCCTTCACAAAAA
* *
6444718 GGATCGATCCCTTCCCAAAAA
1 GGATCGACCCCTTCACAAAAA
6444739 GGATCGA
1 GGATCGA
6444746 TTTCTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (21 bp):
GGATCGACCCCTTCACAAAAA
Found at i:6447804 original size:16 final size:16
Alignment explanation
Indices: 6447783--6447855 Score: 112
Period size: 16 Copynumber: 4.6 Consensus size: 16
6447773 CCAAAGCCTC
6447783 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
6447799 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
6447815 GGAATCATTCAGCATT
1 TGAATCATTCAGCATT
* *
6447831 TGAATCATTTAGCACT
1 TGAATCATTCAGCATT
6447847 T-AATCATTC
1 TGAATCATTC
6447856 TAAAGTAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
15 7 0.13
16 45 0.87
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:6449090 original size:3 final size:3
Alignment explanation
Indices: 6449082--6449154 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
6449072 CTACAAACGA
6449082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6449130 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
6449155 CAGTCCACGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6454317 original size:13 final size:13
Alignment explanation
Indices: 6454301--6454330 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6454291 GATAATTATG
6454301 TTTAAATTATGCC
1 TTTAAATTATGCC
*
6454314 TTTAAATTATGTC
1 TTTAAATTATGCC
6454327 TTTA
1 TTTA
6454331 GGAAAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTAAATTATGCC
Found at i:6457742 original size:55 final size:55
Alignment explanation
Indices: 6457628--6457814 Score: 202
Period size: 55 Copynumber: 3.4 Consensus size: 55
6457618 CTATACGGAA
* * * * * *
6457628 ATTCATCAACTCATGATGAATTCTGTGG-GTTACACACATATTGTC-TGTACGGTG
1 ATTCATCAACCCATAATGAATTCTGTGGATTTGCACACAAAGTG-CATGTACGGTG
*
6457682 ATTCATCAACTCATAATGAATT-TCGTGGATTTGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACCCATAATGAATTCT-GTGGATTTGCACACAAAGTGCATGTACGGTG
* * * * *
6457737 ATTCATCAACCCATGAA-GAATTCTGTGAATATGTACACAAAGTCCATGTATGGTG
1 ATTCATCAACCCAT-AATGAATTCTGTGGATTTGCACACAAAGTGCATGTACGGTG
*
6457792 ATTCATCAACCCATGATGAATTC
1 ATTCATCAACCCATAATGAATTC
6457815 CGTTGATGAA
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
53 1 0.01
54 27 0.23
55 84 0.73
56 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (55 bp):
ATTCATCAACCCATAATGAATTCTGTGGATTTGCACACAAAGTGCATGTACGGTG
Found at i:6457823 original size:13 final size:13
Alignment explanation
Indices: 6457805--6457830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6457795 CATCAACCCA
6457805 TGATGAATTCCGT
1 TGATGAATTCCGT
6457818 TGATGAATTCCGT
1 TGATGAATTCCGT
6457831 GAATATGCAC
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:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
TGATGAATTCCGT
Found at i:6457863 original size:68 final size:68
Alignment explanation
Indices: 6457754--6457882 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 68
6457744 AACCCATGAA
* * * *
6457754 GAATTCTGTGAATATGTACACAAAGTCCATGTATGGTGATTCATCAACCCATGATGAATTCCGTT
1 GAATTCCGTGAATATGCACACAAAGTCCATATACGGTGATTCATCAACCCATGATGAATTCCGTT
6457819 GAT
66 GAT
* *
6457822 GAATTCCGTGAATATGCACACAAATTGCATATACGGTGATTCATCAACCCATGATGAATTC
1 GAATTCCGTGAATATGCACACAAAGTCCATATACGGTGATTCATCAACCCATGATGAATTC
6457883 TGTGAATATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (68 bp):
GAATTCCGTGAATATGCACACAAAGTCCATATACGGTGATTCATCAACCCATGATGAATTCCGTT
GAT
Found at i:6457906 original size:55 final size:55
Alignment explanation
Indices: 6457818--6457959 Score: 239
Period size: 55 Copynumber: 2.6 Consensus size: 55
6457808 TGAATTCCGT
*
6457818 TGATGAATTCCGTGAATATGCACACAAATTGCATATACGGTGATTCATCAACCCA
1 TGATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCA
* *
6457873 TGATGAATTCTGTGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCA
1 TGATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCA
* *
6457928 TGATGAATTCCGTGAATATGCACGCAAGGTGC
1 TGATGAATTCCGTGAATATGCACACAAAGTGC
6457960 CTGTAGTACA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 81 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (55 bp):
TGATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCA
Found at i:6457916 original size:123 final size:123
Alignment explanation
Indices: 6457697--6457940 Score: 407
Period size: 123 Copynumber: 2.0 Consensus size: 123
6457687 TCAACTCATA
* * * *
6457697 ATGAATTTCGTGGATTTGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGAAGAATTCTG
1 ATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCATGAAGAATTCTG
* *
6457762 TGAATATGTACACAAAGTCCATGTATGGTGATTCATCAACCCATGATGAATTCCGTTG
66 TGAATATGCACACAAAGTCCATGTACGGTGATTCATCAACCCATGATGAATTCCGTTG
* *
6457820 ATGAATTCCGTGAATATGCACACAAATTGCATATACGGTGATTCATCAACCCATGATGAATTCTG
1 ATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCATGAAGAATTCTG
*
6457885 TGAATATGCACACAAAGTGCATGTACGGTGATTCATCAACCCATGATGAATTCCGT
66 TGAATATGCACACAAAGTCCATGTACGGTGATTCATCAACCCATGATGAATTCCGT
6457941 GAATATGCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 112 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (123 bp):
ATGAATTCCGTGAATATGCACACAAAGTGCATATACGGTGATTCATCAACCCATGAAGAATTCTG
TGAATATGCACACAAAGTCCATGTACGGTGATTCATCAACCCATGATGAATTCCGTTG
Found at i:6458408 original size:20 final size:20
Alignment explanation
Indices: 6458383--6458434 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
6458373 CGATGTTGCC
6458383 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
6458403 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
