Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 164 of 290
Found at i:53083016 original size:16 final size:16
Alignment explanation
Indices: 53082995--53083025 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53082985 AATTTATTTT
*
53082995 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
53083011 AATTAAATAATTTTC
1 AATTAAATAATTTTC
53083026 TCAACCTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:53088206 original size:2 final size:2
Alignment explanation
Indices: 53088194--53088225 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53088184 CATAGTGTTA
*
53088194 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53088226 AGTGAGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:53091482 original size:36 final size:36
Alignment explanation
Indices: 53091435--53091508 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
53091425 TAGCATAAGG
53091435 ATTGCTAATAATGGATTGGTGAAAAAATTTGATTTA
1 ATTGCTAATAATGGATTGGTGAAAAAATTTGATTTA
**
53091471 ATTGCTAATAATGGATTGGTGAAAATTTTTGATTTA
1 ATTGCTAATAATGGATTGGTGAAAAAATTTGATTTA
53091507 AT
1 AT
53091509 GAATAGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (36 bp):
ATTGCTAATAATGGATTGGTGAAAAAATTTGATTTA
Found at i:53094300 original size:42 final size:41
Alignment explanation
Indices: 53094221--53094360 Score: 113
Period size: 43 Copynumber: 3.3 Consensus size: 41
53094211 TCCCGGACGT
* * * * * *
53094221 GGTCTTACATGTAACTCAATATCGATGCCTCTATCCCAGACAG
1 GGTCTTACACGAAACTC-A-ATCGAGGCCTGTGTCCCAGACAC
* *
53094264 GGTCTTACACGAAA-TCAGATACGATG-CTGATGTCCCAGACAT
1 GGTCTTACACGAAACTCA-AT-CGAGGCCTG-TGTCCCAGACAC
* *
53094306 GGTCTTATACATAAATCTCAATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACAC-GAAA-CTCAATCGAGGCCTGTGTCCCAGACAC
53094349 GGTCTTACACGA
1 GGTCTTACACGA
53094361 TGTCTCAGAC
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
41 5 0.06
42 27 0.34
43 39 0.49
44 5 0.06
45 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (41 bp):
GGTCTTACACGAAACTCAATCGAGGCCTGTGTCCCAGACAC
Found at i:53094954 original size:15 final size:15
Alignment explanation
Indices: 53094934--53094965 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53094924 AGCCTTCATA
53094934 ATTCATTCCAAAAAC
1 ATTCATTCCAAAAAC
53094949 ATTCATTCCAAAAAC
1 ATTCATTCCAAAAAC
53094964 AT
1 AT
53094966 CACAAAACTC
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:0.25, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTCATTCCAAAAAC
Found at i:53100615 original size:15 final size:15
Alignment explanation
Indices: 53100595--53100626 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
53100585 AGCCTTCATA
53100595 ATTCATTCCAAAAAC
1 ATTCATTCCAAAAAC
53100610 ATTCATTCCAAAAAC
1 ATTCATTCCAAAAAC
53100625 AT
1 AT
53100627 CACAAAACTC
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:0.25, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTCATTCCAAAAAC
Found at i:53100818 original size:6 final size:6
Alignment explanation
Indices: 53100807--53100834 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53100797 TGGCTTTCTC
53100807 CTTTTT CTTTTT CTTTTT CTTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTT
53100835 GACTTTCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:53118141 original size:2 final size:2
Alignment explanation
Indices: 53118134--53118165 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53118124 TACTATTTTC
53118134 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53118166 TGCGCGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:53121906 original size:23 final size:23
Alignment explanation
Indices: 53121880--53121925 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53121870 TTCGGGCTCA
* *
53121880 ATTCATTTAGCGATCGCGAACAT
1 ATTCATTTAACGATCGCAAACAT
53121903 ATTCATTTAACGATCGCAAACAT
1 ATTCATTTAACGATCGCAAACAT
53121926 GTTTGCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (23 bp):
ATTCATTTAACGATCGCAAACAT
Found at i:53121944 original size:24 final size:24
Alignment explanation
Indices: 53121916--53121961 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
53121906 CATTTAACGA
*
53121916 TCGCAAACATGTTTGCTTATATGT
1 TCGCAAACATGTTCGCTTATATGT
*
53121940 TCGCAAACATGTTCGTTTATAT
1 TCGCAAACATGTTCGCTTATAT
53121962 ATATATTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (24 bp):
TCGCAAACATGTTCGCTTATATGT
Found at i:53123297 original size:12 final size:11
Alignment explanation
Indices: 53123276--53123314 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
53123266 TAAATACATA
53123276 AGTTATAAACG
1 AGTTATAAACG
53123287 AGTTAATAAACG
1 AGTT-ATAAACG
*
53123299 AGTTTTGAAACG
1 AGTTAT-AAACG
53123311 AGTT
1 AGTT
53123315 TGTTTGAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.31
Consensus pattern (11 bp):
AGTTATAAACG
Found at i:53133575 original size:163 final size:163
Alignment explanation
Indices: 53133385--53133703 Score: 503
Period size: 163 Copynumber: 2.0 Consensus size: 163
53133375 TACCAAAGTA
* *
53133385 CCCTCGATTTACAGAATTACTATTTTACCCTCGATTGACAGAATTACCATTTTATCCTCGATTTA
1 CCCTCGATTTACAGAATTACCATTTTACCCTCGATTGACAGAATTACCATTTTACCCTCGATTTA
* * * * * *
53133450 TAGAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTAATTTATAGAATTACCG
66 TAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCAATTTACAGAATTACCG
* *
53133515 TTTTACCCTCGATTTACAGAATTACTGTTTTAC
131 TTTTACCCTCAATTTACAAAATTACTGTTTTAC
* * *
53133548 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTA
1 CCCTCGATTTACAGAATTACCATTTTACCCTCGATTGACAGAATTACCATTTTACCCTCGATTTA
* *
53133613 TAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTG
66 TAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCAATTTACAGAATTACCG
53133678 TTTTACCCTCAATTTACAAAATTACT
131 TTTTACCCTCAATTTACAAAATTACT
53133704 AAAATACCAT
Statistics
Matches: 141, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
163 141 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (163 bp):
CCCTCGATTTACAGAATTACCATTTTACCCTCGATTGACAGAATTACCATTTTACCCTCGATTTA
TAGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCAATTTACAGAATTACCG
TTTTACCCTCAATTTACAAAATTACTGTTTTAC
Found at i:53133703 original size:27 final size:27
Alignment explanation
Indices: 53133383--53133702 Score: 424
Period size: 27 Copynumber: 11.8 Consensus size: 27
53133373 ATTACCAAAG
*
53133383 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
53133410 TACCCTCGATTGACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
53133437 TATCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* **
53133464 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
** * *
53133491 TACCCTTAATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
**
53133518 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
*
53133545 TACCCCTCGATTTATAGAATTACCATTT
1 TA-CCCTCGATTTACAGAATTACCATTT
*
53133573 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
53133600 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
53133627 TACCCTCAATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCATTT
**
53133654 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
53133681 TACCCTCAATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
53133703 TAAAATACCA
Statistics
Matches: 265, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
27 241 0.91
28 24 0.09
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:53133711 original size:27 final size:27
Alignment explanation
Indices: 53133573--53133848 Score: 144
Period size: 27 Copynumber: 10.2 Consensus size: 27
53133563 ATTACCATTT
* * * ***
53133573 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAAAATTACCAAAA
* * * ***
53133600 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAAAATTACCAAAA
****
53133627 TACCCTCAATTTACAAAATTACCGTTT
1 TACCCTCAATTTACAAAATTACCAAAA
* * *****
53133654 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCAATTTACAAAATTACCAAAA
*
53133681 TACCCTCAATTTACAAAATTACTAAAA
1 TACCCTCAATTTACAAAATTACCAAAA
* ***
53133708 TACCATTGGTTTACAAAATTACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAA
* * **
53133735 TACCCTTAGTTTGTAAAATTACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAA
** ***
53133762 TACCACT-GGTTTTTGAAATTACCAAAA
1 TACC-CTCAATTTACAAAATTACCAAAA
**
53133789 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTACAAAATTACCAAAA
*
53133816 TACCC-CTGATTTACAAAATTA-CAGAAA
1 TACCCTC-AATTTACAAAATTACCA-AAA
53133843 TACCCT
1 TACCCT
53133849 AACTTTCTAA
Statistics
Matches: 212, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
26 5 0.02
27 205 0.97
28 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (27 bp):
TACCCTCAATTTACAAAATTACCAAAA
Found at i:53133721 original size:54 final size:54
Alignment explanation
Indices: 53133370--53133837 Score: 258
Period size: 54 Copynumber: 8.6 Consensus size: 54
53133360 CTCAAATTGT
* * * * *
53133370 AAAATTACCAAAGTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTGAC
1 AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* *** * * *
53133424 AGAATTACCATTTTATCC-TCGATTTATAGAATTACCATTTTACCCTCGATTTAT
1 AAAATTACCAAAATA-CCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* ***** * ** * * *
53133478 AGAATTACTGTTTTACCCTTAATTTATAGAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* ***** * * * *
53133532 AGAATTACTGTTTTACCCCTCGATTTATAGAATTACCATTTTACCCTCGATTTAT
1 AAAATTACCAAAATA-CCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* *** * *
53133587 AGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTAC
1 AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
**** * **
53133641 AAAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCAATTTAC
1 AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* * * * *** * * **
53133695 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* * ** *** **
