Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1267
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1050379
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.28
Warning! 150710 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:22142 original size:15 final size:16
Alignment explanation
Indices: 22117--22150 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
22107 TGTAAATATC
22117 TTTACAACTTTTAATT
1 TTTACAACTTTTAATT
*
22133 TTTA-AACTTTTGATT
1 TTTACAACTTTTAATT
22148 TTT
1 TTT
22151 TGTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTACAACTTTTAATT
Found at i:25629 original size:11 final size:12
Alignment explanation
Indices: 25612--25646 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
25602 TTAAGATTCA
25612 AAAAGTAAACCC
1 AAAAGTAAACCC
25624 -AAAGTAAACCC
1 AAAAGTAAACCC
25635 AGAAAGTAAACC
1 A-AAAGTAAACC
25647 AGGGGTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (12 bp):
AAAAGTAAACCC
Found at i:29672 original size:21 final size:21
Alignment explanation
Indices: 29647--31034 Score: 1493
Period size: 21 Copynumber: 65.0 Consensus size: 21
29637 AGAAATCATA
*
29647 ACAACACCAGAACTTACCACC
1 ACAACACCAGAACCTACCACC
*
29668 ACAACATCAGAACCTACAACTACC
1 ACAACACCAGAACCTAC--C-ACC
* *
29692 ACAACACAAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* * *
29713 ACAACAACAGAAACTACCACT
1 ACAACACCAGAACCTACCACC
29734 ACAACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
*
29755 ACAACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* **
29776 ACAACATCAGAGTCTACCACC
1 ACAACACCAGAACCTACCACC
* * *
29797 TCAACACCAGAACCTACAACT
1 ACAACACCAGAACCTACCACC
29818 ACAACACCAGAACCTACCATCAC
1 ACAACACCAGAACCTACCA-C-C
29841 TACAACACCAGAACCTACCACC
1 -ACAACACCAGAACCTACCACC
29863 ACAACACCAGAACCTACCATCAC
1 ACAACACCAGAACCTACCA-C-C
29886 TACAACACCAGAACCTACCATCAC
1 -ACAACACCAGAACCTACCA-C-C
29910 TACAACACCAGAACCTACCACC
1 -ACAACACCAGAACCTACCACC
*
29932 ACAACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
29953 ACAACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* *
29974 ACAACAGCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* **
29995 ACAACATCAGAGTCTACCACC
1 ACAACACCAGAACCTACCACC
* * *
30016 TCAACACCAGAACCTACAACT
1 ACAACACCAGAACCTACCACC
30037 ACAACACCAGAACCTACCATCAC
1 ACAACACCAGAACCTACCA-C-C
30060 TACAACACCAGAACCTACCACC
1 -ACAACACCAGAACCTACCACC
30082 ACAACACCAGAACCTACCATCAC
1 ACAACACCAGAACCTACCA-C-C
30105 TACAACACCAGAACCTACCATCAC
1 -ACAACACCAGAACCTACCA-C-C
30129 TACAACACCAGAACCTACCACC
1 -ACAACACCAGAACCTACCACC
*
30151 ACAACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
30172 ACAACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* * *
30193 ACAACACTAGAACTTACCACT
1 ACAACACCAGAACCTACCACC
* *
30214 TCAACAGCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* * * *
30235 ACGACACCAGAACTTACAACG
1 ACAACACCAGAACCTACCACC
* * *
30256 ACAACACTAGAACTTACCACT
1 ACAACACCAGAACCTACCACC
* * *
30277 ACAACACCAGAACCGATCACT
1 ACAACACCAGAACCTACCACC
* * *
30298 ACAACATCAGAATCTACCACT
1 ACAACACCAGAACCTACCACC
*
30319 ACGACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* *
30340 ACGACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
*
30361 ACAACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* *
30382 TCAACACCGGAACCTACCACC
1 ACAACACCAGAACCTACCACC
** * *
30403 ACAACATTAGAAACTACCACT
1 ACAACACCAGAACCTACCACC
* * *
30424 ACGACACCAGTACCTACCACT
1 ACAACACCAGAACCTACCACC
*
30445 ACAACACCGGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* *
30466 ACAGCACCAGAACCAACCACC
1 ACAACACCAGAACCTACCACC
* *
30487 ACAACACCCGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* *
30508 ACAACCCCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
**
30529 ACAACACCAGAACCTACCATT
1 ACAACACCAGAACCTACCACC
* * *
30550 ACAACAGCTGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* **
30571 ACAACATCAGAGTCTACCACC
1 ACAACACCAGAACCTACCACC
* *
30592 ACGACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
* *
30613 ACAACACCTGAACCTACCACA
1 ACAACACCAGAACCTACCACC
* *
30634 ACAACACCAAAACCCACCACC
1 ACAACACCAGAACCTACCACC
* *
30655 ACGACACCAGAACTTACCACC
1 ACAACACCAGAACCTACCACC
30676 ACAACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
* * * *
30697 ACAACATCAGAACCTTCAACT
1 ACAACACCAGAACCTACCACC
* * * *
30718 AAAACACCGGAACCAACCACT
1 ACAACACCAGAACCTACCACC
* * *
30739 ACAACATCA-AAGTCTACAACC
1 ACAACACCAGAA-CCTACCACC
*
30760 ACAACACCAGAACCTACCACT
1 ACAACACCAGAACCTACCACC
**
30781 ACAACACCAGAACCTACCATA
1 ACAACACCAGAACCTACCACC
*
30802 ACAACACCAAAACCTACCACC
1 ACAACACCAGAACCTACCACC
* *
30823 ACGACACCAGAACTTACCACC
1 ACAACACCAGAACCTACCACC
* * *
30844 ACGACACCAGAATCTACCACTAAA
1 ACAACACCAGAACCTACCAC---C
*
30868 ACAACACAAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
30889 ACAACACCAGAACCTACCACC
1 ACAACACCAGAACCTACCACC
30910 ACAACACCAGAACCTACCACTC
1 ACAACACCAGAACCTACCAC-C
** *
30932 -CAACACCAGAACAAACCACT
1 ACAACACCAGAACCTACCACC
* * *
30952 ACAACACAAGAACCTACAACG
1 ACAACACCAGAACCTACCACC
* * *
30973 ACAACACTAGAACTTACCACT
1 ACAACACCAGAACCTACCACC
* * * **
30994 TCAACACCAGGACCCACCAGT
1 ACAACACCAGAACCTACCACC
* *
31015 ACAACAGCAGAAACTACCAC
1 ACAACACCAGAACCTACCAC
31035 ATCAATTCCA
Statistics
Matches: 1153, Mismatches: 192, Indels: 44
0.83 0.14 0.03
Matches are distributed among these distances:
20 2 0.00
21 973 0.84
22 12 0.01
23 7 0.01
24 159 0.14
ACGTcount: A:0.43, C:0.41, G:0.06, T:0.10
Consensus pattern (21 bp):
ACAACACCAGAACCTACCACC
Found at i:45213 original size:26 final size:26
Alignment explanation
Indices: 45177--45389 Score: 365
Period size: 26 Copynumber: 8.2 Consensus size: 26
45167 GTAAAGCTTG
*
45177 AATGTGTTGTACATGTACCGGTAGAT
1 AATGTGTTGTATATGTACCGGTAGAT
45203 AATGTGTTGTATATGTACCGGTAGAT
1 AATGTGTTGTATATGTACCGGTAGAT
45229 AATGTGTTGTATATGTACCGGTAGAT
1 AATGTGTTGTATATGTACCGGTAGAT
*
45255 AATGTGTTGTATATGTACCGGTATAT
1 AATGTGTTGTATATGTACCGGTAGAT
*
45281 AATGTGTTGTTTATGTACCGGTAGAT
1 AATGTGTTGTATATGTACCGGTAGAT
* *
45307 AATGTGTTGTACATGTACCGGTATAT
1 AATGTGTTGTATATGTACCGGTAGAT
45333 AATGTGTTGCT-TATGTACCGGTAGAT
1 AATGTGTTG-TATATGTACCGGTAGAT
45359 AATGTGTTGTATATGTACCGGTAGAT
1 AATGTGTTGTATATGTACCGGTAGAT
45385 AATGT
1 AATGT
45390 CTTTTTTCAG
Statistics
Matches: 176, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
25 1 0.01
26 174 0.99
27 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (26 bp):
AATGTGTTGTATATGTACCGGTAGAT
Found at i:48778 original size:105 final size:106
Alignment explanation
Indices: 48596--48808 Score: 410
Period size: 105 Copynumber: 2.0 Consensus size: 106
48586 CATATCGTAT
48596 ATTTGTTCAATTCATCTGGGTTCTATGATGTATTCTAAAGCTTATTATTTCTTTTGATGGTCCCG
1 ATTTGTTCAATTCATCTGGGTTCTATGATGTATTCTAAAGCTTATTATTTCTTTTGATGGTCCCG
48661 ATTTTCAATTTCATTTCGATATTG-TTTTTTTTTTATTGTC