6458423 TGGTATCGATAC
1 TGGTATCGATAC
6458435 TATCATACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:6458491 original size:114 final size:116
Alignment explanation
Indices: 6458285--6458529 Score: 332
Period size: 115 Copynumber: 2.1 Consensus size: 116
6458275 ATTTCTGGCT
* * * * * *
6458285 CCATAGTATCGATACTATTTCCCTGGTACCGATACTTTTATACTATGGTATCGATACCCCCATCC
1 CCATGGTATCGATACCATTACCATGGTACCGATACTATCATACTATGGTATCGATACCCCCATCC
* *
6458350 GATATCGATACCAAAATTAGGTTCGATGTTGCCTGGTATCGATA-CCCTTA
66 GATATCGATACCAAAATTAGATTCGATGTTGCCTGGTATAGATACCCCTTA
* * *
6458400 CCATGGTATCGATACCCTTACCATGGTATCGATACTATCATACTATGGTA-CGATACCCCCTTCC
1 CCATGGTATCGATACCATTACCATGGTACCGATACTATCATACTATGGTATCGATACCCCCATCC
* * *
6458464 GGTATCGATATCAAAATTAGATTCGATGTTGCTTGGTATAGATACCCCTTA
66 GATATCGATACCAAAATTAGATTCGATGTTGCCTGGTATAGATACCCCTTA
* *
6458515 TCATGGTATGGATAC
1 CCATGGTATCGATAC
6458530 TACCTCGTCG
Statistics
Matches: 113, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 52 0.46
115 61 0.54
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (116 bp):
CCATGGTATCGATACCATTACCATGGTACCGATACTATCATACTATGGTATCGATACCCCCATCC
GATATCGATACCAAAATTAGATTCGATGTTGCCTGGTATAGATACCCCTTA
Found at i:6458549 original size:115 final size:114
Alignment explanation
Indices: 6458308--6458529 Score: 320
Period size: 114 Copynumber: 1.9 Consensus size: 114
6458298 ACTATTTCCC
* * * *
6458308 TGGTACCGATACTTTTATACTATGGTATCGATACCCCCATCCGATATCGATACCAAAATTAGGTT
1 TGGTATCGATACTATCATACTATGGTATCGATACCCCCATCCGATATCGATACCAAAATTAGATT
*
6458373 CGATGTTGCCTGGTATCGATACCCTTACCATGGTATCGATACCCTTACCA
66 CGATGTTGCCTGGTATAGATACCCTTACCATGGTATCGATACCCTTA-CA
* * *
6458423 TGGTATCGATACTATCATACTATGGTA-CGATACCCCCTTCCGGTATCGATATCAAAATTAGATT
1 TGGTATCGATACTATCATACTATGGTATCGATACCCCCATCCGATATCGATACCAAAATTAGATT
* * *
6458487 CGATGTTGCTTGGTATAGATACCCCTTATCATGGTATGGATAC
66 CGATGTTGCCTGGTATAGATA-CCCTTACCATGGTATCGATAC
6458530 TACCTCGTCG
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
114 52 0.55
115 43 0.45
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (114 bp):
TGGTATCGATACTATCATACTATGGTATCGATACCCCCATCCGATATCGATACCAAAATTAGATT
CGATGTTGCCTGGTATAGATACCCTTACCATGGTATCGATACCCTTACA
Found at i:6462209 original size:21 final size:21
Alignment explanation
Indices: 6462183--6462233 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
6462173 GAACAAGGGC
*
6462183 TATCGGTTCCCCTCTATGGGG
1 TATCGGTACCCCTCTATGGGG
6462204 TATCGGTACCCCTCTATGGGG
1 TATCGGTACCCCTCTATGGGG
*
6462225 TATCAGTAC
1 TATCGGTAC
6462234 TACCTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.31
Consensus pattern (21 bp):
TATCGGTACCCCTCTATGGGG
Found at i:6462703 original size:21 final size:19
Alignment explanation
Indices: 6462674--6462730 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 19
6462664 ATGTTTAATG
6462674 AAAAAGATATCAATTGTTT
1 AAAAAGATATCAATTGTTT
*
6462693 ACAAAAGGATACCAATTG-TT
1 A-AAAA-GATATCAATTGTTT
6462713 AAAAAGATATCAATTGTT
1 AAAAAGATATCAATTGTT
6462731 GGAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 10 0.30
19 6 0.18
20 7 0.21
21 10 0.30
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTT
Found at i:6463405 original size:23 final size:22
Alignment explanation
Indices: 6463354--6463412 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
6463344 ACATATATGA
*
6463354 GATTAAAACAATAATGCATAAT
1 GATTAAAACAAAAATGCATAAT
*
6463376 TATTTAAAACAAAAACT-CATACAT
1 GA-TTAAAACAAAAA-TGCATA-AT
6463400 GATTAAAATCAAA
1 GATTAAAA-CAAA
6463413 TGTGCAACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 21 0.70
24 8 0.27
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (22 bp):
GATTAAAACAAAAATGCATAAT
Found at i:6465222 original size:24 final size:20
Alignment explanation
Indices: 6465195--6465248 Score: 54
Period size: 24 Copynumber: 2.5 Consensus size: 20
6465185 CTGCTTAAGG
*
6465195 GGTATCGGTACTACTTTGCACTA
1 GGTATCGGTAC--CCTTGC-CTA
*
6465218 TGGTATCGATACCCTTGCCTA
1 -GGTATCGGTACCCTTGCCTA
6465239 GGTATCGGTA
1 GGTATCGGTA
6465249 TCAAATTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.33
21 3 0.11
22 5 0.19
24 10 0.37
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
GGTATCGGTACCCTTGCCTA
Found at i:6469226 original size:29 final size:29
Alignment explanation
Indices: 6469184--6469279 Score: 147
Period size: 29 Copynumber: 3.3 Consensus size: 29
6469174 TAAATGGAAT
** *
6469184 CATTCAGCACTGAATGTTGAACCGTTCAG
1 CATTCAGCGTTGAATGTTGAACCATTCAG
* *
6469213 CATTCAGTGTTGAATGTTGAATCATTCAG
1 CATTCAGCGTTGAATGTTGAACCATTCAG
6469242 CATTCAGCGTTGAATGTTGAACCATTCAG
1 CATTCAGCGTTGAATGTTGAACCATTCAG
6469271 CATTCAGCG
1 CATTCAGCG
6469280 CGTTTGTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (29 bp):
CATTCAGCGTTGAATGTTGAACCATTCAG
Found at i:6469681 original size:32 final size:32
Alignment explanation
Indices: 6469644--6469709 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
6469634 AATAAAACTT
* * *
6469644 AAATAAAATGTTAGAT-ATATTTTTTTAACAAA
1 AAATAAAAT-TTAAATAACATTTTGTTAACAAA
*
6469676 AAATAAAGTTTAAATAACATTTTGTTAACAAA
1 AAATAAAATTTAAATAACATTTTGTTAACAAA
6469708 AA
1 AA
6469710 TAATAGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (32 bp):
AAATAAAATTTAAATAACATTTTGTTAACAAA
Found at i:6470975 original size:18 final size:16
Alignment explanation
Indices: 6470945--6470979 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
6470935 TGTGTGGGAA
6470945 TATGTATAATATATAG
1 TATGTATAATATATAG
6470961 TATGTATATAGTATATAG
1 TATGTATA-A-TATATAG
6470979 T
1 T