53133749 AAAATTACCAAAATACCACTGGTTTTTGA-AATTACCAAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCA-TCGATTTACAGAATTACCATTTTACCCTCAATTTAC
* *
53133803 AAAATTACCAAAATACC-CCTGATTTACAAAATTAC
1 AAAATTACCAAAATACCATC-GATTTACAGAATTAC
53133838 AGAAATACCC
Statistics
Matches: 351, Mismatches: 57, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
53 7 0.02
54 288 0.82
55 56 0.16
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (54 bp):
AAAATTACCAAAATACCATCGATTTACAGAATTACCATTTTACCCTCAATTTAC
Found at i:53133739 original size:81 final size:81
Alignment explanation
Indices: 53133370--53133837 Score: 188
Period size: 81 Copynumber: 5.8 Consensus size: 81
53133360 CTCAAATTGT
* * * * * *** *
53133370 AAAATTACCAAAGTACCCTCGATTTACAGAATTACTATTTTACCCTCGATTGACAGAATTACCAT
1 AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCCTCGATTTACAGAATTACCAT
* * *
53133435 TTTATCCTCGATTTAT
66 TTTACCCTCAATTTAC
* *** * * * * ***** ** * *
53133451 AGAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTAATTTATAGAATTACCGT
1 AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCCTCGATTTACAGAATTACCAT
*
53133516 TTTACCCTCGATTTAC
66 TTTACCCTCAATTTAC
* ***** * * * * *** *
53133532 AGAATTACTGTTTTACCCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACCA
1 AAAATTACCAAAATA-CCATCAATTTACAAAATTACCAAAATACCCTCGATTTACAGAATTACCA
* *
53133597 TTTTACCCTCGATTTAT
65 TTTTACCCTCAATTTAC
* *** * **** **
53133614 AGAATTACCATTTTACCCTCAATTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACTGT
1 AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCCTCGATTTACAGAATTACCAT
53133679 TTTACCCTCAATTTAC
66 TTTACCCTCAATTTAC
* *** * *
53133695 AAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAATACCCTTAGTTTGTA-A-AATTACC
1 AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCC-TCGATT-TACAGAATTACC
*** ** **
53133758 AAAATACCACT-GGTTTTT
64 ATTTTACC-CTCAATTTAC
* * ** *
53133776 GAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCC-CTGATTTACAAAATTAC
1 AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCCTC-GATTTACAGAATTAC
53133838 AGAAATACCC
Statistics
Matches: 314, Mismatches: 66, Indels: 14
0.80 0.17 0.04
Matches are distributed among these distances:
79 2 0.01
80 4 0.01
81 226 0.72
82 80 0.25
83 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCATCAATTTACAAAATTACCAAAATACCCTCGATTTACAGAATTACCAT
TTTACCCTCAATTTAC
Found at i:53133844 original size:54 final size:54
Alignment explanation
Indices: 53133681--53133903 Score: 254
Period size: 54 Copynumber: 4.1 Consensus size: 54
53133671 ATTACTGTTT
** * *
53133681 TACCCTCAATTTACAAAATTACTAAAATACCATTGGTTTACAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACCAAAA
* * ***
53133735 TACCCTTAGTTTGTAAAATTACCAAAATACCACTGGTTTTTGAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACCAAAA
* *
53133789 TACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTA-CAGAAA
1 TACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACCA-AAA
* * * *
53133843 TACCCT-AACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTAAAA
1 TACCCTCAA-TTTGT-AAAATTACCA-AAATACCACTGGTTTACAAAATTACCAAAA
53133898 TACCCT
1 TACCCT
53133904 TGGCTTGTAG
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
53 4 0.03
54 100 0.70
55 37 0.26
56 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAAAATTACCAAAA
Found at i:53133898 original size:27 final size:27
Alignment explanation
Indices: 53133690--53133906 Score: 172
Period size: 27 Copynumber: 8.0 Consensus size: 27
53133680 TTACCCTCAA
* *
53133690 TTTACAAAATTACTAAAATACCATTGG
1 TTTACAAAATTACCAAAATACCCTTGG
*
53133717 TTTACAAAATTACCAAAATACCCTTAG
1 TTTACAAAATTACCAAAATACCCTTGG
**
53133744 TTTGTAAAATTACCAAAATACCAC-TGG
1 TTTACAAAATTACCAAAATACC-CTTGG
*** ***
53133771 TTTTTGAAATTACCAAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTTGG
** * *
53133798 TTTGTAAAATTACCAAAATACCCCTGA
1 TTTACAAAATTACCAAAATACCCTTGG
***
53133825 TTTACAAAATTA-CAGAAATACCCTAAC
1 TTTACAAAATTACCA-AAATACCCTTGG
* *
53133852 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACCA-AAATACCCTTGG
*
53133880 TTTACAAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTTGG
53133907 CTTGTAGATT
Statistics
Matches: 155, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.03
27 127 0.82
28 23 0.15
29 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTTGG
Found at i:53133984 original size:27 final size:27
Alignment explanation
Indices: 53133954--53134005 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
53133944 GACTAAAATA
53133954 CCCCTA-ATAGGTAAAGAGACCGTAAAG
1 CCCCTATA-AGGTAAAGAGACCGTAAAG
* *
53133981 CCCCTGTAAGGTAAAGTGACCGTAA
1 CCCCTATAAGGTAAAGAGACCGTAA
53134006 TACCCTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (27 bp):
CCCCTATAAGGTAAAGAGACCGTAAAG
Found at i:53134015 original size:27 final size:27
Alignment explanation
Indices: 53133962--53134022 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
53133952 TACCCCTAAT
53133962 AGGTAAAGAGACCGTAAAGCCCCTGTA
1 AGGTAAAGAGACCGTAAAGCCCCTGTA
* *
53133989 AGGTAAAGTGACCGTAATA-CCCTTGTA
1 AGGTAAAGAGACCGTAA-AGCCCCTGTA
*
53134016 TGGTAAA
1 AGGTAAA
53134023 ATGATGAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
AGGTAAAGAGACCGTAAAGCCCCTGTA
Found at i:53134876 original size:25 final size:24
Alignment explanation
Indices: 53134838--53134907 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
53134828 AGGAAGTGCT
53134838 AAAAGGGCTTTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
* *
53134862 GAAAAGGGCTCTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
*
53134887 AGAAAGGGTTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
53134908 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:53135117 original size:42 final size:42
Alignment explanation
Indices: 53135054--53135143 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
53135044 TACTCCCCAG
* ** * **
53135054 ATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTGAA
1 ATGGGCTTGCATACATCCATTGACATTACATACGATATTGAA
53135096 ATGGGCTTGCATACATCCATTGACATTACATACGATATTGAA
1 ATGGGCTTGCATACATCCATTGACATTACATACGATATTGAA
53135138 ATGGGC
1 ATGGGC
53135144 CTAAGTGCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (42 bp):
ATGGGCTTGCATACATCCATTGACATTACATACGATATTGAA
Found at i:53135205 original size:31 final size:31
Alignment explanation
Indices: 53135167--53135245 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
53135157 CGTTTACAGT
53135167 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53135198 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
53135229 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
53135246 AACTGTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:53138370 original size:5 final size:5
Alignment explanation
Indices: 53138356--53138389 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
53138346 AAAATTAAAA
* *
53138356 TATAT TATTT TATTT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
53138390 AATAAATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TATAT
Found at i:53138610 original size:22 final size:22
Alignment explanation
Indices: 53138585--53138626 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
53138575 GAAACAGGGG
53138585 AAAGAAAGAAGAAAA-AGAAAGA
1 AAAGAAA-AAGAAAAGAGAAAGA
53138607 AAAGAAAAAGAAAAGAGAAA
1 AAAGAAAAAGAAAAGAGAAA
53138627 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAGAAAAGAGAAAGA
Found at i:53138613 original size:15 final size:13
Alignment explanation
Indices: 53138585--53138619 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
53138575 GAAACAGGGG
53138585 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
53138598 AAAGAAAGAAAAGAA
1 AAAGAAAG--AAGAA
53138613 AAAGAAA
1 AAAGAAA
53138620 AGAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
15 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:53143908 original size:25 final size:25
Alignment explanation
Indices: 53143880--53143931 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
53143870 AACGAGGTGT
53143880 TTGCTAAGAGTATTATTGACCCAGA
1 TTGCTAAGAGTATTATTGACCCAGA
53143905 TTGCTAAGAGTATTATTGACCCAGA
1 TTGCTAAGAGTATTATTGACCCAGA
53143930 TT
1 TT
53143932 TGAATAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (25 bp):
TTGCTAAGAGTATTATTGACCCAGA
Found at i:53147911 original size:42 final size:41
Alignment explanation
Indices: 53147798--53147911 Score: 106
Period size: 43 Copynumber: 2.7 Consensus size: 41
53147788 CATCTGTCTG
* * *
53147798 AGATATCGTGTAAGACCGTGTCTGGGACACAAGCCTCGATT
1 AGATTTCGTGTAAGACCATGTCTGGGACACAAGCATCGATT
* * *
53147839 GAGATTTACGTATAAGACCATGTCTAGGACATC-GGCATCGTATCT
1 -AGATTT-CGTGTAAGACCATGTCTGGGACA-CAAGCATCG-AT-T
*
53147884 -GATTTCGTGTAAGACCCTGTCTGGGACA
1 AGATTTCGTGTAAGACCATGTCTGGGACA
53147912 GAGGTATCGA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
42 25 0.42
43 30 0.51
44 3 0.05
45 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (41 bp):
AGATTTCGTGTAAGACCATGTCTGGGACACAAGCATCGATT
Found at i:53149714 original size:22 final size:22
Alignment explanation
Indices: 53149689--53149736 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
53149679 GGCGTATCAT
*
53149689 TGGTGGAAAACTTTAATATCTA
1 TGGTGGAAAAATTTAATATCTA
53149711 TGGTGGAAAAATTTAATATCTA
1 TGGTGGAAAAATTTAATATCTA
53149733 TGGT
1 TGGT
53149737 TCCGAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (22 bp):
TGGTGGAAAAATTTAATATCTA
Found at i:53165286 original size:17 final size:17
Alignment explanation
Indices: 53165266--53165357 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
53165256 ATTTTAATAG
53165266 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
53165283 ATTTAATACTT--ATCTTA
1 ATTTAATA-TTAAAT-TTA
* **
53165300 A--TAGTATTTTA-TTA
1 ATTTAATATTAAATTTA
*
53165314 ATTTAATAATAAAGTGATT-