66 ATTTTCAATTTCATTTCGATATTGTTTTTTTTTTTATTGTC
48701 ATTTGTTCAATTCATCTGGGTTCTATGATGTATTCTAAAGCTTATTATTTCTTTTGATGGTCCCG
1 ATTTGTTCAATTCATCTGGGTTCTATGATGTATTCTAAAGCTTATTATTTCTTTTGATGGTCCCG
*
48766 ATTTTCAATTTCATTTCGATGTTGTTTTTTTTTTTATTGTC
66 ATTTTCAATTTCATTTCGATATTGTTTTTTTTTTTATTGTC
48807 AT
1 AT
48809 CCATTTCTTT
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 88 0.83
106 18 0.17
ACGTcount: A:0.19, C:0.13, G:0.14, T:0.54
Consensus pattern (106 bp):
ATTTGTTCAATTCATCTGGGTTCTATGATGTATTCTAAAGCTTATTATTTCTTTTGATGGTCCCG
ATTTTCAATTTCATTTCGATATTGTTTTTTTTTTTATTGTC
Found at i:51636 original size:5 final size:5
Alignment explanation
Indices: 51589--51658 Score: 54
Period size: 5 Copynumber: 14.0 Consensus size: 5
51579 TTTTTTTCAT
* * * * * *
51589 CATAG TATAC CATAG CATAT CATAC CATAC CATAG CAAAG CATAG CATA-
1 CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG
51638 CTATAG CATA- CTATAG CATAG
1 C-ATAG CATAG C-ATAG CATAG
51659 GATTTCATAC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
4 2 0.04
5 48 0.92
6 2 0.04
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.24
Consensus pattern (5 bp):
CATAG
Found at i:51676 original size:10 final size:10
Alignment explanation
Indices: 51589--51657 Score: 75
Period size: 10 Copynumber: 6.9 Consensus size: 10
51579 TTTTTTTCAT
*
51589 CATAGTATAC
1 CATAGCATAC
*
51599 CATAGCATAT
1 CATAGCATAC
*
51609 CATACCATAC
1 CATAGCATAC
* *
51619 CATAGCAAAG
1 CATAGCATAC
51629 CATAGCATAC
1 CATAGCATAC
*
51639 TATAGCATAC
1 CATAGCATAC
*
51649 TATAGCATA
1 CATAGCATA
51658 GGATTTCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (10 bp):
CATAGCATAC
Found at i:60531 original size:2 final size:2
Alignment explanation
Indices: 60524--60584 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
60514 TATGCAACTA
60524 CT CT CT CT CT 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 CT CT CT CT CT
60566 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
60585 ATTGGTCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:61908 original size:4 final size:4
Alignment explanation
Indices: 61894--61942 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
61884 AACTGAAGTG
* * * *
61894 GGAC AGAC GGAC GGAC GGAC AGAC AGAC GGAC GAAC GGAC GGAC GGAC
1 GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC GGAC
61942 G
1 G
61943 CAGAGGAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.43, T:0.00
Consensus pattern (4 bp):
GGAC
Found at i:61915 original size:16 final size:16
Alignment explanation
Indices: 61894--61942 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
61884 AACTGAAGTG
61894 GGACAGACGGACGGAC
1 GGACAGACGGACGGAC
*
61910 GGACAGACAGACGGAC
1 GGACAGACGGACGGAC
* *
61926 GAACGGACGGACGGAC
1 GGACAGACGGACGGAC
61942 G
1 G
61943 CAGAGGAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.43, T:0.00
Consensus pattern (16 bp):
GGACAGACGGACGGAC
Found at i:61920 original size:20 final size:20
Alignment explanation
Indices: 61895--61933 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
61885 ACTGAAGTGG
*
61895 GACAGACGGACGGACGGACA
1 GACAGACGGACGAACGGACA
61915 GACAGACGGACGAACGGAC
1 GACAGACGGACGAACGGAC
61934 GGACGGACGC
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:0.26, G:0.38, T:0.00
Consensus pattern (20 bp):
GACAGACGGACGAACGGACA
Found at i:62225 original size:10 final size:10
Alignment explanation
Indices: 62210--62241 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
62200 AGTGGTTGGA
62210 GTACATACAG
1 GTACATACAG
62220 GTACATACA-
1 GTACATACAG
62229 GTACATACAG
1 GTACATACAG
62239 GTA
1 GTA
62242 GAGTCGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (10 bp):
GTACATACAG
Found at i:62234 original size:9 final size:9
Alignment explanation
Indices: 62209--62238 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
62199 TAGTGGTTGG
62209 AGTACATAC
1 AGTACATAC
62218 AGGTACATAC
1 A-GTACATAC
62228 AGTACATAC
1 AGTACATAC
62237 AG
1 AG
62239 GTAGAGTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (9 bp):
AGTACATAC
Found at i:63913 original size:3 final size:3
Alignment explanation
Indices: 63905--64038 Score: 112
Period size: 3 Copynumber: 43.7 Consensus size: 3
63895 AAACATTTGT
* * *
63905 TTG TTG TTG TTG TTG TCG TGTG TTG TTC TTG TCG TGTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG T-TG TTG TTG TTG TTG T-TG TTG TTG TTG
* * *
63952 TCG TGTG TTG TTG TTG TCG TATG TTG TTG TTG TCG TGTG TTG TTG TTG
1 TTG T-TG TTG TTG TTG TTG T-TG TTG TTG TTG TTG T-TG TTG TTG TTG
* * *
64000 TCG TGTG TTG TTG TT- TTG -TG GTG TT- TTT TTG TTG TTG TT
1 TTG T-TG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
64039 TTTTATGTCA
Statistics
Matches: 106, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
2 6 0.06
3 88 0.83
4 12 0.11
ACGTcount: A:0.01, C:0.05, G:0.34, T:0.60
Consensus pattern (3 bp):
TTG
Found at i:64034 original size:16 final size:16
Alignment explanation
Indices: 63909--64014 Score: 194
Period size: 16 Copynumber: 6.6 Consensus size: 16
63899 ATTTGTTTGT
63909 TGTTGTTGTTGTCGTG
1 TGTTGTTGTTGTCGTG
*
63925 TGTTGTTCTTGTCGTG
1 TGTTGTTGTTGTCGTG
63941 TGTTGTTGTTGTCGTG
1 TGTTGTTGTTGTCGTG
*
63957 TGTTGTTGTTGTCGTA
1 TGTTGTTGTTGTCGTG
63973 TGTTGTTGTTGTCGTG
1 TGTTGTTGTTGTCGTG
63989 TGTTGTTGTTGTCGTG
1 TGTTGTTGTTGTCGTG
64005 TGTTGTTGTT
1 TGTTGTTGTT
64015 TTGTGGTGTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 86 1.00
ACGTcount: A:0.01, C:0.07, G:0.35, T:0.58
Consensus pattern (16 bp):
TGTTGTTGTTGTCGTG
Found at i:64648 original size:11 final size:13
Alignment explanation
Indices: 64620--64650 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
64610 AGCACCGTAT
64620 ACACAAACATACC
1 ACACAAACATACC
64633 ACACAAACATACC
1 ACACAAACATACC
64646 ACACA
1 ACACA
64651 GCCCTGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.39, G:0.00, T:0.06
Consensus pattern (13 bp):
ACACAAACATACC
Found at i:65117 original size:204 final size:203
Alignment explanation
Indices: 64767--65161 Score: 781
Period size: 204 Copynumber: 1.9 Consensus size: 203
64757 TAGAAGGATT
64767 TAACGAGAATCTTCCTTTGCCCGGGGGAGGGGGGTATGCATCTATTTAATTGATATTCGTAGATC
1 TAACGAGAATCTTCCTTTGCCCGGGGGAGGGGGGTATGCATCTATTTAATTGATATTCGTAGATC
64832 GAAAGAGAAATTTGATCTCCATGTGCAGTGAGAAAAGAGAAGGAGTGTTAAAATGTTAACATTAG
66 GAAAGAGAAATTTGATCTCCATGTGCAGTGAGAAAAGAGAAGGAGTGTTAAAATGTTAACATTAG
64897 CGATCCGCGGTCTGAGTGGAATAACTGATATAAAATATTTAAGCGATGATAACTGGCATAGAAGT
131 CGATCCGCGGTCTGAGTGGAATAACTGATATAAAATATTTAAGCGATGATAACTGGCATAGAAGT
64962 TAAGGTGG
196 TAAGGTGG
64970 NTAACGAGAATCTTCCTTTGCCCGGGGGAGGGGGGTATGCATCTATTTAATTGATATTCGTAGAT
1 -TAACGAGAATCTTCCTTTGCCCGGGGGAGGGGGGTATGCATCTATTTAATTGATATTCGTAGAT
65035 CGAAAGAGAAATTTGATCTCCATGTGCAGTGAGAAAAGAGAAGGAGTGTTAAAATGTTAACATTA
65 CGAAAGAGAAATTTGATCTCCATGTGCAGTGAGAAAAGAGAAGGAGTGTTAAAATGTTAACATTA