6470980 TGGCATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (16 bp):
TATGTATAATATATAG
Found at i:6471124 original size:15 final size:15
Alignment explanation
Indices: 6471087--6471125 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6471077 TAATAGTTGC
*
6471087 ATTGCATATCATATA
1 ATTGCATATCAAATA
* *
6471102 GTTTCATATCAAATA
1 ATTGCATATCAAATA
6471117 ATTGCATAT
1 ATTGCATAT
6471126 TATATTAGAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTGCATATCAAATA
Found at i:6471880 original size:2 final size:2
Alignment explanation
Indices: 6471873--6472735 Score: 133
Period size: 2 Copynumber: 426.5 Consensus size: 2
6471863 ATATGTAAAC
* *
6471873 AT AT AT AT AT AT AGT -T CAT AT GT AA ACT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT -AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
6471915 AT CA- ACT AT AGT AT AT A- AT AT AT AA AT AT AA ACT AT AGT TT AT
1 AT -AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT
* *
6471958 AT AT AT AGT AT AT ACT AT AT AA AA ACT AT AT AT AT A- AT -T CAT
1 AT AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT -AT
* * * * *
6472000 AT GT AA ACT AT AT AGT TT AT AT AT AT AGT -T CAT AT GT AA ACT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT -AT AT AT AT A-T AT
* * *
6472044 AT AT AT -T AT AT A- AT AC AT AA AT TT CA- ACT AT AGT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT A-T AT AT A-T
* * * * *
6472085 TT AT AT AT AA AGT AT A- AT TT AT AT AGT TT TT AT AT AT AT A- AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
6472127 -T TT AT AT AT A- AT -T CAT AT AT AA ACT AT AT AT AGT TT AT GT
1 AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT AT AT A-T AT AT AT
* * *
6472167 AGT TT AT AT AT AT AT AT AT AG AT AT A- AT TT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
6472209 AT AT AT AG AT AT A- AT TT TT AT AT AT TT TT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
6472251 AT AGT AT AT AT AGT TT AT AT AT GA- AT AT AA ACT AC AT AT A- AT
1 AT A-T AT AT AT A-T AT AT AT AT -AT AT AT AT A-T AT AT AT AT AT
* * * * * *
6472293 -T AC AT AA AT -T A- ACC CT AA ACC AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T
* * * * **
6472333 TT AT AT TT A- AT AA ACT AT AT AT ACT AT AT AT AT AA ACT GC AT
1 AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT A-T AT AT
* * * *
6472375 AT AT AA ACT AT AT AGT TT AT AT AC AT A- AT AT AT AT ACT TT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
6472417 AT AT AA ACT AT A- AT A- AGT -T AT AT A- AT TT AT AC AT A- AT AT
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
6472456 AT -T A- AT AT AT AGT TT AT AT AT AT AT -T A- AT GA- ACT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT -AT A-T AT AT
* * *
6472494 A- AT AT AT AGT TT AT AT GA- ACT AT AT A- AT TT AT AT AT AGT TT
1 AT AT AT AT A-T AT AT AT -AT A-T AT AT AT AT AT AT AT AT A-T AT
* *
6472535 AT AT CT AT -T A- AT GA- ACT AT AT A- AT AT AT A- AT TT AT AT AT
1 AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
6472574 ACT A- AT GA- ACT AT AGT TT AT -T A- AT AT AA ACT AT AT AT AT AT
1 A-T AT AT -AT A-T AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
6472615 AT AT AT AT AT AT AT AT A- AT -T CAT AT AT ACT CT AC AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT A-T AT
* * * * *
6472656 AT AT AC A- AT AT AT A- AA ACT AT AA AT AT AA ACT AT AT AGT TT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT
6472697 AT AT AT AT -T AT AT -T A- AT AT AT ACT -T AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
6472735 A
1 A
6472736 GTTGTTTTAA
Statistics
Matches: 614, Mismatches: 129, Indels: 236
0.63 0.13 0.24
Matches are distributed among these distances:
1 54 0.09
2 493 0.80
3 67 0.11
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6471885 original size:27 final size:28
Alignment explanation
Indices: 6471844--6472055 Score: 135
Period size: 28 Copynumber: 7.5 Consensus size: 28
6471834 CGTTTTTTAG
6471844 TATATACTATATATAGTTCATATGTAAAC
1 TATATA-TATATATAGTTCATATGTAAAC
6471873 -ATATATATATATAGTTCATATGTAAAC
1 TATATATATATATAGTTCATATGTAAAC
* * *
6471900 TATATATATATATA-TATCA-A-CTATAG
1 TATATATATATATAGT-TCATATGTAAAC
*
6471926 TATATA-ATATATA----A-ATATAAAC
1 TATATATATATATAGTTCATATGTAAAC
*
6471948 TATAGTTTATATATATAGTAT-ATACTATATAA-
1 TATA---TATATATATAGT-TCATA-TGTA-AAC
* *
6471980 -AAACTATATATATAATTCATATGTAAAC
1 TATA-TATATATATAGTTCATATGTAAAC
6472008 TATATAGTTTATATATATAGTTCATATGTAAAC
1 --TATA---TATATATATAGTTCATATGTAAAC
6472041 TATATATATTATATA
1 TATATATA-TATATA
6472056 ATACATAAAT
Statistics
Matches: 148, Mismatches: 13, Indels: 44
0.72 0.06 0.21
Matches are distributed among these distances:
21 2 0.01
22 7 0.05
25 9 0.06
26 16 0.11
27 26 0.18
28 29 0.20
29 20 0.14
30 1 0.01
31 9 0.06
32 4 0.03
33 25 0.17
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (28 bp):
TATATATATATATAGTTCATATGTAAAC
Found at i:6472021 original size:33 final size:33
Alignment explanation
Indices: 6471984--6472055 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
6471974 ATATAAAAAC
6471984 TATATATATAATTCATATGTAAACTATATAGT-T
1 TATATATATAATTCATATGTAAACTATATA-TAT
*
6472017 TATATATATAGTTCATATGTAAACTATATATAT
1 TATATATATAATTCATATGTAAACTATATATAT
6472050 TATATA
1 TATATA
6472056 ATACATAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
TATATATATAATTCATATGTAAACTATATATAT
Found at i:6472124 original size:15 final size:14
Alignment explanation
Indices: 6472112--6472272 Score: 65
Period size: 13 Copynumber: 11.7 Consensus size: 14