1 ATTTAATATTAAA-T--TTA
53165333 ATCTTAATATTAAATTTA
1 AT-TTAATATTAAATTTA
53165351 ATTTAAT
1 ATTTAAT
53165358 GTTTATCTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 24
0.66 0.07 0.28
Matches are distributed among these distances:
14 6 0.11
15 4 0.07
16 9 0.16
17 19 0.33
18 4 0.07
19 3 0.05
20 12 0.21
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:53165768 original size:13 final size:13
Alignment explanation
Indices: 53165746--53165799 Score: 81
Period size: 13 Copynumber: 4.2 Consensus size: 13
53165736 AGAAGACTAC
* *
53165746 TCGGTTGAAGCAT
1 TCGGTCGAAGCGT
53165759 TCGGTCGAAGCGT
1 TCGGTCGAAGCGT
53165772 TCGGTCGAAGCGT
1 TCGGTCGAAGCGT
*
53165785 TCGGTTGAAGCGT
1 TCGGTCGAAGCGT
53165798 TC
1 TC
53165800 ATCCTAGACG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (13 bp):
TCGGTCGAAGCGT
Found at i:53168655 original size:21 final size:21
Alignment explanation
Indices: 53168626--53168674 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
53168616 AATATCTATG
53168626 AAATGTTAGTAATGTGGTATTA
1 AAAT-TTAGTAATGTGGTATTA
53168648 AAATTTAGTAATGTGGTATTA
1 AAATTTAGTAATGTGGTATTA
53168669 AAATTT
1 AAATTT
53168675 CGTTAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (21 bp):
AAATTTAGTAATGTGGTATTA
Found at i:53171188 original size:23 final size:23
Alignment explanation
Indices: 53171162--53171206 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53171152 TGGGTATGTG
*
53171162 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
53171185 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
53171207 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:53173924 original size:27 final size:27
Alignment explanation
Indices: 53173876--53173980 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
53173866 GCGAGGCTAC
* *
53173876 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
53173903 CAGATATTGTCGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
53173929 CAGATATATGTGGCAGAGCCACTAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
53173956 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
53173981 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
26 8 0.12
27 56 0.84
28 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:53175634 original size:26 final size:26
Alignment explanation
Indices: 53175599--53175706 Score: 164
Period size: 26 Copynumber: 4.2 Consensus size: 26
53175589 TGAAATGCCC
53175599 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
53175625 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
53175651 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
53175677 ATCATGGAACATTTACCT-AACCTATT
1 ATCATGGAACATTTACCTAAACC-ATT
53175703 ATCA
1 ATCA
53175707 ATTTGTATCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
25 3 0.04
26 71 0.96
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:53180055 original size:73 final size:75
Alignment explanation
Indices: 53179936--53180085 Score: 175
Period size: 73 Copynumber: 2.0 Consensus size: 75
53179926 AAATTAAAAT
*
53179936 ATTTGGGATTTTTTTTAAAATATAGTGGCTATGAATTTTCATAAGTA-GT-TGCGCATATAAAG-
1 ATTTGGGATTCTTTTTAAAATATAGTGGCTATGAATTTTCATAAGTATGTGTGCG--TATAAAGA
53179998 ACTTTTAT-ATA
64 ACTTTTATGATA
* * * **
53180009 ATTTGGGATTCTTTTTAAACT-TAGTGGTTATGGATTTTTTTTAAGTATGTGTGCGTATAAAGAA
1 ATTTGGGATTCTTTTTAAAATATAGTGGCTAT-GAATTTTCATAAGTATGTGTGCGTATAAAGAA
*
53180073 GTTTTATGATA
65 CTTTTATGATA
53180084 AT
1 AT
53180086 GTCTTTAGCC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
72 9 0.14
73 38 0.58
74 9 0.14
75 9 0.14
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (75 bp):
ATTTGGGATTCTTTTTAAAATATAGTGGCTATGAATTTTCATAAGTATGTGTGCGTATAAAGAAC
TTTTATGATA
Found at i:53180190 original size:17 final size:17
Alignment explanation
Indices: 53180164--53180196 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53180154 TTATTATAAT
*
53180164 TGTGTGTATATATTATG
1 TGTGTATATATATTATG
53180181 TGTGTATATATATTAT
1 TGTGTATATATATTAT
53180197 ATGCATATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (17 bp):
TGTGTATATATATTATG
Found at i:53190814 original size:27 final size:27
Alignment explanation
Indices: 53190784--53190961 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53190774 ATATTGAGTC
* * * *
53190784 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
53190811 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53190838 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53190866 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53190893 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53190920 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53190947 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53190962 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53190923 original size:82 final size:81
Alignment explanation
Indices: 53190805--53190960 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53190795 TGCTATATAA
* *
53190805 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53190870 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53190887 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53190951 CACTTAGTGC
65 CACTTAGTGC
53190961 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:53203798 original size:16 final size:18
Alignment explanation
Indices: 53203779--53203811 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53203769 CATATGAATT
53203779 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
53203795 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
53203812 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:53204450 original size:43 final size:43
Alignment explanation
Indices: 53204379--53204485 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
53204369 TTGAACTCAT
*
53204379 TCACCGGCATTA-CGCCTGCTAGGCTCGAAGCCCAATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAAC
* *
53204421 TCACCGGCATTATAGCCTGCTAGGTTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAAC
53204464 TC-CCTGGCATTATAGCCTGCTA
1 TCACC-GGCATTATAGCCTGCTA
53204486 ATCAACAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
42 14 0.23
43 46 0.77
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCAATATTAAC
Found at i:53218340 original size:56 final size:56
Alignment explanation
Indices: 53218254--53218373 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
53218244 ACAAGGGATG
53218254 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
53218310 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
53218366 ATGGGCAA
1 ATGGGCAA
53218374 TAAACTAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:53219631 original size:40 final size:40
Alignment explanation
Indices: 53219503--53219708 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
53219493 TCGAATGATG
* * *
53219503 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
53219543 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TTACTATA
* *
53219584 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
53219624 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * **
53219664 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
53219704 TCCGG
1 TCCGG
53219709 TTAAATTCCG
Statistics
Matches: 145, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
39 2 0.01
40 103 0.71
41 40 0.28
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:53219696 original size:80 final size:80
Alignment explanation
Indices: 53219503--53219722 Score: 252
Period size: 81 Copynumber: 2.7 Consensus size: 80
53219493 TCGAATGATG
* * * **
53219503 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGCATT
53219567 TGTGCGAGATTACTAAA
64 TGTGCGAGATTACTAAA
* *
53219584 TTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGT-CCGAAGGCATTT
53219649 GTGCGAG-TTACTATAA
65 GTGCGAGATTACTA-AA
* ** *
53219665 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG
53219723 TACGTGATTT
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
79 13 0.11
80 44 0.36
81 57 0.47
82 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTTG
TGCGAGATTACTAAA
Found at i:53226241 original size:56 final size:56
Alignment explanation
Indices: 53226155--53226329 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
53226145 ACAAGGGATG
53226155 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
53226211 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGG-AAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
53226266 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
53226322 ATGGGCAA
1 ATGGGCAA
53226330 TAAACTAATA
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
55 55 0.47
56 62 0.53
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:53227540 original size:40 final size:40
Alignment explanation
Indices: 53227457--53227642 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
53227447 TCGAATGATG
* * * *
53227457 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
53227497 TCCGGACTAAGAT-CCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53227537 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
53227577 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53227618 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53227643 AACGAGTAGC
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 121 0.92
41 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53227649 original size:80 final size:79
Alignment explanation
Indices: 53227510--53227675 Score: 219
Period size: 80 Copynumber: 2.1 Consensus size: 79
53227500 GGACTAAGAT
* **
53227510 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
53227574 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
* *
53227590 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
53227654 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