65100 GCGATCCGCGGTCTGAGTGGAATAACTGATATAAAATATTTAAGCGATGATAACTGGCATAG
130 GCGATCCGCGGTCTGAGTGGAATAACTGATATAAAATATTTAAGCGATGATAACTGGCATAG
65162 NNNNNNNNNN
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
204 191 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (203 bp):
TAACGAGAATCTTCCTTTGCCCGGGGGAGGGGGGTATGCATCTATTTAATTGATATTCGTAGATC
GAAAGAGAAATTTGATCTCCATGTGCAGTGAGAAAAGAGAAGGAGTGTTAAAATGTTAACATTAG
CGATCCGCGGTCTGAGTGGAATAACTGATATAAAATATTTAAGCGATGATAACTGGCATAGAAGT
TAAGGTGG
Found at i:66221 original size:21 final size:21
Alignment explanation
Indices: 66165--66488 Score: 396
Period size: 21 Copynumber: 15.2 Consensus size: 21
66155 NNNNNNNNNN
66165 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
** *
66186 AGAAAATTATCTCGTAATAACG
1 AG-ATCTTTTCTCGTAATAACG
66208 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
** *
66229 AGAAAATTATCTCGTAATAACG
1 AG-ATCTTTTCTCGTAATAACG
66251 AGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACG
* *
66272 AGATAATTTACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
* *
66294 AGATCTTTTCTCGTTATTACG
1 AGATCTTTTCTCGTAATAACG
*
66315 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
*
66336 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
* *
66357 AGATATTTAACTCGTAATAACG
1 AGATCTTT-TCTCGTAATAACG
* * *
66379 AGATCTTTTCTTGTTATTACG
1 AGATCTTTTCTCGTAATAACG
* *
66400 AGATCTTTTCTCGTTATTACG
1 AGATCTTTTCTCGTAATAACG
*
66421 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
* *
66442 AGATAATTTACTCGTAATAACG
1 AGAT-CTTTTCTCGTAATAACG
*
66464 AGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACG
66485 AGAT
1 AGAT
66489 AAAAATATTA
Statistics
Matches: 263, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
21 172 0.65
22 91 0.35
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATAACG
Found at i:66360 original size:85 final size:85
Alignment explanation
Indices: 66165--66488 Score: 499
Period size: 85 Copynumber: 3.8 Consensus size: 85
66155 NNNNNNNNNN
* *
66165 AGATCTTTTCTCGTAATAACGAGA-AAATTATCTCGTAATAACGAGATCTTTTCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGATAATTTA-CTCGTAATAACGAGATCTTTTCTCGTAATTACG
** * *
66229 AGAAAATTATCTCGTAATAACG
65 AG-ATCTTTTCTCGTAATTACG
*
66251 AGATCTTTTCTCGTAATAACGAGATAATTTACTCGTAATAACGAGATCTTTTCTCGTTATTACGA
1 AGATCTTTTCTCGTAATAACGAGATAATTTACTCGTAATAACGAGATCTTTTCTCGTAATTACGA
66316 GATCTTTTCTCGTAATTACG
66 GATCTTTTCTCGTAATTACG
* * *
66336 AGATCTTTTCTCGTAATTACGAGAT-ATTTAACTCGTAATAACGAGATCTTTTCTTGTTATTACG
1 AGATCTTTTCTCGTAATAACGAGATAATTT-ACTCGTAATAACGAGATCTTTTCTCGTAATTACG
*
66400 AGATCTTTTCTCGTTATTACG
65 AGATCTTTTCTCGTAATTACG
*
66421 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACGAGATCTTTTCTCGTAATTACGA
1 AGATCTTTTCTCGTAATAACGAGATAATTTACTCGTAATAACGAGATCTTTTCTCGTAATTACGA
66486 GAT
66 GAT
66489 AAAAATATTA
Statistics
Matches: 223, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
84 4 0.02
85 153 0.69
86 61 0.27
87 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (85 bp):
AGATCTTTTCTCGTAATAACGAGATAATTTACTCGTAATAACGAGATCTTTTCTCGTAATTACGA
GATCTTTTCTCGTAATTACG
Found at i:66488 original size:43 final size:43
Alignment explanation
Indices: 66165--66490 Score: 455
Period size: 43 Copynumber: 7.6 Consensus size: 43
66155 NNNNNNNNNN
* *
66165 AGATCTTTTCTCGTAATAACGAGA-AAATTATCTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTA-CTCGTAATAACG
* *
66208 AGATCTTTTCTCGTAATAACGAGA-AAATTATCTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTA-CTCGTAATAACG
*
66251 AGATCTTTTCTCGTAATAACGAGATAATTTACTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
* * * *
66294 AGATCTTTTCTCGTTATTACGAGAT-CTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
66336 AGATCTTTTCTCGTAATTACGAGAT-ATTTAACTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTT-ACTCGTAATAACG
* * * * * *
66379 AGATCTTTTCTTGTTATTACGAGAT-CTTTTCTCGTTATTACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
66421 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
1 AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
66464 AGATCTTTTCTCGTAATTACGAGATAA
1 AGATCTTTTCTCGTAATTACGAGATAA
66491 AAATATTATT
Statistics
Matches: 258, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
42 74 0.29
43 179 0.69
44 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (43 bp):
AGATCTTTTCTCGTAATTACGAGATAATTTACTCGTAATAACG
Found at i:66786 original size:2 final size:2
Alignment explanation
Indices: 66779--66835 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
66769 ATAGGTCAAA
*
66779 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC AC ATC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC
66822 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
66836 GTTTAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.04, C:0.49, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:69375 original size:2 final size:2
Alignment explanation
Indices: 69368--69410 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
69358 ATTCATGCAC
69368 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
69410 A
1 A
69411 TACCAGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:70567 original size:2 final size:2
Alignment explanation
Indices: 70560--70599 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
70550 AATCGAAGTA
70560 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
70600 AGATAAAAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:72240 original size:2 final size:2
Alignment explanation
Indices: 72233--72279 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
72223 TTTGTGCTCG
72233 CT CT CT CT CT 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 CT CT CT CT CT
72275 CT CT C
1 CT CT C
72280 ACACACACAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:74011 original size:1 final size:1
Alignment explanation
Indices: 74007--74032 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
73997 GTTTTTGAGT
74007 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
74033 ACTTCGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:79728 original size:2 final size:2
Alignment explanation
Indices: 79721--79787 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
79711 TATATCACAT
79721 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
79763 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
79788 GCGAGGGTCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:80550 original size:11 final size:11
Alignment explanation
Indices: 80534--80558 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80524 GGCGATGTTT
80534 TTTTTTTTTTG
1 TTTTTTTTTTG
80545 TTTTTTTTTTG
1 TTTTTTTTTTG
80556 TTT
1 TTT
80559 AAACTTGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:81161 original size:39 final size:40
Alignment explanation