6472102 TTTATATAGT
6472112 TTTTATATATATAA
1 TTTTATATATATAA
6472126 -TTT-TATATATAA
1 TTTTATATATATAA
*
6472138 -TTCATATATA-AA
1 TTTTATATATATAA
* * *
6472150 CTATATATAGTTTATGTA
1 -T-TTTATA-TATAT-AA
*
6472168 GTTTATATATAT-A
1 TTTTATATATATAA
* *
6472181 -TATATAGATATAA
1 TTTTATATATATAA
6472194 -TTTATATATATATA
1 TTTTATATATATA-A
* *
6472208 TATATATAGATATAA
1 T-TTTATATATATAA
6472223 TTTT-TATATAT--
1 TTTTATATATATAA
6472234 TTTTATATATA-AA
1 TTTTATATATATAA
* *
6472247 CTATATAGTATATATA
1 TTTTATA-TATATA-A
*
6472263 GTTTATATAT
1 TTTTATATAT
6472273 GAATATAAAC
Statistics
Matches: 110, Mismatches: 20, Indels: 33
0.67 0.12 0.20
Matches are distributed among these distances:
11 4 0.04
12 28 0.25
13 32 0.29
14 7 0.06
15 14 0.13
16 24 0.22
18 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (14 bp):
TTTTATATATATAA
Found at i:6472135 original size:54 final size:55
Alignment explanation
Indices: 6472072--6472477 Score: 168
Period size: 56 Copynumber: 7.4 Consensus size: 55
6472062 AAATTTCAAC
* * *
6472072 TATAGTATATAGTTTATATATAAA-GTATA-A-TTTATATAGTTTTTATATATATAA
1 TATA-TATATAATTTATATATAAACATATATAGTTTATATAGTTTATATATATAT-A
* * *
6472126 TTTTATATATAATTCATATATAAACTATATATAGTTTATGTAGTTTATATATATATA
1 -TATATATATAATTTATATATAAAC-ATATATAGTTTATATAGTTTATATATATATA
* * * ** * *
6472183 TATAGATATAATTTATATATATATATATATA-TAGATATAATTT-T-TATATATT
1 TATATATATAATTTATATATAAACATATATAGTTTATATAGTTTATATATATATA
* ** ** * *
6472235 TTTATATATAA---ACTATAT-AGTATATATAGTTTATATA-TGAATATAAACTACA
1 TATATATATAATTTA-TATATAAACATATATAGTTTATATAGTTTATATATA-TATA
* * ** *
6472287 TATAATTACATAAATTA-ACCCTAAACCATATATA-TATATATATAGTTTATATTTA-ATA
1 TAT-A-TATATAATTTATA-TATAAA-CATATATAGT-T-TATATAGTTTATATATATATA
* * * *** *
6472345 AACTATATATACTATATATATAAACTGCATATATAAACTATATAG-TT-TATATACATA
1 TA-TATATATAATTTATATATAAA---CATATATAGTTTATATAGTTTATATATATATA
* * *
6472402 -ATATATATACTTTATATATAAAC-TATAATAAG-TTATATAATTTATACATA-ATA
1 TATATATATAATTTATATATAAACATAT-AT-AGTTTATATAGTTTATATATATATA
*
6472455 TATTAATATATAGTTTATATATA
1 TA-T-ATATATAATTTATATATA
6472478 TATTAATGAA
Statistics
Matches: 263, Mismatches: 55, Indels: 65
0.69 0.14 0.17
Matches are distributed among these distances:
49 10 0.04
50 12 0.05
51 6 0.02
52 29 0.11
53 8 0.03
54 37 0.14
55 32 0.12
56 47 0.18
57 21 0.08
58 40 0.15
59 15 0.06
60 6 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (55 bp):
TATATATATAATTTATATATAAACATATATAGTTTATATAGTTTATATATATATA
Found at i:6472203 original size:29 final size:29
Alignment explanation
Indices: 6472072--6472244 Score: 121
Period size: 29 Copynumber: 6.1 Consensus size: 29
6472062 AAATTTCAAC
*
6472072 TATAGTATATAGTTTATATATA-A-AGTATA
1 TATAG-ATATAATTTATATATATATA-TATA
** * *
6472101 -ATTTATATAGTTTTTATATATATA-AT-
1 TATAGATATAATTTATATATATATATATA
* * *
6472127 TTTATATATAATTCATATATA-A-ACTATA
1 TATAGATATAATTTATATATATATA-TATA
* * *
6472155 TATAG-T-TTATGTAGTTTATATATATATA
1 TATAGATATAATTTA-TATATATATATATA
6472183 TATAGATATAATTTATATATATATATATA
1 TATAGATATAATTTATATATATATATATA
* * *
6472212 TATAGATATAATTTTTATATATTTTTATA
1 TATAGATATAATTTATATATATATATATA
6472241 TATA
1 TATA
6472245 AACTATATAG
Statistics
Matches: 113, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
25 1 0.01
26 5 0.04
27 40 0.35
28 16 0.14
29 46 0.41
30 5 0.04
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (29 bp):
TATAGATATAATTTATATATATATATATA
Found at i:6472209 original size:27 final size:27
Alignment explanation
Indices: 6472072--6472242 Score: 105
Period size: 27 Copynumber: 6.1 Consensus size: 27
6472062 AAATTTCAAC
* *
6472072 TATAGTATATAGTTTATATATAAAGTATA
1 TATAG-ATATAATTTATATATATA-TATA
** * *
6472101 -ATTTATATAGTTTTTATATATATA-A
1 TATAGATATAATTTATATATATATATA
* * * *
6472126 TTTTATATATAATTCATATATAAACTATA
1 -TATAGATATAATTTATATATATA-TATA
* * *
6472155 TATAGTTTATGTAGTT-TATATATATATA
1 TATAG-ATAT-AATTTATATATATATATA
6472183 TATAGATATAATTTATATATATATATATA
1 TATAGATATAA-TT-TATATATATATATA
* * *
6472212 TATAGATATAATTTTTATATATTTTTA
1 TATAGATATAATTTATATATATATATA
6472239 TATA
1 TATA
6472243 TAAACTATAT
Statistics
Matches: 110, Mismatches: 23, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
25 1 0.01
26 3 0.03
27 51 0.46
28 19 0.17
29 34 0.31
30 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (27 bp):
TATAGATATAATTTATATATATATATA
Found at i:6472509 original size:33 final size:33
Alignment explanation
Indices: 6472453--6472587 Score: 147
Period size: 33 Copynumber: 4.1 Consensus size: 33
6472443 TTATACATAA
*
6472453 TATATTAATATATAGTTTATATATATATTAATGAAC
1 TATA-TAATATATAG-TT-TATATATACTAATGAAC
6472489 TATATAATATATAGTTTATATGA-ACTATAT-AA-
1 TATATAATATATAGTTTATAT-ATACTA-ATGAAC
* *
6472521 T-T-T-ATATATAGTTTATATCTATTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
6472551 TATATAATATATAATTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
6472584 TATA
1 TATA
6472588 GTTTATTAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 19
0.77 0.05 0.17
Matches are distributed among these distances:
28 2 0.02
29 20 0.24
30 2 0.02
31 2 0.02
32 2 0.02
33 38 0.45
34 5 0.06
35 10 0.12
36 4 0.05
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:6472517 original size:25 final size:24
Alignment explanation
Indices: 6472471--6472529 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 24
6472461 TATATAGTTT
6472471 ATATATATATTAATGAACTATATA
1 ATATATATATTAATGAACTATATA
6472495 ATATATAGT-TTATATGAACTATATA
1 ATATATA-TATTA-ATGAACTATATA
*
6472520 ATTTATATAT
1 ATATATATAT
6472530 AGTTTATATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (24 bp):