53227669 CCGAAGG
1 CCGAAGG
53227676 TACGTGATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 16 0.21
80 58 0.76
81 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTGGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:53233785 original size:21 final size:20
Alignment explanation
Indices: 53233723--53233793 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
53233713 ATCAACAAAT
53233723 AATTTAAAATT-TATAAAAAA
1 AATTTAAAATTAT-TAAAAAA
* * **
53233743 TATTTAAAAATAAAAAATAAA
1 AATTTAAAATTATTAAA-AAA
53233764 AATTATAAAATTATTAAAAAA
1 AATT-TAAAATTATTAAAAAA
*
53233785 AATTCAAAA
1 AATTTAAAA
53233794 AAATAGCCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
20 16 0.41
21 13 0.33
22 10 0.26
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTTAAAATTATTAAAAAA
Found at i:53234559 original size:6 final size:7
Alignment explanation
Indices: 53234542--53234567 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53234532 TGCTGTTGTT
53234542 TTTTTTA
1 TTTTTTA
53234549 TTTTTTA
1 TTTTTTA
53234556 TTTTTTA
1 TTTTTTA
53234563 TTTTT
1 TTTTT
53234568 GAAATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:53236908 original size:33 final size:33
Alignment explanation
Indices: 53236871--53236938 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
53236861 GAGTGCAAAG
53236871 ATAGAACATTATAGAAACTATTGAGTTAAATCA
1 ATAGAACATTATAGAAACTATTGAGTTAAATCA
53236904 ATAGAACATTATAGAAACTATTGAGTTAAATCA
1 ATAGAACATTATAGAAACTATTGAGTTAAATCA
53236937 AT
1 AT
53236939 CTTACAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.31
Consensus pattern (33 bp):
ATAGAACATTATAGAAACTATTGAGTTAAATCA
Found at i:53238113 original size:6 final size:6
Alignment explanation
Indices: 53238102--53238135 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
53238092 ATTCAAACAC
*
53238102 AGATTG AGATTG AGATTG AGTTTG AGATTG AGAT
1 AGATTG AGATTG AGATTG AGATTG AGATTG AGAT
53238136 CAAATGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
AGATTG
Found at i:53241421 original size:13 final size:13
Alignment explanation
Indices: 53241403--53241428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53241393 ATGAAGTGTT
53241403 GAAGATCAAGCTG
1 GAAGATCAAGCTG
53241416 GAAGATCAAGCTG
1 GAAGATCAAGCTG
53241429 CTATATTATT
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:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GAAGATCAAGCTG
Found at i:53246097 original size:8 final size:9
Alignment explanation
Indices: 53246050--53246132 Score: 53
Period size: 9 Copynumber: 8.7 Consensus size: 9
53246040 TATAATTTAC
*
53246050 AAATAAAAT
1 AAATAATAT
*
53246059 ATATAATAT
1 AAATAATAT
53246068 AAATCATATAAT
1 AAAT-A-AT-AT
53246080 AAATAATAT
1 AAATAATAT
53246089 AAA-AATAT
1 AAATAATAT
53246097 ATATATAATA-
1 A-A-ATAATAT
*
53246107 AAATCTATAT
1 AAAT-AATAT
53246117 AATATAATAT
1 AA-ATAATAT
*
53246127 ATATAA
1 AAATAA
53246133 GAAACATACA
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
8 8 0.14
9 24 0.41
10 12 0.20
11 9 0.15
12 6 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATAATAT
Found at i:53246123 original size:16 final size:15
Alignment explanation
Indices: 53246054--53246132 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 15
53246044 ATTTACAAAT
53246054 AAAATATATAATATA
1 AAAATATATAATATA
53246069 AATCATATAATAAATAATATA
1 AA--A-AT-AT--ATAATATA
53246090 AAAATATATATATAATA
1 AAAATATATA-AT-ATA
*
53246107 AAATCTATATAATAT-
1 AAA-ATATATAATATA
*
53246122 AATATATATAA
1 AAAATATATAA
53246133 GAAACATACA
Statistics
Matches: 52, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
14 7 0.13
15 7 0.13
16 4 0.08
17 11 0.21
18 10 0.19
19 3 0.06
21 10 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATATATAATATA
Found at i:53246172 original size:14 final size:14
Alignment explanation
Indices: 53246057--53246171 Score: 80
Period size: 14 Copynumber: 8.2 Consensus size: 14
53246047 TACAAATAAA
53246057 ATATATAATATAAAT
1 ATATATAATA-AAAT
*
53246072 -CATATAAT-AAAT
1 ATATATAATAAAAT
53246084 A-ATATAA-AAATAT
1 ATATATAATAAA-AT
53246097 ATATATAATAAAAT
1 ATATATAATAAAAT
* *
53246111 CTATATAATATAAT
1 ATATATAATAAAAT
*
53246125 ATATATAAGAAACAT
1 ATATATAATAAA-AT
*
53246140 ACAT-T-ATAAGGAAT
1 ATATATAATAA--AAT
*
53246154 AATAGATAATAAAAT
1 -ATATATAATAAAAT
53246169 ATA
1 ATA
53246172 GTATGTGGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 23
0.71 0.09 0.21
Matches are distributed among these distances:
12 12 0.15
13 6 0.08
14 42 0.53
15 14 0.18
16 1 0.01
17 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATATAATAAAAT
Found at i:53246222 original size:3 final size:3
Alignment explanation
Indices: 53246214--53246253 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
53246204 TGAAATATGA
53246214 AAT AAT AAT AAT -AT AA- AA- AAT AAT AAT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53246254 GTACTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.24
3 26 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53246235 original size:9 final size:11
Alignment explanation
Indices: 53246215--53246253 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
53246205 GAAATATGAA
53246215 ATAATAATAAT
1 ATAATAATAAT
53246226 ATAA-AA-AAT
1 ATAATAATAAT
53246235 AATAATAATAAT
1 -ATAATAATAAT
53246247 ATAATAA
1 ATAATAA
53246254 GTACTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 3 0.12
10 6 0.24
11 13 0.52
12 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:53246235 original size:15 final size:15
Alignment explanation
Indices: 53246181--53246241 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
53246171 AGTATGTGGT
53246181 AAAAATACATAA-ATA
1 AAAAATA-ATAATATA
*
53246196 AAATATAATGAAATATGA
1 AAAAATAAT--AATAT-A
*
53246214 AATAATAATAATATA
1 AAAAATAATAATATA
53246229 AAAAATAATAATA
1 AAAAATAATAATA
53246242 ATAATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.05
15 19 0.50
16 7 0.18
17 2 0.05
18 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAAATAATAATATA
Found at i:53251324 original size:6 final size:6
Alignment explanation
Indices: 53251313--53251341 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53251303 GATGCTCCCA
53251313 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
53251342 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:53256233 original size:28 final size:28
Alignment explanation
Indices: 53256200--53256327 Score: 184
Period size: 29 Copynumber: 4.5 Consensus size: 28
53256190 ATAGTAAGTC
*
53256200 CGCACACTTAGTGTTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53256228 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
53256257 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
** * *
53256285 CGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53256314 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53256328 CAATCTCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
28 45 0.49
29 46 0.51
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53256288 original size:57 final size:57
Alignment explanation
Indices: 53256199--53256327 Score: 197
Period size: 57 Copynumber: 2.3 Consensus size: 57
53256189 TATAGTAAGT
*
53256199 CCGCACACTTAGTGTTATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * *
53256256 TCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
53256313 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
53256328 CAATCTCATG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 62 0.95
58 3 0.05
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:53264171 original size:28 final size:28
Alignment explanation
Indices: 53264087--53264212 Score: 175
Period size: 29 Copynumber: 4.5 Consensus size: 28
53264077 ATAGTAAGTC
53264087 CGCACACTTAGT--TATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
53264113 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGC-TATATAATCAAACT
53264142 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
** * *
53264170 CGCACACTTAGTGCTATGCAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
53264199 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53264213 CAATCTCATG
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
26 12 0.13
28 32 0.36
29 46 0.51
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:53264173 original size:57 final size:57
Alignment explanation
Indices: 53264086--53264212 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 57
53264076 TATAGTAAGT
53264086 CCGCACACTTAGT--TATATAATCAAACTCGCACACTTAGTGCT-TACATAATCAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACA-AATCAAAC
* * * *
53264141 TCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATGCAATTTAAAC
1 CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
53264198 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
53264213 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
55 12 0.19
57 49 0.77
58 3 0.05
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (57 bp):
CCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTATACAAATCAAAC
Found at i:53272047 original size:29 final size:29
Alignment explanation
Indices: 53271989--53272117 Score: 190
Period size: 29 Copynumber: 4.5 Consensus size: 29
53271979 ATAGTAAGTC
*
53271989 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
53272017 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
53272046 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * *
53272075 CGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
53272104 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53272118 CAATCTCATG
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
28 13 0.14
29 78 0.83
30 3 0.03
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:53275427 original size:15 final size:16
Alignment explanation
Indices: 53275386--53275428 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