Indices: 81005--81166 Score: 188
Period size: 40 Copynumber: 4.1 Consensus size: 40
80995 AAGAAACATT
*
81005 ACATGTATTCAGATTTTGTTAATTGTATC-ATATTATTGAAA
1 ACAT-TATTCAGATTTTGTTAATTGTATCTATATTA-TGGAA
* * * * *
81046 ACATTAGTCATATTTTGTTAATTGTATGT-TATGATAGAA
1 ACATTATTCAGATTTTGTTAATTGTATCTATATTATGGAA
*
81085 ACATTATTTCAGATTTTGTTAATTGTAT-TATACTATGGAA
1 ACATTA-TTCAGATTTTGTTAATTGTATCTATATTATGGAA
* *
81125 GCATTATTCAGATTTTGTTAATT-AATCTATATTATGGAA
1 ACATTATTCAGATTTTGTTAATTGTATCTATATTATGGAA
81164 ACA
1 ACA
81167 ATAATCGTAG
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 40 0.39
40 56 0.55
41 4 0.04
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (40 bp):
ACATTATTCAGATTTTGTTAATTGTATCTATATTATGGAA
Found at i:81165 original size:79 final size:80
Alignment explanation
Indices: 81012--81166 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 80
81002 ATTACATGTA
* * * *
81012 TTCAGATTTTGTTAATTGTATCATATTATTGAAAACATTAGTCATATTTTGTTAATTGTATGTTA
1 TTCAGATTTTGTTAATTGTATCATACTATTGAAAACATTAGTCAGATTTTGTTAATTGAATCTTA
81077 TGATAGAAACATTAT
66 TGATAGAAACATTAT
* * * *
81092 TTCAGATTTTGTTAATTGTATTATACTA-TGGAAGCATTATTCAGATTTTGTTAATT-AATCTAT
1 TTCAGATTTTGTTAATTGTATCATACTATTGAAAACATTAGTCAGATTTTGTTAATTGAATCT-T
* *
81155 ATTATGGAAACA
65 ATGATAGAAACA
81167 ATAATCGTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 3 0.05
79 35 0.55
80 26 0.41
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (80 bp):
TTCAGATTTTGTTAATTGTATCATACTATTGAAAACATTAGTCAGATTTTGTTAATTGAATCTTA
TGATAGAAACATTAT
Found at i:81871 original size:13 final size:13
Alignment explanation
Indices: 81853--81881 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
81843 AAAAACGATG
81853 CTACGTGCCTGTA
1 CTACGTGCCTGTA
81866 CTACGTGCCTGTA
1 CTACGTGCCTGTA
81879 CTA
1 CTA
81882 TGTAGCCTAA
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:0.17, C:0.31, G:0.21, T:0.31
Consensus pattern (13 bp):
CTACGTGCCTGTA
Found at i:87176 original size:4 final size:4
Alignment explanation
Indices: 87167--87262 Score: 192
Period size: 4 Copynumber: 24.0 Consensus size: 4
87157 TTGTATCTTT
87167 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
87215 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
87263 TTTTTTTGTG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:89865 original size:11 final size:11
Alignment explanation
Indices: 89843--89880 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
89833 TGGGTTAACT
*
89843 AGAGTGAACCC
1 AGAGTAAACCC
*
89854 AGCGTAAACCC
1 AGAGTAAACCC
89865 AGAGTAAACCC
1 AGAGTAAACCC
89876 AGAGT
1 AGAGT
89881 GGATACAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.11
Consensus pattern (11 bp):
AGAGTAAACCC
Found at i:90109 original size:11 final size:11
Alignment explanation
Indices: 90087--90221 Score: 92
Period size: 11 Copynumber: 12.0 Consensus size: 11
90077 AAATTTTCAA
90087 AAAGTAAACCC
1 AAAGTAAACCC
* *
90098 AGAGTAAGCCC
1 AAAGTAAACCC
90109 AAAGTAAACCC
1 AAAGTAAACCC
* *
90120 CAAGTTAACCC
1 AAAGTAAACCC
90131 AAAGTAAACCC
1 AAAGTAAACCC
** **
90142 TGAGTGGACCC
1 AAAGTAAACCC
*** **
90153 AAA-TTTTCAA
1 AAAGTAAACCC
*
90163 AAAGAAAACCC
1 AAAGTAAACCC
90174 AGAAAGTAAACCC
1 --AAAGTAAACCC
90187 AGAAAGTAAACCC
1 --AAAGTAAACCC
*
90200 AGAGTAAACCC
1 AAAGTAAACCC
90211 AAAGTAAACCC
1 AAAGTAAACCC
90222 CTAGTGGACC
Statistics
Matches: 93, Mismatches: 28, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
10 5 0.05
11 65 0.70
13 23 0.25
ACGTcount: A:0.48, C:0.26, G:0.14, T:0.12
Consensus pattern (11 bp):
AAAGTAAACCC
Found at i:90184 original size:13 final size:13
Alignment explanation
Indices: 90163--90221 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
90153 AAATTTTCAA
*
90163 AAAGAAAACCCAG
1 AAAGTAAACCCAG
90176 AAAGTAAACCCAG
1 AAAGTAAACCCAG
90189 AAAGTAAACCCAG
1 AAAGTAAACCCAG
90202 --AGTAAACCC--
1 AAAGTAAACCCAG
90211 AAAGTAAACCC
1 AAAGTAAACCC
90222 CTAGTGGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
11 18 0.42
13 25 0.58
ACGTcount: A:0.54, C:0.25, G:0.14, T:0.07
Consensus pattern (13 bp):
AAAGTAAACCCAG
Found at i:90229 original size:80 final size:79
Alignment explanation
Indices: 90045--90266 Score: 312
Period size: 80 Copynumber: 2.8 Consensus size: 79
90035 AGCAATTTTC
* *
90045 GAGTAAACCCAAAGTAAACCCCGAGTGGACCCAAATTTTCAAAAAGTAAACCCAG--AGTAAGCC
1 GAGTAAACCCAAAGTAAACCCCTAGTGGACCCAAATTTTCAAAAAGTAAACCCAGAAAGTAAACC
90108 CAAAGTAAACCCCA
66 CAAAGTAAACCCCA
* *
90122 -AGTTAACCCAAAGTAAA-CCCTGAGTGGACCCAAATTTTCAAAAAGAAAACCCAGAAAGTAAAC
1 GAGTAAACCCAAAGTAAACCCCT-AGTGGACCCAAATTTTCAAAAAGTAAACCCAGAAAGTAAAC
90185 CCAGAAAGTAAA-CCCA
65 CC--AAAGTAAACCCCA
* *
90201 GAGTAAACCCAAAGTAAACCCCTAGTGGACCCAAATTTTTATAAATGTAAA-CCAGAAAGTAAAC
1 GAGTAAACCCAAAGTAAACCCCTAGTGGACCCAAATTTTCA-AAAAGTAAACCCAGAAAGTAAAC
90265 CC
65 CC
90267 GAGGTTTACG
Statistics
Matches: 129, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
75 3 0.02
76 47 0.36
78 8 0.06
79 4 0.03
80 56 0.43
81 11 0.09
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.15
Consensus pattern (79 bp):
GAGTAAACCCAAAGTAAACCCCTAGTGGACCCAAATTTTCAAAAAGTAAACCCAGAAAGTAAACC
CAAAGTAAACCCCA
Found at i:90285 original size:11 final size:11
Alignment explanation
Indices: 90269--90293 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
90259 GTAAACCCGA
90269 GGTTTACGTGG
1 GGTTTACGTGG
90280 GGTTTACGTGG
1 GGTTTACGTGG
90291 GGT
1 GGT
90294 GTTAAGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.48, T:0.36
Consensus pattern (11 bp):
GGTTTACGTGG
Found at i:108213 original size:12 final size:12
Alignment explanation
Indices: 108196--108250 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
108186 TGACATGGAT
108196 GGATGGATAGAG
1 GGATGGATAGAG
***
108208 GGATGGCCGGAG
1 GGATGGATAGAG
*
108220 GGATGGATAGCG
1 GGATGGATAGAG
108232 GGATGGATAGAG
1 GGATGGATAGAG
108244 GGATGGA
1 GGATGGA
108251 GGGATAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.27, C:0.05, G:0.53, T:0.15
Consensus pattern (12 bp):
GGATGGATAGAG
Found at i:109444 original size:3 final size:3
Alignment explanation
Indices: 109436--109462 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
109426 ATTCAGGTCT
109436 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
109463 CATTCAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:117695 original size:168 final size:168
Alignment explanation
Indices: 117416--117728 Score: 554
Period size: 168 Copynumber: 1.9 Consensus size: 168
117406 NNNNNNNNNN
*
117416 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCTAGAGCCT
1 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
* * *
117481 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACATCATAATC
66 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACC
*
117546 ATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAG
131 ATGCATTCAGTTTTTAACAAATATATATGGTAGTAGAG
117584 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
1 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
* * *
117649 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGAAATTATAACC
66 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACC
117714 ATGCATTCAGTTTTT
131 ATGCATTCAGTTTTT
117729 TCCTCACATG
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 137 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (168 bp):
AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACC
ATGCATTCAGTTTTTAACAAATATATATGGTAGTAGAG
Found at i:117793 original size:168 final size:167
Alignment explanation
Indices: 117416--117771 Score: 516
Period size: 168 Copynumber: 2.1 Consensus size: 167
117406 NNNNNNNNNN
* *
117416 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCTAGAGCCT
1 AAGAAGATTTTCTAAAATTTAATA-ATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
* * *
117481 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACATCATAATC
65 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACC
* * *
117546 ATGCATTTAGTTTTTAACAAATATATATGGTAGTAGAG
130 ATGCATTCAGTTTTTAACAAACATATATGGAAGTAGAG
*
117584 AAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
1 AAGAAGATTTTCTAAAATTTAATA-ATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCT
* * *
117649 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGAAATTATAACC
65 GAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACC
** ** * *
117714 ATGCATTCAGTTTTTTCCTCACATGTGTGGAAGTAGAG
130 ATGCATTCAGTTTTTAACAAACATATATGGAAGTAGAG
117752 AAGAAGATTTT-TGAAAATTT
1 AAGAAGATTTTCT-AAAATTT
117772 GGCTTTTTTT
Statistics
Matches: 170, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
167 1 0.01
168 169 0.99
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (167 bp):
AAGAAGATTTTCTAAAATTTAATAATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAGCCTG
AATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCCTCATGGAAATCATAACCA
TGCATTCAGTTTTTAACAAACATATATGGAAGTAGAG
Found at i:119526 original size:2 final size:2
Alignment explanation
Indices: 119519--119544 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
119509 TGAAACCCAC
119519 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
119545 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:119591 original size:2 final size:2
Alignment explanation
Indices: 119584--119648 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
119574 NNNNNNNNNN
119584 CT CT CT CT CT 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 CT CT CT CT CT
119626 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
119649 CTTACCGTGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:120476 original size:22 final size:22
Alignment explanation
Indices: 120448--120493 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
120438 CTAGTAGTTG
120448 AATTCAAGTTGTAACATTGCTT
1 AATTCAAGTTGTAACATTGCTT
120470 AATTCAAGTTGTAACATTGCTT
1 AATTCAAGTTGTAACATTGCTT
120492 AA
1 AA
120494 GTATTTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (22 bp):
AATTCAAGTTGTAACATTGCTT
Found at i:129405 original size:12 final size:11
Alignment explanation
Indices: 129381--129414 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
129371 GCCTGTTCTG
129381 ATTAACTTAATA
1 ATTAA-TTAATA
129393 ATTAATTATATA
1 ATTAATTA-ATA
129405 ATTAATTAAT
1 ATTAATTAAT
129415 GTAATCTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAATTAATA
Found at i:131922 original size:2 final size:2
Alignment explanation
Indices: 131909--131970 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
131899 GTGTTTAGAT
* * *
131909 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TT TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
131951 TC TC T- TT TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
131971 GACACAGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (2 bp):
TC
Found at i:132017 original size:2 final size:2
Alignment explanation
Indices: 132010--132050 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
132000 GTATACTCAT
132010 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
132051 GACACAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:134383 original size:113 final size:113
Alignment explanation
Indices: 134185--134443 Score: 500
Period size: 113 Copynumber: 2.3 Consensus size: 113
134175 AGACCAACGG
* *
134185 TCCCCGCGAGGCAGAACATTCCAATAACCACGTATACTGCAATAGAGTGAACCTCGCTATAGTAT
1 TCCCCGCGAGGCAGAACATTCCAATAACCACTTATACTGCAAAAGAGTGAACCTCGCTATAGTAT
134250 ACACAATAGTCTCTACATAGTTACGGTAATATAACAAATGACCGGCCC
66 ACACAATAGTCTCTACATAGTTACGGTAATATAACAAATGACCGGCCC
134298 TCCCCGCGAGGCAGAACATTCCAATAACCACTTATACTGCAAAAGAGTGAACCTCGCTATAGTAT
1 TCCCCGCGAGGCAGAACATTCCAATAACCACTTATACTGCAAAAGAGTGAACCTCGCTATAGTAT
134363 ACACAATAGTCTCTACATAGTTACGGTAATATAACAAATGACCGGCCC
66 ACACAATAGTCTCTACATAGTTACGGTAATATAACAAATGACCGGCCC
134411 TCCCCGCGAGGCAGAACATTCCAATAACCACTT
1 TCCCCGCGAGGCAGAACATTCCAATAACCACTT
134444 NNNNNNNNNN
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 144 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (113 bp):
TCCCCGCGAGGCAGAACATTCCAATAACCACTTATACTGCAAAAGAGTGAACCTCGCTATAGTAT
ACACAATAGTCTCTACATAGTTACGGTAATATAACAAATGACCGGCCC
Found at i:137639 original size:112 final size:113
Alignment explanation
Indices: 137443--137647 Score: 358
Period size: 112 Copynumber: 1.8 Consensus size: 113
137433 ACCTTGTGTA
* *
137443 TATGTTACAATTGTGTTAGGGTATGCAAAGACTCATTTTATTGTGGTCCTTTTTACGTTGCATCT
1 TATGTTACAATTGTGTTAGAGTATGCAAAGACTCATTTTATTATGGTCCTTTTTACGTTGCATCT
*
137508 CTATACATATTTTGTAAAGACTCGTTGTCTATATTCACTTAGCACGTG
66 CTATACATATTTTGTAAAGACTCATTGTCTATATTCACTTAGCACGTG
*
137556 TATGTTACAATTGTGTTAGAGTATGCAAAGACTCATTTTA-TATGGTCCTTTTTATGTTGCATCT
1 TATGTTACAATTGTGTTAGAGTATGCAAAGACTCATTTTATTATGGTCCTTTTTACGTTGCATCT
*
137620 CTATGCATATTTTGTAAAGACTCATTGT
66 CTATACATATTTTGTAAAGACTCATTGT
137648 TTAGTACTCT
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
112 48 0.55
113 39 0.45
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (113 bp):
TATGTTACAATTGTGTTAGAGTATGCAAAGACTCATTTTATTATGGTCCTTTTTACGTTGCATCT
CTATACATATTTTGTAAAGACTCATTGTCTATATTCACTTAGCACGTG
Found at i:165342 original size:2 final size:2
Alignment explanation
Indices: 165335--165384 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
165325 CTTTACCACC
165335 CT CT CT CT CT 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 CT CT CT CT CT
165377 CT CT CT CT
1 CT CT CT CT
165385 GTTGGTGTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:166233 original size:416 final size:415
Alignment explanation
Indices: 165462--166292 Score: 1601
Period size: 416 Copynumber: 2.0 Consensus size: 415
165452 CCGGCTTACG