ATATATATATTAATGAACTATATA
Found at i:6472573 original size:64 final size:63
Alignment explanation
Indices: 6472452--6472571 Score: 190
Period size: 62 Copynumber: 1.9 Consensus size: 63
6472442 TTTATACATA
6472452 ATATATTAATATATAGTTTATATATATATTAATGAACTATATAATATATAGTTTATATGAACT
1 ATATATTAATATATAGTTTATATATATATTAATGAACTATATAATATATAGTTTATATGAACT
* * *
6472515 ATATAATTTATATATAG-TT-TATATCTATTAATGAACTATATAATATATAATTTATAT
1 ATAT-ATTAATATATAGTTTATATATATATTAATGAACTATATAATATATAGTTTATAT
6472572 ATACTAATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 36 0.68
63 6 0.11
64 11 0.21
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (63 bp):
ATATATTAATATATAGTTTATATATATATTAATGAACTATATAATATATAGTTTATATGAACT
Found at i:6472734 original size:11 final size:11
Alignment explanation
Indices: 6472391--6472735 Score: 53
Period size: 11 Copynumber: 31.5 Consensus size: 11
6472381 ACTATATAGT
*
6472391 TTATATACATA
1 TTATATATATA
*
6472402 ATATATATACT-
1 TTATATATA-TA
*
6472413 TTATATATAAA
1 TTATATATATA
*
6472424 CTATA-ATA-A
1 TTATATATATA
6472433 GTTATATA-AT-
1 -TTATATATATA
6472443 TTATACATAATATA
1 TTAT--AT-ATATA
6472457 TTA-ATATATA
1 TTATATATATA
6472467 GTTTATATATATA
1 --TTATATATATA
6472480 TTA-ATGA-ACTA
1 TTATAT-ATA-TA
6472491 -TATAATATATA
1 TTAT-ATATATA
6472502 GTT-TATATGA-A
1 -TTATATAT-ATA
*
6472513 CTATATA-AT-
1 TTATATATATA
*
6472522 TTATATATA-G
1 TTATATATATA
*
6472532 TT-TATATCTA
1 TTATATATATA
6472542 TTA-ATGAACTATA
1 TTATAT--A-TATA
*
6472555 TAATATATA-A
1 TTATATATATA
6472565 TTTATATATACTAA
1 -TTATATATA-T-A
* *
6472579 TGAACTATAGTTTA
1 T-TA-TATA-TATA
*
6472593 TTA-ATATAAA
1 TTATATATATA
*
6472603 CTATATATATA
1 TTATATATATA
6472614 -TATATATATA
1 TTATATATATA
6472624 -TATATATA-A
1 TTATATATATA
*
6472633 TT-CATATATA
1 TTATATATATA
* * *
6472643 CTCTACATAGT-
1 TTATATATA-TA
*
6472654 TTATATACA-A
1 TTATATATATA
*
6472664 -TATATA-AAA
1 TTATATATATA
* *
6472673 CTATAAATATA
1 TTATATATATA
* *
6472684 -AACTATATAGTT
1 TTA-TATATA-TA
6472696 TATATATATTATA
1 T-TATATA-TATA
6472709 TTA-ATATATA
1 TTATATATATA
6472719 CTTATATATATA
1 -TTATATATATA
6472731 TTATA
1 TTATA
6472736 GTTGTTTTAA
Statistics
Matches: 245, Mismatches: 35, Indels: 108
0.63 0.09 0.28
Matches are distributed among these distances:
8 1 0.00
9 30 0.12
10 62 0.25
11 88 0.36
12 23 0.09
13 23 0.09
14 12 0.05
15 5 0.02
16 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATATA
Found at i:6474655 original size:39 final size:39
Alignment explanation
Indices: 6474611--6474715 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
6474601 TACTTTTAGA
* *
6474611 AATAATTTAGATGGTTATGGTGAAATAGCTTAAGAAATT
1 AATAATTTAGATGGTTATGGTGAAATAACTTAAAAAATT
* * *
6474650 AATAATTTAGAAT-GTAATGGTAAAATAATTTAAAAAATT
1 AATAATTTAG-ATGGTTATGGTGAAATAACTTAAAAAATT
* *
6474689 AAGAATTTAGAAGGTTA-GAGTGAAATA
1 AATAATTTAGATGGTTATG-GTGAAATA
6474716 CTTTGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
38 2 0.04
39 50 0.93
40 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.18, T:0.33
Consensus pattern (39 bp):
AATAATTTAGATGGTTATGGTGAAATAACTTAAAAAATT
Found at i:6474751 original size:2 final size:2
Alignment explanation
Indices: 6474746--6474791 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
6474736 AAATTTAATG
6474746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6474788 AT AT
1 AT AT
6474792 CGAATTAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6475568 original size:14 final size:15
Alignment explanation
Indices: 6475549--6475577 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6475539 AATAATTTTG
6475549 AATAATT-AAATAAT
1 AATAATTCAAATAAT
6475563 AATAATTCAAATAAT
1 AATAATTCAAATAAT
6475578 TACAAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTCAAATAAT
Found at i:6481769 original size:31 final size:31
Alignment explanation
Indices: 6481727--6481817 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
6481717 TCATACGTAA
* *
6481727 CGTTTATTTTTTGTTTCATTTTAGTACCCGG
1 CGTTTACTTTTTGTTTCATTTTAGTACCCAG
* *
6481758 CGTTTACTTTTTATTTCATTTTAGTACCCCAT
1 CGTTTACTTTTTGTTTCATTTTAGTA-CCCAG
* * *
6481790 TGTTAACTTTTTGTCTCATTTTAGTACC
1 CGTTTACTTTTTGTTTCATTTTAGTACC
6481818 TAAATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 26 0.51
32 25 0.49
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (31 bp):
CGTTTACTTTTTGTTTCATTTTAGTACCCAG
Found at i:6481799 original size:32 final size:32
Alignment explanation
Indices: 6481734--6481817 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 32
6481724 TAACGTTTAT
* *
6481734 TTTTTGTTTCATTTTAGTA-CCCGGCGTTTAC
1 TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
* **
6481765 TTTTTATTTCATTTTAGTACCCCATTGTTAAC
1 TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
*
6481797 TTTTTGTCTCATTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
6481818 TAAATTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 18 0.40
32 27 0.60
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.54
Consensus pattern (32 bp):
TTTTTGTTTCATTTTAGTACCCCAGCGTTAAC
Found at i:6487212 original size:32 final size:33
Alignment explanation
Indices: 6487167--6487255 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 33
6487157 AAAATTTTGT
6487167 TCGACTC-TTGCTCGTTAAG-AAAATTTGTTGC
1 TCGACTCGTTGCTCGTTAAGTAAAATTTGTTGC
6487198 TCGACTCGTTGCTCGTTAAGGTTGTTAAAATTTGTTGC
1 TCGACTCGTTGCTCGTTAA----G-TAAAATTTGTTGC
6487236 TCGACTCGTTGCTCGTTAAG
1 TCGACTCGTTGCTCGTTAAG
6487256 CTTTTTGCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
31 7 0.14