53275376 AAAAACATTA
*
53275386 TATAATAACAAATCAAC
1 TATAA-AACAAAACAAC
53275403 TATAAAACAAAACAA-
1 TATAAAACAAAACAAC
*
53275418 TATAACACAAA
1 TATAAAACAAA
53275429 TATATCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 5 0.21
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (16 bp):
TATAAAACAAAACAAC
Found at i:53278924 original size:10 final size:10
Alignment explanation
Indices: 53278909--53278963 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
53278899 CCACAAATGT
53278909 TTTTTTTTAA
1 TTTTTTTTAA
53278919 -TTTTTTTAA
1 TTTTTTTTAA
*
53278928 TCTTTTTTTAC
1 T-TTTTTTTAA
*
53278939 TTTTCTTT-A
1 TTTTTTTTAA
**
53278948 TTTTTTCAAA
1 TTTTTTTTAA
53278958 TTTTTT
1 TTTTTT
53278964 GTGGGAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 14 0.39
10 13 0.36
11 9 0.25
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:53287715 original size:20 final size:20
Alignment explanation
Indices: 53287687--53287725 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53287677 TGTGAAACTT
*
53287687 ATTGGTGAATATTTTATATA
1 ATTGATGAATATTTTATATA
53287707 ATTGATGAATATTTTATAT
1 ATTGATGAATATTTTATAT
53287726 TGCAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTGATGAATATTTTATATA
Found at i:53292000 original size:50 final size:50
Alignment explanation
Indices: 53291944--53292043 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
53291934 CCACATCCAC
53291944 CAAGAAGAAAGCTAAAGAAGTTCTATGTTCTCCATAGCACCAATTGAAAA
1 CAAGAAGAAAGCTAAAGAAGTTCTATGTTCTCCATAGCACCAATTGAAAA
53291994 CAAGAAGAAAGCTAAAGAAGTTCTATGTTCTCCATAGCACCAATTGAAAA
1 CAAGAAGAAAGCTAAAGAAGTTCTATGTTCTCCATAGCACCAATTGAAAA
53292044 GGATGGGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (50 bp):
CAAGAAGAAAGCTAAAGAAGTTCTATGTTCTCCATAGCACCAATTGAAAA
Found at i:53294671 original size:3 final size:3
Alignment explanation
Indices: 53294663--53294690 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
53294653 ATATTAAGAG
53294663 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
53294691 TAGGAAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:53303886 original size:40 final size:41
Alignment explanation
Indices: 53303784--53303929 Score: 174
Period size: 40 Copynumber: 3.6 Consensus size: 41
53303774 TTGAATGATG
* * *
53303784 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
53303825 TCCGCGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCG-GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
53303866 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
53303907 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
53303930 GAACGAGTAG
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
39 1 0.01
40 49 0.54
41 12 0.13
42 20 0.22
43 8 0.09
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:53311587 original size:40 final size:40
Alignment explanation
Indices: 53311435--53311580 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
53311425 TTGAATGATG
* * * *
53311435 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
53311475 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
53311515 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
53311556 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53311581 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.01
40 80 0.88
41 10 0.11
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:53311587 original size:80 final size:80
Alignment explanation
Indices: 53311435--53311613 Score: 186
Period size: 80 Copynumber: 2.2 Consensus size: 80
53311425 TTGAATGATG
* * *
53311435 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
53311500 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
53311515 TCCGGGTTAAGTCCCGAAGGCAATTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-ATTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
53311578 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
53311595 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53311614 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.72
81 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:53314726 original size:7 final size:7
Alignment explanation
Indices: 53314714--53314740 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
53314704 TTCTTTTTCA
53314714 TATTTTT
1 TATTTTT
53314721 TATTTTT
1 TATTTTT
53314728 TATTTTT
1 TATTTTT
53314735 TATTTT
1 TATTTT
53314741 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:53316130 original size:38 final size:38
Alignment explanation
Indices: 53316079--53316157 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
53316069 TTCACCTCCG
*
53316079 TATAGGATAGTGGATCGCTTCCTGGATACATCTATACC
1 TATAGGATAGTGGATCGCTTCCGGGATACATCTATACC
53316117 TATAGGATAGTGGATCGCTTCCGGGATACATCTATACC
1 TATAGGATAGTGGATCGCTTCCGGGATACATCTATACC
53316155 TAT
1 TAT
53316158 GTATTTGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (38 bp):
TATAGGATAGTGGATCGCTTCCGGGATACATCTATACC
Found at i:53318700 original size:19 final size:18
Alignment explanation
Indices: 53318676--53318719 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
53318666 ACCTTTTTTC
*
53318676 TGCATTCATCCCATGCATT
1 TGCATTCATCCCAT-CATA
*
53318695 TGCATTTCATCGCATCATA
1 TGCA-TTCATCCCATCATA
53318714 TGCATT
1 TGCATT
53318720 AAGTCTCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (18 bp):
TGCATTCATCCCATCATA
Found at i:53327094 original size:95 final size:95
Alignment explanation
Indices: 53326953--53327126 Score: 215
Period size: 95 Copynumber: 1.8 Consensus size: 95
53326943 CATAATAAGT
* * * ** *
53326953 CTTATCTCCCTAAAGTTGCAGTGGACCAGATTAAAGATAGCGAATCTTATTTCCCTGAAATTGCA
1 CTTATCTCCCTAAAGTTGCAGTGGACCAGATAAAAGATAGCAAATCTCAACTCCCTGAAATTACA
*
53327018 GTGGAACAGATTGACATTATCATGACGAGC
66 GTAGAACAGATTGACATTATCATGACGAGC
* * * * *
53327048 CTTATCTCCTTAAAGTTGCAGTGGAGCAGGTCAAAAGTTA-CAAATCTCAACTCCCTGAAGTTAC
1 CTTATCTCCCTAAAGTTGCAGTGGACCAGAT-AAAAGATAGCAAATCTCAACTCCCTGAAATTAC
*
53327112 AGTAGAGCAGATTGA
65 AGTAGAACAGATTGA
53327127 AGTTAGATCT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
95 59 0.91
96 6 0.09
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (95 bp):
CTTATCTCCCTAAAGTTGCAGTGGACCAGATAAAAGATAGCAAATCTCAACTCCCTGAAATTACA
GTAGAACAGATTGACATTATCATGACGAGC
Found at i:53327242 original size:44 final size:44
Alignment explanation
Indices: 53327180--53327289 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 44
53327170 GATAGAAAAT
* *
53327180 CTTATCTCTCTGATGTTGCAGTAAAGCAGATACAAATTACAAGC
1 CTTATCTCCCTGAAGTTGCAGTAAAGCAGATACAAATTACAAGC
** ** * * *
53327224 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTCAAGT
1 CTTATCTCCCTGAAGTTGCAGTAAAGCAGATACAAATTACAAGC
53327268 CTTATCTCCCTGAAGTTGCAGT
1 CTTATCTCCCTGAAGTTGCAGT
53327290 GGAGCAGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTAAAGCAGATACAAATTACAAGC
Found at i:53327290 original size:44 final size:44
Alignment explanation
Indices: 53326949--53327303 Score: 209
Period size: 45 Copynumber: 7.9 Consensus size: 44
53326939 CTACCATAAT
* * * **
53326949 AAGTCTTATCTCCCTAAAGTTGCAGTGGACCAGATTAAAGATAGC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TTTC
* * *
53326994 GAA-TCTTATTTCCCTGAAATTGCAGTGGAACAGATTGACA-TTATC
1 -AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGTT-TC
* * * * ** *
53327039 ATGACGAGCCTTATCTCCTTAAAGTTGCAGTGGAGCAGGTCAAAAGTTAC
1 ---A--AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TGAAGTTTC
* * * * *
53327089 AAATCTCAACTCCCTGAAGTTACAGTAGAGCAGATTGAAG-TT-
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTC
** * * ***
53327131 -AGATCTTATCTCCCTGAAGTTGCAGTGGAATAGA-TCAGGGATAGA
1 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AG-TTTC
* * * ** ** * *
53327176 AAATCTTATCTCTCTGATGTTGCAGTAAAGCAGATACAAATTAC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTC
*
53327220 AAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTC
*
53327264 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
53327304 ATAGCGAATC
Statistics
Matches: 228, Mismatches: 65, Indels: 34
0.70 0.20 0.10
Matches are distributed among these distances:
41 3 0.01
42 26 0.11
43 1 0.00
44 77 0.34
45 81 0.36
46 6 0.03
47 3 0.01
49 1 0.00
50 27 0.12
51 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTC
Found at i:53327314 original size:133 final size:131
Alignment explanation
Indices: 53327098--53327343 Score: 320
Period size: 133 Copynumber: 1.9 Consensus size: 131
53327088 CAAATCTCAA
*
53327098 CTCCCTGAAGTTACAGTAGAGCAGATTGAAGTTAGATCTTATCTCCCTGAAGTTGCAGTGGAATA
1 CTCCCTGAAGTTACAGTAGAGCAGATTGAAGTTAGATCTTATCTCCCTGAAGTTGCAGTGGAACA
* *
53327163 GATCAGGGATAGAAAATCTTATCT-CTCTGATGTTGCAGTA-AAGCAGATACAAATTACAAGCCT
66 GATCAGAGATAGAAAATCTTATCTACT-TGAAGTTGCAGTAGAA-CAGATACAAATTACAAGCCT
53327226 TAT
129 TAT
* *
53327229 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTTCA-AGTCTTATCTCCCTGAAGTTGCAGTGGA
1 CTCCCTGAAGTTACAGTAGAGCAGATTGAAG-TT-AGA-TCTTATCTCCCTGAAGTTGCAGTGGA
* * ** *
53327293 GCAGA-CTGAAGATAGCGAATCTTATTTACTTGAAGTTGCAGTAGAACAGAT
63 ACAGATCAG-AGATAGAAAATCTTATCTACTTGAAGTTGCAGTAGAACAGAT
53327344 TAAAGCTATA
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
131 29 0.29
132 5 0.05
133 61 0.62
134 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (131 bp):
CTCCCTGAAGTTACAGTAGAGCAGATTGAAGTTAGATCTTATCTCCCTGAAGTTGCAGTGGAACA
GATCAGAGATAGAAAATCTTATCTACTTGAAGTTGCAGTAGAACAGATACAAATTACAAGCCTTA
T
Found at i:53327331 original size:45 final size:44
Alignment explanation
Indices: 53327219--53327334 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
53327209 ATACAAATTA
* * * **
53327219 CAAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTT
1 CAAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTGAAGTAG
*
53327263 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