165462 GAGACAACGTTTGCAAAGAGTATAAAGACTGGGCCCAGGTCAACTGCAGAAAACACTGTGGCTTC
1 GAGACAACGTTTGCAAAGAGTATAAAGACTGGGCCCAGGTCAACTGCAGAAAACACTGTGGCTTC
165527 TGCAGCAGTGCGGGTAACCAATGGTGTTTGATTGTGATGGCGACTGGTTTTACAAACTAGCAATT
66 TGCAGCAGTGCGGGTAACCAATGGTGTTTGATTGTGATGGCGACTGGTTTTACAAACTAGCAATT
*
165592 CCAACTCATTTTTAGTTTTAAAAAATATTTTCAGCACATTATGGTATAACGAAAACTCATGGTTC
131 CCAACTCATTTTTAGTTTAAAAAAATATTTTCAGCACATTATGGTATAACGAAAACTCATGGTTC
165657 ATATAAAATTAAAAGTTCAAATTCTCATCAGTAATAAGTACATGCATATACTGGTAATTCTTTAG
196 ATATAAAATTAAAAGTTCAAATTCTCATCAGTAATAAGTACATGCATATACTGGTAATTCTTTAG
165722 GTTTACTAGCTGTATTCAAAGTCTTAAAGAAACAATTCTGTTTATATAAAGGTAACGTGAATGTT
261 GTTTACTAGCTGTATTCAAAGTCTTAAAGAAACAATTCTGTTTATATAAAGGTAACGTGAATGTT
165787 GGGAGTTGCTCAGACAAAGTCAACTGCGACGATTATCAAGACGATATTTGTACAAACCCAACGTA
326 GGGAGTTGCTCAGACAAAGTCAACTGCGACGATTATCAAGACGATATTTGTACAAACCCAACGTA
165852 TGCAAAATGGTCCAAAGAAAACTGT
391 TGCAAAATGGTCCAAAGAAAACTGT
165877 NGAGACAACGTTTGCAAAGAGTATAAAGACTGGGCCCAGGTCAACTGCAGAAAACACTGTGGCTT
1 -GAGACAACGTTTGCAAAGAGTATAAAGACTGGGCCCAGGTCAACTGCAGAAAACACTGTGGCTT
*
165942 CTGCAGCAGTGGGGGTAACCAATGGTGTTTGATTGTGATGGCGACTGGTTTTACAAACTAGCAAT
65 CTGCAGCAGTGCGGGTAACCAATGGTGTTTGATTGTGATGGCGACTGGTTTTACAAACTAGCAAT
*
166007 TCCAAC-CTATTTTTAGTTTAAAAAAATATTTTCAGCACATTATGGTATAAGGAAAACTCATGGT
130 TCCAACTC-ATTTTTAGTTTAAAAAAATATTTTCAGCACATTATGGTATAACGAAAACTCATGGT
*
166071 TCATATAAAATTACAAGTTCAAATTCTCATCAGTAATAAGTACATGCATATACTGGTAATTCTTT
194 TCATATAAAATTAAAAGTTCAAATTCTCATCAGTAATAAGTACATGCATATACTGGTAATTCTTT
166136 AGGTTTACTAGCTGTATTCAAAGTCTTAAAGAAACAATTCTGTTTATATAAAGGTAACGTGAATG
259 AGGTTTACTAGCTGTATTCAAAGTCTTAAAGAAACAATTCTGTTTATATAAAGGTAACGTGAATG
166201 TTGGGAGTTGCTCAGACAAAGTCAACTGCGACGATTATCAAGACGATATTTGTACAAACCCAACG
324 TTGGGAGTTGCTCAGACAAAGTCAACTGCGACGATTATCAAGACGATATTTGTACAAACCCAACG
166266 TATGCAAAATGGTCCAAAGAAAACTGT
389 TATGCAAAATGGTCCAAAGAAAACTGT
166293 CCAAACTATT
Statistics
Matches: 410, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
415 1 0.00
416 409 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (415 bp):
GAGACAACGTTTGCAAAGAGTATAAAGACTGGGCCCAGGTCAACTGCAGAAAACACTGTGGCTTC
TGCAGCAGTGCGGGTAACCAATGGTGTTTGATTGTGATGGCGACTGGTTTTACAAACTAGCAATT
CCAACTCATTTTTAGTTTAAAAAAATATTTTCAGCACATTATGGTATAACGAAAACTCATGGTTC
ATATAAAATTAAAAGTTCAAATTCTCATCAGTAATAAGTACATGCATATACTGGTAATTCTTTAG
GTTTACTAGCTGTATTCAAAGTCTTAAAGAAACAATTCTGTTTATATAAAGGTAACGTGAATGTT
GGGAGTTGCTCAGACAAAGTCAACTGCGACGATTATCAAGACGATATTTGTACAAACCCAACGTA
TGCAAAATGGTCCAAAGAAAACTGT
Found at i:167774 original size:12 final size:12
Alignment explanation
Indices: 167757--167782 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
167747 CCTTTTATCT
167757 TGAATTAGGTTG
1 TGAATTAGGTTG
167769 TGAATTAGGTTG
1 TGAATTAGGTTG
167781 TG
1 TG
167783 TCATGCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (12 bp):
TGAATTAGGTTG
Found at i:172411 original size:39 final size:40
Alignment explanation
Indices: 172331--172414 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
172321 CGAACAAAAA
* *
172331 AAACTATAGTGAACGACGATAATCTGTATTTCACATCTGT
1 AAACCATAGTGAACGACGATAATCTGTATTTCACAGCTGT
* * * * *
172371 AAACCATAGTTAACG-CGATCATCTGTGTTTCAGAGGTGT
1 AAACCATAGTGAACGACGATAATCTGTATTTCACAGCTGT
172410 AAACC
1 AAACC
172415 TAAATTAACA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 24 0.65
40 13 0.35
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (40 bp):
AAACCATAGTGAACGACGATAATCTGTATTTCACAGCTGT
Found at i:187905 original size:44 final size:44
Alignment explanation
Indices: 187857--187974 Score: 121
Period size: 46 Copynumber: 2.6 Consensus size: 44
187847 TCAATTTTGA
*
187857 TATTCTTCTCATTAGCATATTCAGCAAAAATATGTTAA-TTTTC
1 TATTCTTCTCATTAGCATATTCAGCAAAAACATGTTAATTTTTC
* * * * ** * *
187900 GTATTCTTCACATTATCATATATTAATCAAATGCGTTTTAATTTTTC
1 -TATTCTTCTCATTAGC--ATATTCAGCAAAAACATGTTAATTTTTC
187947 TATTCTTCTCATTAGCATATTCAGCAAA
1 TATTCTTCTCATTAGCATATTCAGCAAA
187975 GATGACGGCC
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
44 24 0.41
46 29 0.50
47 5 0.09
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (44 bp):
TATTCTTCTCATTAGCATATTCAGCAAAAACATGTTAATTTTTC
Found at i:192657 original size:26 final size:26
Alignment explanation
Indices: 192628--192741 Score: 99
Period size: 26 Copynumber: 4.4 Consensus size: 26
192618 TAAACTTTTT
*
192628 ATCAAATTTTCACTGAATTATATACC
1 ATCAAATTTTCACTGAATCATATACC
**
192654 ATC-AATTTGTCACTGAA-CTATATAAA
1 ATCAAATTT-TCACTGAATC-ATATACC
* * *
192680 ATCAATTTTTTACTAAATCATATACC
1 ATCAAATTTTCACTGAATCATATACC
* *
192706 ATC-AATTTGTCACTGTATCATATAGC
1 ATCAAATTT-TCACTGAATCATATACC
*
192732 ATCAATTTTT
1 ATCAAATTTT
192742 GTCAGAAGCA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
25 9 0.13
26 50 0.74
27 9 0.13
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (26 bp):
ATCAAATTTTCACTGAATCATATACC
Found at i:196866 original size:26 final size:25
Alignment explanation
Indices: 196792--196905 Score: 79
Period size: 26 Copynumber: 4.4 Consensus size: 25
196782 TAAACTTTTT
* *
196792 ATCAATTTTTCACTGAATTATATACC
1 ATCAATTTTTCACTAAATCATATA-C
* * * *
196818 CTTAATTTGTCACTGAA-CAATATAC
1 ATCAATTTTTCACTAAATC-ATATAC
*
196843 AATCAATTTTTTACTAAATCATATACC
1 -ATCAATTTTTCACTAAATCATATA-C
* *
196870 AT-ACATTTGTCACTATATCATATAGC
1 ATCA-ATTTTTCACTAAATCATATA-C
196896 ATCAATTTTT
1 ATCAATTTTT
196906 GTCAGAAGCA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
25 2 0.03
26 63 0.93
27 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.41
Consensus pattern (25 bp):
ATCAATTTTTCACTAAATCATATAC
Found at i:196893 original size:52 final size:52
Alignment explanation
Indices: 196792--196905 Score: 128
Period size: 52 Copynumber: 2.2 Consensus size: 52
196782 TAAACTTTTT
* * *
196792 ATCAATTTTTCACTGAATTATATACCCTTAATTTGTCACTGAACAATATA-C
1 ATCAATTTTTCACTAAATCATATACCCATAATTTGTCACTGAACAATATAGC
*
196843 AATCAATTTTTTACTAAATCATATA-CCATACATTTGTCACT-ATATC-ATATAGC
1 -ATCAATTTTTCACTAAATCATATACCCATA-ATTTGTCACTGA-A-CAATATAGC
196896 ATCAATTTTT
1 ATCAATTTTT
196906 GTCAGAAGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 5 0.09
52 47 0.87
53 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.41
Consensus pattern (52 bp):
ATCAATTTTTCACTAAATCATATACCCATAATTTGTCACTGAACAATATAGC
Found at i:201177 original size:21 final size:21
Alignment explanation
Indices: 201147--201194 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
201137 TACAAGATGA
* * *
201147 ACGATGGGATAGGATTCACGC
1 ACGATAGGATAAGATTAACGC
201168 ACGATAGGATAAGATTAACGC
1 ACGATAGGATAAGATTAACGC
201189 ACGATA
1 ACGATA
201195 AAACAGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (21 bp):
ACGATAGGATAAGATTAACGC
Found at i:203199 original size:84 final size:84
Alignment explanation
Indices: 203056--203219 Score: 283
Period size: 84 Copynumber: 2.0 Consensus size: 84