32 11 0.22
34 1 0.02
36 1 0.02
38 31 0.61
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (33 bp):
TCGACTCGTTGCTCGTTAAGTAAAATTTGTTGC
Found at i:6487622 original size:6 final size:6
Alignment explanation
Indices: 6487611--6487653 Score: 77
Period size: 6 Copynumber: 7.0 Consensus size: 6
6487601 GACAAAGCAA
6487611 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGGAGAT
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT -GGAGAT
6487654 TTCCCACCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GGAGAT
Found at i:6487720 original size:12 final size:14
Alignment explanation
Indices: 6487687--6487716 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6487677 TCATAACACC
6487687 TCCTTTCCCTCTCT
1 TCCTTTCCCTCTCT
6487701 TCCTTTCCCTCTCT
1 TCCTTTCCCTCTCT
6487715 TC
1 TC
6487717 TTCCTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (14 bp):
TCCTTTCCCTCTCT
Found at i:6487720 original size:17 final size:15
Alignment explanation
Indices: 6487687--6487724 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
6487677 TCATAACACC
6487687 TCCTTT-CCCTCTCT
1 TCCTTTCCCCTCTCT
6487701 TCCTTTCCCTCTCTTCT
1 TCCTTTCCC-CTC-TCT
6487718 TCCTTTC
1 TCCTTTC
6487725 TAACCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 2 0.10
16 3 0.14
17 10 0.48
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCCTTTCCCCTCTCT
Found at i:6495100 original size:3 final size:3
Alignment explanation
Indices: 6495092--6495141 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
6495082 AATCAAAATG
6495092 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6495140 AA
1 AA
6495142 ATTCCTAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6496559 original size:19 final size:21
Alignment explanation
Indices: 6496535--6496574 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6496525 AGTATGAATA
6496535 TGATG-AA-TAATATCGATAC
1 TGATGAAAGTAATATCGATAC
*
6496554 TGATGAAAGTAGTATCGATAC
1 TGATGAAAGTAATATCGATAC
6496575 CAAGATGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (21 bp):
TGATGAAAGTAATATCGATAC
Found at i:6497377 original size:53 final size:53
Alignment explanation
Indices: 6497304--6497415 Score: 170
Period size: 53 Copynumber: 2.1 Consensus size: 53
6497294 GTGTACTTTC
* * *
6497304 GACACTATGTATGCACCCATGGTATTCATATTGAGTTTGTGAATTACCATTTT
1 GACACTATGTACGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
* * *
6497357 GGCACTATGTGCGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
1 GACACTATGTACGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
6497410 GACACT
1 GACACT
6497416 TAGGTTTTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
GACACTATGTACGCACCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
Found at i:6502234 original size:26 final size:26
Alignment explanation
Indices: 6502194--6502249 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
6502184 GCCTTGGAAG
*
6502194 AAAGTATTACGGTTTGGGCGCAAAAC
1 AAAGTATTACAGTTTGGGCGCAAAAC
* *
6502220 AAAGTATTGCAGTTTGGGCGCAAAAG
1 AAAGTATTACAGTTTGGGCGCAAAAC
6502246 AAAG
1 AAAG
6502250 CTGAGTCCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (26 bp):
AAAGTATTACAGTTTGGGCGCAAAAC
Found at i:6504297 original size:53 final size:53
Alignment explanation
Indices: 6504217--6504321 Score: 167
Period size: 53 Copynumber: 2.0 Consensus size: 53
6504207 GTGTACTTTC
* * *
6504217 GGCACTATGTGTGCACCTATGGTATTCATAATGAGTTTGTTAATTACCATTTT
1 GGCACTATGTGCGCACCTATGGAATTCATAATGAGTTTGTGAATTACCATTTT
6504270 GGCACTATGTGCGCATCC-ATGGAATTCATAATGAGTTTGTGAATTACCATTT
1 GGCACTATGTGCGCA-CCTATGGAATTCATAATGAGTTTGTGAATTACCATTT
6504322 CGACACTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 46 0.96
54 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (53 bp):
GGCACTATGTGCGCACCTATGGAATTCATAATGAGTTTGTGAATTACCATTTT
Found at i:6506084 original size:23 final size:20
Alignment explanation
Indices: 6506022--6506074 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
6506012 TGACCCTAGG
6506022 GTATCAATACTACAAGTAGA
1 GTATCAATACTACAAGTAGA
6506042 GTATCAATACTACAAGTAGA
1 GTATCAATACTACAAGTAGA
6506062 GTATCAATACTAC
1 GTATCAATACTAC
6506075 TTACTTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (20 bp):
GTATCAATACTACAAGTAGA
Found at i:6511477 original size:20 final size:20
Alignment explanation
Indices: 6511452--6511501 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
6511442 CCAAGGGGAG
*
6511452 TATCGATACTACCATTGAAA
1 TATCGATACTACCATAGAAA
*
6511472 TATCGATACTACCATAGAAG
1 TATCGATACTACCATAGAAA
*
6511492 TATCGTTACT
1 TATCGATACT
6511502 TAGGGTGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
TATCGATACTACCATAGAAA
Found at i:6512428 original size:5 final size:5
Alignment explanation
Indices: 6512420--6512452 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
6512410 GGAATGATGG
6512420 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
1 TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGT
6512453 GGCAGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TGTAA
Found at i:6522143 original size:23 final size:23
Alignment explanation
Indices: 6522109--6522158 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
6522099 GGAATCGATA
6522109 CCCC-TTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
6522131 CCCCTTTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
6522154 CCCCT
1 CCCCT
6522159 AGGGGAATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTC
Found at i:6522178 original size:20 final size:19
Alignment explanation
Indices: 6522117--6522182 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