1 CAAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTGAAG-TAG
* *
53327308 CGAA-TCTTATTTACTTGAAGTTGCAGT
1 C-AAGTCTTATCTACCTGAAGTTGCAGT
53327335 AGAACAGATT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 39 0.62
45 22 0.35
46 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (44 bp):
CAAGTCTTATCTACCTGAAGTTGCAGTGGAGCAGACTGAAGTAG
Found at i:53328276 original size:3 final size:3
Alignment explanation
Indices: 53328268--53328319 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
53328258 TAGATTTCAA
* ** *
53328268 TAT TAT TAT TAT TGT GGT TTT TAAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
53328313 TAT TAT T
1 TAT TAT T
53328320 CCCTATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:53336786 original size:40 final size:40
Alignment explanation
Indices: 53336742--53336928 Score: 320
Period size: 40 Copynumber: 4.7 Consensus size: 40
53336732 GCAAACACAT
* * *
53336742 TTGCCTTCGGGTCTTAACCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
53336782 TTGCCTTCGGGTCTTAGCCCGGATATATCATCCCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
53336822 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53336862 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
53336902 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
53336929 ATCCAATGTT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 138 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:53343490 original size:40 final size:40
Alignment explanation
Indices: 53343435--53343558 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
53343425 ATCGAACACA
*
53343435 CCAAACAAAAACTCATAAGAGTTTATCCAACCGAAATACG
1 CCAAACAAAAGCTCATAAGAGTTTATCCAACCGAAATACG
* ** *
53343475 CCAAACAAAAGCTCATAAGAGCTGGTCCACCCGAAATACG
1 CCAAACAAAAGCTCATAAGAGTTTATCCAACCGAAATACG
* * *
53343515 CC-AACAGAAGCTCATAAAAGTTTATCC-ACCCAAATCACG
1 CCAAACAAAAGCTCATAAGAGTTTATCCAACCGAAAT-ACG
53343554 CCAAA
1 CCAAA
53343559 TAGAAAGTAT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 6 0.09
39 25 0.36
40 39 0.56
ACGTcount: A:0.44, C:0.29, G:0.12, T:0.15
Consensus pattern (40 bp):
CCAAACAAAAGCTCATAAGAGTTTATCCAACCGAAATACG
Found at i:53346723 original size:57 final size:57
Alignment explanation
Indices: 53346635--53346767 Score: 232
Period size: 57 Copynumber: 2.3 Consensus size: 57
53346625 TCAATAGTTG
*
53346635 AAAGATGTTATGGCATCAAGTGATGATTTGACAGTAGAATGAGTAAGTCTATAGCTA
1 AAAGATGTTATGGCATCAAGTGATGATTTGACAGTAGAATGAGTAAGTCCATAGCTA
53346692 AAAGATGTTATGGCATCAAGTGATGATTTGACAGTAGAATGAGTAAGTCCATAGCTA
1 AAAGATGTTATGGCATCAAGTGATGATTTGACAGTAGAATGAGTAAGTCCATAGCTA
*
53346749 AAAGA-GACTATGGCATCAA
1 AAAGATG-TTATGGCATCAA
53346768 AGATTGTCCG
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
56 1 0.01
57 72 0.99
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (57 bp):
AAAGATGTTATGGCATCAAGTGATGATTTGACAGTAGAATGAGTAAGTCCATAGCTA
Found at i:53358760 original size:21 final size:23
Alignment explanation
Indices: 53358736--53358784 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
53358726 AACCAAATTC
53358736 TTAA-TAATTAAAAA-TATTGCA
1 TTAATTAATTAAAAATTATTGCA
**
53358757 TTAATTTCTTTAAAAATTATTGCA
1 TTAA-TTAATTAAAAATTATTGCA
53358781 TTAA
1 TTAA
53358785 AATGGACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATTAATTAAAAATTATTGCA
Found at i:53363172 original size:19 final size:19
Alignment explanation
Indices: 53363136--53363190 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
53363126 AATCATATCT
*
53363136 TCTAATATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
53363154 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53363173 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
53363191 TAAAGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 11 0.31
19 24 0.69
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53363198 original size:17 final size:19
Alignment explanation
Indices: 53363142--53363198 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
53363132 ATCTTCTAAT
*
53363142 ATTGCA-ATCATATCTAAG
1 ATTGCATATCATATCAAAG
*
53363160 ATTGCATATCATATCTAAG
1 ATTGCATATCATATCAAAG
53363179 ATTGCATATCAT-T-AAAG
1 ATTGCATATCATATCAAAG
53363196 ATT
1 ATT
53363199 ATATTTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
17 6 0.16
18 7 0.19
19 24 0.65
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (19 bp):
ATTGCATATCATATCAAAG
Found at i:53363346 original size:21 final size:20
Alignment explanation
Indices: 53363309--53363347 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
53363299 TTGGACTTCG
**
53363309 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
53363329 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
53363348 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:53363602 original size:45 final size:45
Alignment explanation
Indices: 53363546--53363739 Score: 228
Period size: 45 Copynumber: 4.3 Consensus size: 45
53363536 CGATATTTGC
*
53363546 TATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * * *
53363591 TATCTTCGATCTACTCCCCGTCTAATACAGAGATGCTAAATCTGC
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * * *
53363636 T-TCTTCAATCTGCTCCCTGTCTAATACAGAAATGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* * * * * *
53363680 TATCTCCAATTTACTCCACGTCTAATACAGAGACACCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
* *
53363725 CATCTTGGATCTGCT
1 TATCTTCGATCTGCT
53363740 TCGATGTAAA
Statistics
Matches: 123, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
44 38 0.31
45 85 0.69
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGT
Found at i:53363721 original size:89 final size:89
Alignment explanation
Indices: 53363554--53363723 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
53363544 GCTATCTTTG
* * * *
53363554 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTTCGATCTACTCCCCGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAGAAACGCCAAATCTGTTATCTCCAATCTACTCCACGTCTAATAC
** *
53363619 AGAGATGCTAAATCTGCTTCTTCA
66 AGAGACACCAAATCTGCTTCTTCA
* * *
53363643 ATCTGCTCCCTGTCTAATACAGAAATGCCAAATCTGTTATCTCCAATTTACTCCACGTCTAATAC
1 ATCTGCTCCCCGTCTAATACAGAAACGCCAAATCTGTTATCTCCAATCTACTCCACGTCTAATAC
53363708 AGAGACACCAAATCTG
66 AGAGACACCAAATCTG
53363724 TCATCTTGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (89 bp):
ATCTGCTCCCCGTCTAATACAGAAACGCCAAATCTGTTATCTCCAATCTACTCCACGTCTAATAC
AGAGACACCAAATCTGCTTCTTCA
Found at i:53363885 original size:78 final size:78
Alignment explanation
Indices: 53363753--53364046 Score: 419
Period size: 78 Copynumber: 3.8 Consensus size: 78
53363743 ATGTAAACAC
* **
53363753 ATGAAGGTCAGATCTGCTATGTCTTCGGTCTGCTCATCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
53363818 TGAATCTGCTTCA
66 TGGATCTGCTTCA
* * *
53363831 ATAAAGGTCCA-ATCTGTTATGTCATCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
53363895 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* * ** *
53363909 ATGAAGGTTAGATCTGCTGTGTCTTCGATCTGCTCCCTATCTAATACAAAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
53363974 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* * * **
53363987 ATGAAGGTCAGATCTGCTATGTCTTCGATATGCTCTCCGTCGAATATGGAGATGCCAAAT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
53364047 TTATTTTTTT
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
77 1 0.01
78 186 0.98
79 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:53372661 original size:17 final size:17
Alignment explanation
Indices: 53372639--53372671 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53372629 GATATGATAC
53372639 TAAAAT-TATTAAAAAAT
1 TAAAATATA-TAAAAAAT
53372656 TAAAATATATAAAAAA
1 TAAAATATATAAAAAA
53372672 AATCAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:53372672 original size:18 final size:17
Alignment explanation
Indices: 53372639--53372672 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53372629 GATATGATAC
*
53372639 TAAAATTATTAAAAAAT
1 TAAAATTATAAAAAAAT
53372656 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
53372673 ATCAGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAATTATAAAAAAAT
Found at i:53373020 original size:35 final size:37
Alignment explanation
Indices: 53372964--53373054 Score: 150
Period size: 35 Copynumber: 2.5 Consensus size: 37
53372954 AATCGTATCT
53372964 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCATA
53373001 TCTAAGATTG-TATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCATA
53373037 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
53373055 TGAAGATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 19 0.37
36 16 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCATA
Found at i:53373062 original size:17 final size:19
Alignment explanation
Indices: 53372964--53373054 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
53372954 AATCGTATCT
53372964 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53372983 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
53373001 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
53373018 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53373037 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
53373055 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53381466 original size:95 final size:93
Alignment explanation
Indices: 53381315--53381724 Score: 498
Period size: 95 Copynumber: 4.4 Consensus size: 93
53381305 AATGGCAACT
* *
53381315 GATGTGGATGAATGATAAAAGATGTTATATATGTGATAAGGCCTAATAGCCGATGTGATGGAATG
1 GATGT-GATGAATG-TGAAAG-TG-TATATATGTGAT-AGGCCTAATGGCCGATGTGAT-GAATG
53381380 TGAAATGTATATATATGTGAT-AGGCCTAATGGCC
60 TGAAA-GTATATATATGTGATAAGGCCTAATGGCC
*
53381414 GATGTGATGAATGTGAAACTAGTATATATGTGATAGGCCTAATGGCCGATGTGATTGAATGTGAA
1 GATGTGATGAATGTGAAAGT-GTATATATGTGATAGGCCTAATGGCCGATGTGA-TGAATGTGAA