203046 AGTTTTTAAA
* * *
203056 ACTTTAAGAAGTTGCATTAATTTTTATTAACTTGGTTAATCCAATATTATTTAAGGTAAAAGCTG
1 ACTTTAAGAAGTTGCATTAATTTTTATTAACTTGGTTAATCCAATATCAATTAACGTAAAAGCTG
203121 TGTATATCATCATTCCAAG
66 TGTATATCATCATTCCAAG
* *
203140 ACTTTAAGAAGTTGTATTACTTTTTATTAACTTGGTTAATCCAATATCAATTAACGTAAAAGCTG
1 ACTTTAAGAAGTTGCATTAATTTTTATTAACTTGGTTAATCCAATATCAATTAACGTAAAAGCTG
203205 TGTATATCATCATTC
66 TGTATATCATCATTC
203220 TTGTAAATTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (84 bp):
ACTTTAAGAAGTTGCATTAATTTTTATTAACTTGGTTAATCCAATATCAATTAACGTAAAAGCTG
TGTATATCATCATTCCAAG
Found at i:208693 original size:19 final size:19
Alignment explanation
Indices: 208669--208707 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
208659 CCAATAAAAG
208669 CAATCATTGAGGATTGTAT
1 CAATCATTGAGGATTGTAT
208688 CAATCATTGAGGATTGTAT
1 CAATCATTGAGGATTGTAT
208707 C
1 C
208708 GTTACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (19 bp):
CAATCATTGAGGATTGTAT
Found at i:211357 original size:4 final size:4
Alignment explanation
Indices: 211348--211374 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
211338 CATGATATAC
211348 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
211375 GTATGACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:212455 original size:73 final size:72
Alignment explanation
Indices: 212310--212496 Score: 268
Period size: 73 Copynumber: 2.5 Consensus size: 72
212300 GATCTGTTAA
* * *
212310 AGGTCTGACCCCAGATGGAGTGT-CATCGATCTCCCAAGTTTTCATTGATTTTAGTATGATCTAT
1 AGGTCTGACCCC-GATGGAGTGTCCCT-AATCT-CCAGGTTTTCATTGATTTTAGTATGATCTAT
212374 GGTCTGTTGT
63 GGTCTGTTGT
* *
212384 AGGTCTGACCCCTGATGGAGGGTCCCTAATCTCCAGGTTTTCATTGATTTTAGTATGATCTATGT
1 AGGTCTGACCCC-GATGGAGTGTCCCTAATCTCCAGGTTTTCATTGATTTTAGTATGATCTATGG
*
212449 TTTGTTGT
65 TCTGTTGT
212457 AGGTCTGAACCCCGATGGAGTGTCCCTAATCTCCAGGTTT
1 AGGTCTG-ACCCCGATGGAGTGTCCCTAATCTCCAGGTTT
212497 GTGGACATGA
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
73 71 0.69
74 30 0.29
75 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (72 bp):
AGGTCTGACCCCGATGGAGTGTCCCTAATCTCCAGGTTTTCATTGATTTTAGTATGATCTATGGT
CTGTTGT
Found at i:219636 original size:52 final size:52
Alignment explanation
Indices: 219535--219648 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 52
219525 TAAACTTTTT
* *
219535 ATCAATTTTTCACTGAATTATATACCATTAATTTGTCACTGAACAATATA-C
1 ATCAATTTTTCACTAAATCATATACCATTAATTTGTCACTGAACAATATAGC
*
219586 AATCAATTTTTTACTAAATCATATACCA-TACATTTGTCACT-ATATC-ATATAGC
1 -ATCAATTTTTCACTAAATCATATACCATTA-ATTTGTCACTGA-A-CAATATAGC
219639 ATCAATTTTT
1 ATCAATTTTT
219649 GTCAGAAGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
51 3 0.05
52 50 0.91
53 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (52 bp):
ATCAATTTTTCACTAAATCATATACCATTAATTTGTCACTGAACAATATAGC
Found at i:219646 original size:26 final size:26
Alignment explanation
Indices: 219535--219646 Score: 104
Period size: 26 Copynumber: 4.3 Consensus size: 26
219525 TAAACTTTTT
* *
219535 ATCAATTTTTCACTGAATTATATACC
1 ATCAATTTGTCACTGAATCATATACC
* *
219561 ATTAATTTGTCACTGAA-CAATATACA
1 ATCAATTTGTCACTGAATC-ATATACC
* * *
219587 ATCAATTTTTTACTAAATCATATACC
1 ATCAATTTGTCACTGAATCATATACC
*
219613 AT-ACATTTGTCACT-ATATCATATAGC
1 ATCA-ATTTGTCACTGA-ATCATATACC
219639 ATCAATTT
1 ATCAATTT
219647 TTGTCAGAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.03
26 65 0.94
27 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (26 bp):
ATCAATTTGTCACTGAATCATATACC
Found at i:227063 original size:27 final size:27
Alignment explanation
Indices: 227013--227064 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
227003 TGATCCGTAT
* *
227013 AATAGTATAACTTTTAATCATGTGTAC
1 AATAGTATAACATTTAAACATGTGTAC
227040 AATAGTATAATCATTTAAAC-TGTGT
1 AATAGTATAA-CATTTAAACATGTGT
227065 CTAATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (27 bp):
AATAGTATAACATTTAAACATGTGTAC
Found at i:228484 original size:18 final size:18
Alignment explanation
Indices: 228461--228511 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
228451 TTTTAAAAAG
228461 TCCTATAGGAATTATATT
1 TCCTATAGGAATTATATT
**
228479 TCCTATAGGAGAATGGTATT
1 TCCTATA-G-GAATTATATT
*
228499 TCCTGTAGGAATT
1 TCCTATAGGAATT
228512 TGATTCAGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 11 0.41
19 2 0.07
20 14 0.52
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (18 bp):
TCCTATAGGAATTATATT
Found at i:228661 original size:20 final size:19
Alignment explanation
Indices: 228632--228689 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
228622 TTTCAAATTA
* *
228632 CCTATAGGAATATTGTTTTT
1 CCTATGGGAATATT-ATTTT
*
228652 CCTATGGGAAAAATTATTTT
1 CCTATGGG-AATATTATTTT
228672 CCTATGGGAAT-TTATTTT
1 CCTATGGGAATATTATTTT
228690 TGAAAGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 2 0.06
20 19 0.58
21 5 0.15
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.47
Consensus pattern (19 bp):
CCTATGGGAATATTATTTT
Found at i:229622 original size:73 final size:73
Alignment explanation
Indices: 229511--229774 Score: 465
Period size: 73 Copynumber: 3.6 Consensus size: 73
229501 GTGTGTCTCT
* * *
229511 GATCTCCAAGTTTTCATTGATTTTAGTATGATCTATGGTCTGTTGTAGGTCTGACCTCTGATGGA
1 GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTAGGTCTGACCCCCGATGGA
*
229576 GTGTCCCC
66 GTGTCACC
*
229584 GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTATGTCTGACCCCCGATGGA
1 GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTAGGTCTGACCCCCGATGGA
229649 GTGTCACC
66 GTGTCACC
229657 GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTAGGTCTGACCCCCGATGGA
1 GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTAGGTCTGACCCCCGATGGA
229722 GTGTCACC
66 GTGTCACC
*
229730 GATCTCCCAAGTTTTCATTGATTTTAGTATGATCTATGGTCTGTT
1 GATCT-CCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTT
229775 TCAGTGTTCC
Statistics
Matches: 183, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
73 145 0.79
74 38 0.21
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (73 bp):
GATCTCCAAGTTTTCATTGATTTTAGTATGACCTATGGTCTGTTGTAGGTCTGACCCCCGATGGA
GTGTCACC
Found at i:251004 original size:52 final size:52
Alignment explanation
Indices: 250903--251016 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 52
250893 TAAACTTTTT
* *
250903 ATCAATTTTTCACTGAATTATATACCATTAATTTGTCACTGAACAATATA-C
1 ATCAATTTTTCACTAAATCATATACCATTAATTTGTCACTGAACAATATAGC
*
250954 AATCAATTTTTTACTAAATCATATACCA-TACATTTGTCACT-ATATC-ATATAGC
1 -ATCAATTTTTCACTAAATCATATACCATTA-ATTTGTCACTGA-A-CAATATAGC
251007 ATCAATTTTT
1 ATCAATTTTT
251017 GTCAGAAGCA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
51 3 0.05
52 50 0.91
53 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (52 bp):
ATCAATTTTTCACTAAATCATATACCATTAATTTGTCACTGAACAATATAGC