6522107 TACCCCTTGA
*
6522117 AGGGGAACCGATTCCCCCTTT
1 AGGGGAACCGA-TCCCCC-CT
*
6522138 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATCCCCCCT
*
6522159 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
6522179 -GGGG
1 AGGGG
6522183 TTCTGGTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 15 0.39
20 6 0.16
21 1 0.03
22 5 0.13
23 11 0.29
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.17
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:6528728 original size:45 final size:47
Alignment explanation
Indices: 6528649--6528743 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 47
6528639 GACTAGGGTT
* *
6528649 TTTTTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTAG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGGCTACTAG
* *
6528696 TTTTTTT-TTCTTGATGGAGTG-TTAATGGTTGGTAATGGCTACTGG
1 TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGGCTACTAG
6528741 TTT
1 TTT
6528744 CTCCTCTGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 25 0.57
46 12 0.27
47 7 0.16
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.53
Consensus pattern (47 bp):
TTTTTTTGTTCTTGATGGAGTGTTTAATGATTGGTAATGGCTACTAG
Found at i:6529292 original size:55 final size:55
Alignment explanation
Indices: 6529226--6529592 Score: 432
Period size: 55 Copynumber: 6.7 Consensus size: 55
6529216 TTCGAATGAT
* ** **
6529226 GGGTCCACTCCCTATTCCTTCATTGAGTATA-AGACTCGAACAATCTTCAGCAAAC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAAAAAAC
* * * * *
6529281 GTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAAAAAAC
* * * * * *
6529336 GGGTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCAAACAATCTTCATAAAAT
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAAC
* *
6529391 GGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAAC
* * * *
6529446 GGGTCCTCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAAC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAAC
* * * **
6529501 GAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCAACGAAC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAAC
** *
6529556 TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTC
6529593 AATCTTCAAC
Statistics
Matches: 270, Mismatches: 41, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
55 269 1.00
56 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (55 bp):
GGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAAAC
Found at i:6529485 original size:165 final size:165
Alignment explanation
Indices: 6529224--6529607 Score: 482
Period size: 165 Copynumber: 2.4 Consensus size: 165
6529214 TCTTCGAATG
* ** * *
6529224 ATGGGTCCACTCCCTATTCCTTCATTGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCTG
1 ATGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCTG
* *
6529288 CTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCA-ATAAACGGGTCTGCTCCCTATT
65 CTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCATA-AAACGAGTCCGCTCCCTATT
* *
6529352 CGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AA
129 CCTTCAGAGAGTATAGAACTCAAACAATCTTCA-ACAA
* *
6529389 ATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCCT-
1 ATGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGT-CTG
* *
6529453 CTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAAACGAGTCCGCTCTCTATT
65 CTCCCTATTCATTCAGGGAGTATAAG-ACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTATT
* *
6529517 CCTTCAGAGAGTATAGAACTCGAGCAATCTTCAACGAA
129 CCTTCAGAGAGTATAGAACTCAAACAATCTTCAAC-AA
* * *
6529555 CT-TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 ATGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
6529608 AGTTTGCTTC
Statistics
Matches: 193, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
161 15 0.08
164 3 0.02
165 168 0.87
166 7 0.04
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (165 bp):
ATGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGC
TCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTATTCC
TTCAGAGAGTATAGAACTCAAACAATCTTCAACAA
Found at i:6530979 original size:7 final size:7
Alignment explanation
Indices: 6530959--6531217 Score: 389
Period size: 7 Copynumber: 36.3 Consensus size: 7
6530949 CCTCATTTTA
6530959 TTTC-TT
1 TTTCATT
6530965 TTTC-TT
1 TTTCATT
*
6530971 TTTCTTT
1 TTTCATT
*
6530978 TTTCTTCTT
1 TTTC--ATT
6530987 TTTTCATT
1 T-TTCATT
*
6530995 TTTTATTT
1 TTTCA-TT
*
6531003 TTTTATT
1 TTTCATT
6531010 TTTCATTTT
1 TTTCA--TT
6531019 TTTCATTT
1 TTTCA-TT
6531027 TTTCATTT
1 TTTCA-TT
6531035 TTTCATT
1 TTTCATT
6531042 TTTCATT
1 TTTCATT
6531049 TTTCATT
1 TTTCATT
6531056 TTTCATT
1 TTTCATT
6531063 TTTCATT
1 TTTCATT
6531070 TTTCATT
1 TTTCATT
6531077 TTTCATT
1 TTTCATT
6531084 TTTCATT
1 TTTCATT
6531091 TTTCATT
1 TTTCATT
6531098 TTTCATT
1 TTTCATT
6531105 TTTCATT
1 TTTCATT
6531112 TTTCATT
1 TTTCATT
6531119 TTTCATT
1 TTTCATT
6531126 TTTCATT
1 TTTCATT
6531133 TTTCATT
1 TTTCATT
6531140 TTTCATT
1 TTTCATT
6531147 TTTCATT
1 TTTCATT
6531154 TTTCATT
1 TTTCATT
6531161 TTTCATT
1 TTTCATT
6531168 TTTCATT
1 TTTCATT
6531175 TTTCATT
1 TTTCATT
6531182 TTTCATT
1 TTTCATT
6531189 TTTCATT
1 TTTCATT
6531196 TTTCA-T
1 TTTCATT
6531202 TTTCATT
1 TTTCATT
6531209 TTTCATT
1 TTTCATT
6531216 TT
1 TT
6531218 CTTTTTCTTC
Statistics
Matches: 241, Mismatches: 4, Indels: 15
0.93 0.02 0.06
Matches are distributed among these distances:
6 16 0.07
7 186 0.77
8 26 0.11
9 10 0.04
10 3 0.01
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCATT
Found at i:6531247 original size:7 final size:6