53381479 AGTATATTATATATGTGATAAGGCCTAATGGCC
64 AG--TA-TATATATGTGATAAGGCCTAATGGCC
*
53381512 GATGTGATG-ATG-GAAAGTGTATATATGTGAAAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATATGTG-ATAGGCCTAATGGCCGATGTGATGAATGTGAAA
*
53381575 GTGTA-ATATGTGATAAGGCCTAAT-GCC
65 GTATATATATGTGATAAGGCCTAATGGCC
*
53381602 GATGTGATGAATGTGAAAGTGTATATATGTGAAAGG--TAATGGCCGA--TGATGAATGTGAAAG
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * *
53381663 TGTATATATGTGA-CAGGCCGAGTGGCC
66 TATATATATGTGATAAGGCCTAATGGCC
* * * *
53381690 AACGTGAATGGATGTGAAAGTGTATAAATGTGATA
1 GATGTG-ATGAATGTGAAAGTGTATATATGTGATA
53381725 AGTCCCGAAG
Statistics
Matches: 285, Mismatches: 14, Indels: 34
0.86 0.04 0.10
Matches are distributed among these distances:
87 26 0.09
88 15 0.05
89 35 0.12
90 12 0.04
91 27 0.09
92 19 0.07
93 1 0.00
94 1 0.00
95 52 0.18
96 42 0.15
97 20 0.07
98 30 0.11
99 5 0.02
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (93 bp):
GATGTGATGAATGTGAAAGTGTATATATGTGATAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TATATATATGTGATAAGGCCTAATGGCC
Found at i:53381538 original size:45 final size:47
Alignment explanation
Indices: 53381315--53381726 Score: 515
Period size: 47 Copynumber: 8.8 Consensus size: 47
53381305 AATGGCAACT
* *
53381315 GATGTGGATGAATGATAAAAGATGTTATATATGTGATAAGGCCTAATAGCC
1 GATGT-GATGAATG-TGAAAG-TG-TATATATGTGATAAGGCCTAATGGCC
*
53381366 GATGTGATGGAATGTGAAATGTATATATATGTGAT-AGGCCTAATGGCC
1 GATGTGAT-GAATGTGAAA-GTGTATATATGTGATAAGGCCTAATGGCC
*
53381414 GATGTGATGAATGTGAAACTAGTATATATGTGAT-AGGCCTAATGGCC
1 GATGTGATGAATGTGAAAGT-GTATATATGTGATAAGGCCTAATGGCC
*
53381461 GATGTGATTGAATGTGAAAGTATATTATATATGTGATAAGGCCTAATGGCC
1 GATGTGA-TGAATGTGAAAG--T-GTATATATGTGATAAGGCCTAATGGCC
*
53381512 GATGTGATG-ATG-GAAAGTGTATATATGTGAAAAGGCCTAATGGCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
53381557 GATGTGATGAATGTGAAAGTGTA-ATATGTGATAAGGCCTAAT-GCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
53381602 GATGTGATGAATGTGAAAGTGTATATATGTGA-AAGG--TAATGGCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
* * *
53381646 GA--TGATGAATGTGAAAGTGTATATATGTGA-CAGGCCGAGTGGCC
1 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
* * * *
53381690 AACGTGAATGGATGTGAAAGTGTATAAATGTGATAAG
1 GATGTG-ATGAATGTGAAAGTGTATATATGTGATAAG
53381727 TCCCGAAGGG
Statistics
Matches: 327, Mismatches: 17, Indels: 37
0.86 0.04 0.10
Matches are distributed among these distances:
42 31 0.09
43 4 0.01
44 12 0.04
45 64 0.20
46 33 0.10
47 75 0.23
48 38 0.12
49 15 0.05
50 24 0.07
51 31 0.09
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
Found at i:53381683 original size:36 final size:39
Alignment explanation
Indices: 53381370--53381675 Score: 125
Period size: 45 Copynumber: 6.7 Consensus size: 39
53381360 ATAGCCGATG
*
53381370 TGATGGAATGTGAAATGTATATATATGTGATAGGCCTAATGGCCGA
1 TGAT-GAATGTGAAA-GTGTATATATGTGA-A-G---AATGGCCGA
*
53381416 TGTGATGAATGTGAAACTAGTATATATGTGATAGGCCTAATGGCCGA
1 --TGATGAATGTGAAAGT-GTATATATGTGA-A-G---AATGGCCGA
*
53381463 TGTGATTGAATGTGAAAGTATATTATATATGTGATAAGGCCTAATGGCCGA
1 --TGA-TGAATGTGAAAG--T-GTATATATGTG--AA-G---AATGGCCGA
53381514 TG-TG-ATGATGGAAAGTGTATATATGTGAAAAGGCCTAATGGCCGA
1 TGATGAATG-T-GAAAGTGTATATATGTG--AA-G---AATGGCCGA
53381559 TGTGATGAATGTGAAAGTGTA-ATATGTGATAAGGCCTAAT-GCCGA
1 --TGATGAATGTGAAAGTGTATATATGTG--AA-G---AATGGCCGA
53381604 TGTGATGAATGTGAAAGTGTATATATGTGAAAGGTAATGGCCGA
1 --TGATGAATGTGAAAGTGTATATATGTG-AA-G-AATGGCCGA
53381648 TGATGAATGTGAAAGTGTATATATGTGA
1 TGATGAATGTGAAAGTGTATATATGTGA
53381676 CAGGCCGAGT
Statistics
Matches: 236, Mismatches: 8, Indels: 35
0.85 0.03 0.13
Matches are distributed among these distances:
41 1 0.00
42 27 0.11
43 4 0.02
44 5 0.02
45 57 0.24
46 30 0.13
47 56 0.24
48 23 0.10
49 5 0.02
50 12 0.05
51 15 0.06
52 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (39 bp):
TGATGAATGTGAAAGTGTATATATGTGAAGAATGGCCGA
Found at i:53381908 original size:36 final size:36
Alignment explanation
Indices: 53381841--53381917 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
53381831 TCGAGCTCTA
*
53381841 AAGACCCGATGACTACGTGTGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGATTATGTCCGGGT
*
53381877 AAGACCCGAT-ACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGG-GATTATGTCCGGGT
53381913 AAGAC
1 AAGAC
53381918 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 10 0.26
36 28 0.74
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
AAGACCCGATGACTACGTGTGGGATTATGTCCGGGT
Found at i:53383284 original size:39 final size:39
Alignment explanation
Indices: 53383124--53383385 Score: 331
Period size: 39 Copynumber: 6.7 Consensus size: 39
53383114 TGAGAATGAG
53383124 AGTGAATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCT
1 AGTG-ATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCT
53383164 AGTG--ATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGA-GAGCATTCGTGCT
53383202 AGTGATATATCATCCGGGCTAAGT-CCGAGAGCATTCGTGCT
1 AGTG--ATAT-ATCCGGGCTAAGTCCCGAGAGCATTCGTGCT
53383243 AGTGATATATCC-GGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGA-GAGCATTCGTGCT
*
53383282 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCG-AGAGCATTCGTGCT
* * *
53383322 AGTAATATAT-CGTGCTAA-ACCTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCC-CG-AGAGCATTCGTGCT
* * *
53383361 GGTGTTATAT-CGGGCTAGGTCCCGA
1 AGTGATATATCCGGGCTAAGTCCCGA
53383386 AAGTAATCAT
Statistics
Matches: 199, Mismatches: 11, Indels: 26
0.84 0.05 0.11
Matches are distributed among these distances:
37 28 0.14
38 27 0.14
39 68 0.34
40 39 0.20
41 18 0.09
42 6 0.03
43 13 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
AGTGATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCT
Found at i:53383312 original size:79 final size:79
Alignment explanation
Indices: 53383124--53383385 Score: 351
Period size: 79 Copynumber: 3.3 Consensus size: 79
53383114 TGAGAATGAG
53383124 AGTGAATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCTAGTG--ATATCCGGGCTAAGTCCCG
1 AGTGAATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATATCC-GGCTAAGTCCCG
53383187 AGGAGCATTCGTGCT
65 AGGAGCATTCGTGCT
53383202 AGTGATATATCATCCGGGCTAAGT-CCGAGAGCATTCGTGCTAGTGATATATCCGGCTAAGTCCC
1 AGTGA-ATAT-ATCCGGGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATATCCGGCTAAGTCCC
53383266 GAGGAGCATTCGTGCT
64 GAGGAGCATTCGTGCT
* * *
53383282 AGTG-ATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATATAT-CGTGCTAA-ACCT
1 AGTGAATATATCCGGGCTAAGTCCCG-AGAGCATTCGTGCTAGTGATATATCCG-GCTAAGTCC-
*
53383344 CGAAGAGCATTCGTGCT
63 CGAGGAGCATTCGTGCT
* * *
53383361 GGTG-TTATAT-CGGGCTAGGTCCCGA
1 AGTGAATATATCCGGGCTAAGTCCCGA
53383386 AAGTAATCAT
Statistics
Matches: 169, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
77 14 0.08
78 28 0.17
79 77 0.46
80 44 0.26
81 6 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
AGTGAATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATATCCGGCTAAGTCCCGA
GGAGCATTCGTGCT
Found at i:53383353 original size:118 final size:117
Alignment explanation
Indices: 53383124--53383385 Score: 352
Period size: 118 Copynumber: 2.2 Consensus size: 117
53383114 TGAGAATGAG
*
53383124 AGTGAATATATCCGGGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATCCGGGCTAAGTCCCGAG
1 AGTG-ATATATCC-GGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATCCGGGCTAAGTCCCGAA
**
53383189 GAGCATTCGTGCTAGTGATATATCATCCGGGCTAAGTCCGAGAGCATTCGTGCT
64 GAGCATTCGTGCTAGTGATATATCATCCGGGCTAAACCCGAGAGCATTCGTGCT
*
53383243 AGTGATATATCCGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTTCCGA
1 AGTGATATATCCGGCTAAGTCCCGA-GAGCATTCGTGCTAGTG--ATATCCGGGCTAAGTCCCGA
*
53383308 AGAGCATTCGTGCTAGT-A-ATAT-AT-CGTGCTAAACCTCGAAGAGCATTCGTGCT
63 AGAGCATTCGTGCTAGTGATATATCATCCGGGCTAAACC-CG-AGAGCATTCGTGCT
* * * *
53383361 GGTGTTATATCGGGCTAGGTCCCGA
1 AGTGATATATCCGGCTAAGTCCCGA
53383386 AAGTAATCAT
Statistics
Matches: 129, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
116 8 0.06
117 17 0.13
118 64 0.50
119 5 0.04
120 35 0.27
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (117 bp):
AGTGATATATCCGGCTAAGTCCCGAGAGCATTCGTGCTAGTGATATCCGGGCTAAGTCCCGAAGA
GCATTCGTGCTAGTGATATATCATCCGGGCTAAACCCGAGAGCATTCGTGCT
Found at i:53386934 original size:49 final size:47
Alignment explanation
Indices: 53386786--53387213 Score: 651
Period size: 49 Copynumber: 8.9 Consensus size: 47
53386776 TAGTATGGCG
*
53386786 TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
*
53386833 TAATGGCCGATGTGATGAATGTGAATA-TGTATATATTTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCC
*
53386880 TAATGGCCGATGTGATGAATGTGAAAGTGTTTATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
*
53386929 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
*
53386978 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
53387027 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
53387076 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
53387123 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
53387170 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
53387214 TCCCGAAGGG
Statistics
Matches: 361, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 169 0.47
48 1 0.00
49 190 0.53
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:53387388 original size:37 final size:37
Alignment explanation
Indices: 53387332--53387410 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
53387322 CCGAGCTCTA
* * *
53387332 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
53387369 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
53387406 AAGAC
1 AAGAC
53387411 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:53388470 original size:29 final size:29
Alignment explanation
Indices: 53388437--53388496 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
53388427 GATCATGTGA
*
53388437 GTTTAGATATTAGTAAGTAAATGTTAAGT
1 GTTTAGATATTAGTAAGTAAAAGTTAAGT
53388466 GTTTAGATATTAGTAAGTAAAAGTTAAGT
1 GTTTAGATATTAGTAAGTAAAAGTTAAGT
53388495 GT
1 GT
53388497 GGTTTTAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (29 bp):
GTTTAGATATTAGTAAGTAAAAGTTAAGT
Found at i:53390962 original size:53 final size:52
Alignment explanation
Indices: 53390887--53391037 Score: 155
Period size: 51 Copynumber: 2.9 Consensus size: 52
53390877 ATAACATACT
* * * * *
53390887 GATGCCATATCCTAGATTTGGTCTTATACGGAATCACATTATCACGTCACACC
1 GATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCACATCACACC
* ***
53390940 GATGCCATAGCCCAGCTATGGTCTTATACGGGAACTC-GA-ATCACATTGTACC
1 GATGCCATAGCCCAGCTATGGTCTTATAC-GGAA-TCACATATCACATCACACC
* *
53390992 GATGCTAT-GCCCAGCTATGGTCTTATACGAAATCACATATCACATC
1 GATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATC
53391038 TTTTCCGTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
49 2 0.02
50 4 0.05
51 27 0.33
52 16 0.20
53 25 0.31
54 5 0.06
55 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (52 bp):
GATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATCACACC
Found at i:53397464 original size:20 final size:20
Alignment explanation
Indices: 53397439--53397479 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53397429 TGAAAATAGG
53397439 GGGACATGCCCGTGTGGCCT
1 GGGACATGCCCGTGTGGCCT
*
53397459 GGGACATGCTCGTGTGGCCT
1 GGGACATGCCCGTGTGGCCT
53397479 G
1 G
53397480 CCTATGGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.27, G:0.41, T:0.22
Consensus pattern (20 bp):
GGGACATGCCCGTGTGGCCT
Found at i:53398389 original size:52 final size:52
Alignment explanation
Indices: 53398270--53398412 Score: 164
Period size: 52 Copynumber: 2.7 Consensus size: 52
53398260 ATCACATAAC
* * *
53398270 ATACCGATGCCATATCCTAGATATGGTCTTATACGGAATTACATTATCACATT
1 ATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAACTACA-TATCACATT
* *
53398323 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACT-CGA-ATCACATT
1 ATACCGATGCCATAGCCTAGCTATGGTCTTATAC-GGAACTAC-ATATCACATT
* * * *
53398375 GTACCAATGCCATAGCCTAGCTATGGTGTTATAAGGAA
1 ATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAA
53398413 GCACATTTGA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
51 4 0.05
52 36 0.47
53 31 0.40
54 6 0.08
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (52 bp):
ATACCGATGCCATAGCCTAGCTATGGTCTTATACGGAACTACATATCACATT
Found at i:53401435 original size:12 final size:12
Alignment explanation
Indices: 53401418--53401442 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53401408 ATGTAAGTGA
53401418 TCTTGATGATTT
1 TCTTGATGATTT
53401430 TCTTGATGATTT
1 TCTTGATGATTT
53401442 T
1 T
53401443 TACATTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:53401796 original size:30 final size:30
Alignment explanation
Indices: 53401762--53401819 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
53401752 TTTTTGGGCC
*
53401762 TAGGGGCAAAATGGTCATTTTGCCAAGGTA
1 TAGGGGCAAAATGGTCATTTTACCAAGGTA
53401792 TAGGGGCAAAATGGTCATTTTACCAAGG
1 TAGGGGCAAAATGGTCATTTTACCAAGG
53401820 CTGTGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAGGTA
Found at i:53402301 original size:46 final size:47
Alignment explanation
Indices: 53402201--53402420 Score: 231
Period size: 47 Copynumber: 4.7 Consensus size: 47
53402191 TATGGAAGCT
* * * *
53402201 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACT-GAGACGAGT-GCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTCGAGA-TA-TAGCC
*
53402249 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCAAGATATAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATAT-AGCC
* * *
53402295 AGTGTAAGA-CATGTTTGGGACAT-GCATCG-GCTACGAGATGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCT-CGAGAT-ATAGCC
*
53402341 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGAGATATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATAT-AGCC
*
53402388 AGTGTAAGATCATGTCTGGGACATGGCATCGAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC
53402421 ACCTTACCCA
Statistics
Matches: 149, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
44 1 0.01
45 5 0.03
46 59 0.40
47 67 0.45
48 17 0.11
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACCTCGAGATATAGCC
Found at i:53402380 original size:47 final size:46
Alignment explanation
Indices: 53402155--53402420 Score: 228
Period size: 47 Copynumber: 5.7 Consensus size: 46
53402145 TGTGTGTGCT
* * *
53402155 AGTGTAAGACATGTCAGGGACAT-GCATC-AGC-C-ACATTATGGAAGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGA-CTCGAGA-TAT--AAGCC
* * *
53402201 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACT-GAGACGAGT--GCT
1 AGTGTAAGA-CATGTCTGGGACATGGCATC-G-ACTCGAGA-TA-TAAGCC
*
53402249 AGTGTAAGACATGTCTGGGACAT-GCATCGACCTCAAGATATAAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGA-CTCGAGATATAAGCC
* * *
53402295 AGTGTAAGACATGTTTGGGACAT-GCATCGGCTACGAGATGAT-AGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGACT-CGAGAT-ATAAGCC
* *
53402341 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATATGAGCC
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGACTCGAGATATAAGCC
53402388 AGTGTAAGATCATGTCTGGGACATGGCATCGAC
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGAC
53402421 ACCTTACCCA
Statistics
Matches: 185, Mismatches: 18, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
44 2 0.01
45 6 0.03
46 66 0.36
47 80 0.43
48 25 0.14
50 1 0.01
51 4 0.02
52 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGACTCGAGATATAAGCC
Found at i:53406882 original size:19 final size:19
Alignment explanation
Indices: 53406858--53406895 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
53406848 AATCTCACAA
53406858 AAACATAATTGAGCCAAAT
1 AAACATAATTGAGCCAAAT
53406877 AAACATAATTGAGCCAAAT
1 AAACATAATTGAGCCAAAT
53406896 TTTCAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (19 bp):
AAACATAATTGAGCCAAAT
Found at i:53407119 original size:25 final size:25
Alignment explanation
Indices: 53407060--53407119 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
53407050 TCAAACATGA
* * **
53407060 CAAAACAC-AAATATTCATCAATGT
1 CAAAATACAAAATATTCACCAAAAT
*
53407084 CATAATACAAAATATTCACCAAAAT
1 CAAAATACAAAATATTCACCAAAAT
*
53407109 CAAAATTCAAA
1 CAAAATACAAA
53407120 CATGGGTCGG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.55, C:0.20, G:0.02, T:0.23
Consensus pattern (25 bp):
CAAAATACAAAATATTCACCAAAAT
Found at i:53408062 original size:19 final size:19
Alignment explanation
Indices: 53408033--53408078 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53408023 CCTTTTACTA
**
53408033 AAAAAACTAAAATTAACTTT
1 AAAAAA-TAAAAAAAACTTT
*
53408053 AAAAAATAAAAAAAAGTTT
1 AAAAAATAAAAAAAACTTT
53408072 AAAAAAT
1 AAAAAAT
53408079 TGAAAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAATAAAAAAAACTTT
Found at i:53408107 original size:120 final size:124
Alignment explanation
Indices: 53407954--53408190 Score: 281
Period size: 120 Copynumber: 1.9 Consensus size: 124
53407944 TTTTAGAAGG
* * * *
53407954 AAATTAAAATGATAAAATAGTTTTTCCTATAAAAACCCAAG-CAATTTTCTATAAAACCTTGATT
1 AAATTAAAATGATAAAATAGTTCTTCCTATAAAAA-CCAAGTCAATTCTCTATAAAACC-TCATG
*
53408018 TTTTTC-CTTTTACTA-AAAAAACTAAAATTAACTTTAAAAA-ATAAAA-AAAAGTTTAAA
64 CTTTTCACTTTTACTAGAAAAAACTAAAATTAACTTTAAAAAGATAAAATAAAAGTTTAAA
* * * * *
53408075 AAATTGAAAA-GAT-AAATGGTTCTTCCTATAAAAACCTAGTTAATTCTCTATAAAATCTCCTGC
1 AAATT-AAAATGATAAAATAGTTCTTCCTATAAAAACCAAGTCAATTCTCTATAAAACCTCATGC
* * *
53408138 TTTTCACTTTTATTAGAAAATACTAAAATTAATTTTAAAAAGATAAAATAAAA
65 TTTTCACTTTTACTAGAAAAAACTAAAATTAACTTTAAAAAGATAAAATAAAA
53408191 TAAATTTTCT
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
119 11 0.11
120 41 0.42
121 31 0.32
122 10 0.10
123 4 0.04
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (124 bp):
AAATTAAAATGATAAAATAGTTCTTCCTATAAAAACCAAGTCAATTCTCTATAAAACCTCATGCT
TTTCACTTTTACTAGAAAAAACTAAAATTAACTTTAAAAAGATAAAATAAAAGTTTAAA
Found at i:53408302 original size:25 final size:26
Alignment explanation
Indices: 53408280--53408328 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
53408270 GAAGAAAACT
53408280 AAATTAATTATAAAAAC-TAAAAATA
1 AAATTAATTATAAAAACATAAAAATA
*
53408305 AAATTAATTTTAAAAACATAAAAA
1 AAATTAATTATAAAAACATAAAAA
53408329 AATGACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATTAATTATAAAAACATAAAAATA
Found at i:53408924 original size:24 final size:24
Alignment explanation
Indices: 53408876--53408925 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
53408866 TAAAATTTTC
*
53408876 AATATTTTAAAATACAATTAGTTA
1 AATATTTTAAAATACAATTAATTA
53408900 AATATGTTTAAAA-A-AATTAAATTA
1 AATAT-TTTAAAATACAATT-AATTA
53408924 AA
1 AA
53408926 ATAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
AATATTTTAAAATACAATTAATTA
Found at i:53410380 original size:31 final size:31
Alignment explanation
Indices: 53410343--53410402 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
53410333 TTTAATTTAA
53410343 TCAATTTTAGTTCCTT-TACTTTGTGAATTGG
1 TCAATTTTAG-TCCTTATACTTTGTGAATTGG
*
53410374 TCAATTTTAGTCCTTATACTTTTTGAATT
1 TCAATTTTAGTCCTTATACTTTGTGAATT
53410403 TTGAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.53
Consensus pattern (31 bp):
TCAATTTTAGTCCTTATACTTTGTGAATTGG
Found at i:53410411 original size:31 final size:30
Alignment explanation
Indices: 53410345--53410416 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
53410335 TAATTTAATC
*
53410345 AATTTTAGTTCCTTTACTTTGTGAATTGGTC
1 AATTTTAG-TCCTTTACTTTGTGAATTGGTA
* *
53410376 AATTTTAGTCCTTATACTTTTTGAATT-TTGA
1 AATTTTAGTCCTT-TACTTTGTGAATTGGT-A
53410407 AATTTTAGTC
1 AATTTTAGTC
53410417 TTGTTCCAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.24, C:0.11, G:0.12, T:0.53
Consensus pattern (30 bp):
AATTTTAGTCCTTTACTTTGTGAATTGGTA
Done.