Alignment explanation
Indices: 6530959--6531295 Score: 199
Period size: 7 Copynumber: 52.0 Consensus size: 6
6530949 CCTCATTTTA
* * *
6530959 TTTCTT TTTCTT TTTC-T TTT-TT CTTCTTT TTTCAT TTT-TT ATT-TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT
* **
6531004 TTTATT TTTCATT TTT-TT CAT-TT TTTCATTT TTTCATT TTTCATT TTTCATT
1 TTTCTT TTTC-TT TTTCTT TTTCTT TTTC--TT TTTC-TT TTTC-TT TTTC-TT
6531056 TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT
1 TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT
6531105 TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT
1 TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT
*
6531154 TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCATT TTTCAT
1 TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTCTT
*
6531202 TTTCATT TTTCAT TTTCTT TTTCTT CATTT-TT TTTCTT TATTCTT TTCTCTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT --TTTCTT TTTCTT T-TTCTT TT-TCTT
* *
6531254 TTATCTT TTT-TC TTTCTT TTT-TCT CTT-TT TTTCATT TTTCTT
1 TT-TCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTC-TT TTTCTT
6531296 CAAGCGAAAT
Statistics
Matches: 292, Mismatches: 21, Indels: 36
0.84 0.06 0.10
Matches are distributed among these distances:
5 31 0.11
6 51 0.17
7 201 0.69
8 9 0.03
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:6531280 original size:20 final size:20
Alignment explanation
Indices: 6531219--6531284 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
6531209 TTTCATTTTC
*
6531219 TTTTTC-TTCATTTTTTTTCT
1 TTTTTCTTTC-TTTTTTATCT
* *
6531239 TTATTCTTTTCTCTTTTATCT
1 TTTTTC-TTTCTTTTTTATCT
*
6531260 TTTTTCTTTCTTTTTTCTCT
1 TTTTTCTTTCTTTTTTATCT
6531280 TTTTT
1 TTTTT
6531285 TCATTTTTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 22 0.58
21 13 0.34
22 3 0.08
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCTTTTTTATCT
Found at i:6541022 original size:46 final size:46
Alignment explanation
Indices: 6540925--6541027 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 46
6540915 CGTTATTCAT
* *
6540925 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
1 AAAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
* * *
6540971 AAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCATT-TTCT
1 AAAAAAAAAACCTAACCGCATGATATCTAATTCGCATGC-TTGTTCG
*
6541017 CAAAAAAAAAC
1 AAAAAAAAAAC
6541028 AAAAAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 47 0.96
47 2 0.04
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (46 bp):
AAAAAAAAAACCTAACCGCATGATATCTAATTCGCATGCTTGTTCG
Found at i:6543860 original size:46 final size:47
Alignment explanation
Indices: 6543779--6543871 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 47
6543769 TCGGGTTTTG
* *
6543779 TTTTGTTTTTGATGGATTGTTTAATGATTGGTAATGGCTACTGGTTT
1 TTTTGTTATTGATGGAGTGTTTAATGATTGGTAATGGCTACTGGTTT
*
6543826 TTTTGTTATTGATGGAGTG-TTAATGGTTGGTAATGGCTACTGGTTT
1 TTTTGTTATTGATGGAGTGTTTAATGATTGGTAATGGCTACTGGTTT
6543872 CTCCTCTGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
46 26 0.60
47 17 0.40
ACGTcount: A:0.17, C:0.04, G:0.28, T:0.51
Consensus pattern (47 bp):
TTTTGTTATTGATGGAGTGTTTAATGATTGGTAATGGCTACTGGTTT
Found at i:6556870 original size:11 final size:11
Alignment explanation
Indices: 6556850--6556879 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6556840 GGTTGTTATA
6556850 AATTTAATAAT
1 AATTTAATAAT
*
6556861 AATTTGATAAT
1 AATTTAATAAT
6556872 AATTTAAT
1 AATTTAAT
6556880 GACCTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:6559851 original size:166 final size:167
Alignment explanation
Indices: 6559577--6559912 Score: 647
Period size: 166 Copynumber: 2.0 Consensus size: 167
6559567 AATTATATTC
6559577 GTAAAATCAGAACTGGCAAAATACAAAAAAGGAAACTGATTCATTAGATCACAACATGCATGATA
1 GTAAAATCAGAACTGGCAAAATACAAAAAAGGAAACTGATTCATTAGATCACAACATGCATGATA
6559642 TATGAGTGCATGCATGATAGGAACAGAAGGCGCGGGGAAGGAACTAACCTCTTCTGCCCTTAATG
66 TATGAGTGCATGCATGATAGGAACAGAAGGCGCGGGGAAGGAACTAACCTCTTCTGCCCTTAATG
6559707 TCCAG-TGGTCATTTATATTCTCAATCTTCTCACTAG
131 TCCAGATGGTCATTTATATTCTCAATCTTCTCACTAG
6559743 GTAAAATCAGAACTGGCAAAATACAAAAAAGGAAACTGATTCATTAGATCACAACATGCATGATA
1 GTAAAATCAGAACTGGCAAAATACAAAAAAGGAAACTGATTCATTAGATCACAACATGCATGATA
6559808 TATGAGTGCATGCATGATAGGAACAGAAGGCGCGGGGAAGGAACTAACCTCTTCTGCCCTTAATG
66 TATGAGTGCATGCATGATAGGAACAGAAGGCGCGGGGAAGGAACTAACCTCTTCTGCCCTTAATG
6559873 TCCAGTACTGGTCATTTATATTCTCAATCTTCTCACTAG
131 TCCAG-A-TGGTCATTTATATTCTCAATCTTCTCACTAG
6559912 G
1 G
6559913 CGGGAAAATC
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
166 135 0.81
169 32 0.19
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (167 bp):
GTAAAATCAGAACTGGCAAAATACAAAAAAGGAAACTGATTCATTAGATCACAACATGCATGATA
TATGAGTGCATGCATGATAGGAACAGAAGGCGCGGGGAAGGAACTAACCTCTTCTGCCCTTAATG
TCCAGATGGTCATTTATATTCTCAATCTTCTCACTAG
Found at i:6563865 original size:55 final size:59
Alignment explanation
Indices: 6563751--6563867 Score: 161
Period size: 55 Copynumber: 2.0 Consensus size: 59
6563741 TTTTCTGTAC
*
6563751 ATTTTCTAAAGAGAAAAACATATGTAAATATATATATATATTCATTCAACAGGAAAGGCAT
1 ATTTTCTAAAGAG-AAAACATATGT-AATATATATATAAATTCATTCAACAGGAAAGGCAT
* *
6563812 ATTTTTTAAAGAG-AAACATATGT-ATA-A-ATATAAATTCATTCAACAGGATAGGCAT
1 ATTTTCTAAAGAGAAAACATATGTAATATATATATAAATTCATTCAACAGGAAAGGCAT
6563867 A
1 A
6563868 AAACGATATG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
55 27 0.51
56 1 0.02
57 3 0.06
59 10 0.19
61 12 0.23
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (59 bp):
ATTTTCTAAAGAGAAAACATATGTAATATATATATAAATTCATTCAACAGGAAAGGCAT
Done.