Found at i:251014 original size:26 final size:26
Alignment explanation
Indices: 250903--251014 Score: 104
Period size: 26 Copynumber: 4.3 Consensus size: 26
250893 TAAACTTTTT
* *
250903 ATCAATTTTTCACTGAATTATATACC
1 ATCAATTTGTCACTGAATCATATACC
* *
250929 ATTAATTTGTCACTGAA-CAATATACA
1 ATCAATTTGTCACTGAATC-ATATACC
* * *
250955 ATCAATTTTTTACTAAATCATATACC
1 ATCAATTTGTCACTGAATCATATACC
*
250981 AT-ACATTTGTCACT-ATATCATATAGC
1 ATCA-ATTTGTCACTGA-ATCATATACC
251007 ATCAATTT
1 ATCAATTT
251015 TTGTCAGAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.03
26 65 0.94
27 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (26 bp):
ATCAATTTGTCACTGAATCATATACC
Found at i:252843 original size:14 final size:14
Alignment explanation
Indices: 252826--252867 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
252816 TTAGGATGCT
*
252826 GGATACAGGATATA
1 GGATACAGGATAGA
252840 GGATACAGGATAGA
1 GGATACAGGATAGA
* *
252854 GAATACATGATAGA
1 GGATACAGGATAGA
252868 ATAGAAACGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.29, T:0.19
Consensus pattern (14 bp):
GGATACAGGATAGA
Found at i:262683 original size:10 final size:10
Alignment explanation
Indices: 262666--262705 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
262656 CCTACTAAAC
262666 AGAGAACTCT
1 AGAGAACTCT
*
262676 AAAGAACTCT
1 AGAGAACTCT
262686 AGAGAAC-CAT
1 AGAGAACTC-T
262696 AGAGAACTCT
1 AGAGAACTCT
262706 TGGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (10 bp):
AGAGAACTCT
Found at i:263717 original size:10 final size:10
Alignment explanation
Indices: 263704--263745 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
263694 GAAAAAATCC
263704 CTAGAGTTCT
1 CTAGAGTTCT
263714 CTAGAGTTCT
1 CTAGAGTTCT
*
263724 CTAAAGTTCT
1 CTAGAGTTCT
263734 CTAGAGTTCT
1 CTAGAGTTCT
263744 CT
1 CT
263746 GTTTAGTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (10 bp):
CTAGAGTTCT
Found at i:264024 original size:7 final size:7
Alignment explanation
Indices: 264009--264060 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
263999 ATAGAATAGA
*
264009 ATACTGG
1 ATACAGG
264016 ATACAGG
1 ATACAGG
*
264023 ATATAGG
1 ATACAGG
*
264030 ATAGAGG
1 ATACAGG
264037 ATACAGG
1 ATACAGG
264044 ATACTA-G
1 ATAC-AGG
264051 ATACAGG
1 ATACAGG
264058 ATA
1 ATA
264061 GGATAGGGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 1 0.03
7 37 0.95
8 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (7 bp):
ATACAGG
Found at i:264038 original size:21 final size:21
Alignment explanation
Indices: 264009--264060 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
263999 ATAGAATAGA
*
264009 ATACTGGATACAGGATA-TAGG
1 ATACAGGATACAGGATACTA-G
*
264030 ATAGAGGATACAGGATACTAG
1 ATACAGGATACAGGATACTAG
264051 ATACAGGATA
1 ATACAGGATA
264061 GGATAGGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (21 bp):
ATACAGGATACAGGATACTAG
Found at i:265478 original size:20 final size:20
Alignment explanation
Indices: 265429--265479 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
265419 TCAAAAATAA
265429 ATTCCTATAGGAAAATAATTT
1 ATTCCTATAGGAAAATAA-TT
*
265450 TTTCC-ATAGGAAAATCAA-T
1 ATTCCTATAGGAAAAT-AATT
265469 ATTCCTATAGG
1 ATTCCTATAGG
265480 TAATTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 15 0.58
21 6 0.23
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (20 bp):
ATTCCTATAGGAAAATAATT
Found at i:269068 original size:21 final size:20
Alignment explanation
Indices: 269001--269079 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
268991 GCGCCCCATG
*
269001 CACGAGCGCCCCAAATTTTTT
1 CACGAGCGCCCCAAA-TGTTT
*** *
269022 TTGGAGCGCCCCAATTACGTTT
1 CACGAGCGCCCCAA--ATGTTT
269044 CACGAGCGCCCCAAATGTATT
1 CACGAGCGCCCCAAATGT-TT
269065 CACGAGCGCCCCAAA
1 CACGAGCGCCCCAAA
269080 GTAAAATTAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.07
21 28 0.61
22 14 0.30
23 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (20 bp):
CACGAGCGCCCCAAATGTTT
Found at i:269347 original size:141 final size:141
Alignment explanation
Indices: 269087--269568 Score: 810
Period size: 141 Copynumber: 3.4 Consensus size: 141
269077 AAAGTAAAAT
* * * **
269087 TATCATTATACCTTACGTCTTGGAA-AATTTGCACAAGCGCCCC-AAATTGGATTTGCCAATATT
1 TATCATTACACCTTACGTCAT-GAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCAATATT
* *
269150 GTACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAAATGATTTTCCTGATTATGTCTATCTGCA
65 GTACTAAAATTGGGATCGTTTTCACGAGCGCCCC-AAATGATTTTCCTGATTATGTCTTTCTGAA
269215 TAGAATCTTT-TTG
129 TAGAAT-TTTGTTG
* *
269228 TATCATTACACGTTACGTCATGAATAATTTGCCCGAGCGCCCCAAAATTGGATTTTTCAATATTG
1 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCAATATTG
269293 TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAATGATTTTCCTGATTATGTCTTTCTGAATA
66 TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAATGATTTTCCTGATTATGTCTTTCTGAATA
269358 GAATTTTGTTG
131 GAATTTTGTTG
269369 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCAATATTG
1 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCAATATTG
*
269434 TACTAAAATTGGGATCGTTTTCACGATCGCCCCAAATGATTTTCCTGATTATGTCTTTCTGTAA-
66 TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAATGATTTTCCTGATTATGTCTTTCTG-AAT
269498 AGAATTTTGTTG
130 AGAATTTTGTTG
269510 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCA
1 TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCA
269569 TTGGATTATA
Statistics
Matches: 325, Mismatches: 12, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
140 6 0.02
141 265 0.82
142 54 0.17
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (141 bp):
TATCATTACACCTTACGTCATGAATAATTTGCACGAGCGCCCCAAAATTGGATTTTTCAATATTG
TACTAAAATTGGGATCGTTTTCACGAGCGCCCCAAATGATTTTCCTGATTATGTCTTTCTGAATA
GAATTTTGTTG
Found at i:270031 original size:14 final size:15
Alignment explanation
Indices: 270012--270040 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
270002 AATAAATATC
270012 ATACATC-TATAAAT
1 ATACATCATATAAAT
270026 ATACATCATATAAAT
1 ATACATCATATAAAT
270041 GAAACACTGA
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:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACATCATATAAAT
Found at i:273119 original size:105 final size:105
Alignment explanation
Indices: 272950--273492 Score: 980
Period size: 105 Copynumber: 5.2 Consensus size: 105
272940 GTAAGTAAAC
* *
272950 GACGGCGTTTTTGTGGCACTGGCTGGGAGACTGTTTCCTGGGTTAATCGGCGAGTCACAGATGGT
1 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
273015 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
66 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
* * *
273055 GACGGCGTTTTAGTGGCACTGGCTGGGAGACGGTTTCCTGGGTAAATCGGCGAGGCACATATGGT
1 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
273120 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
66 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
*
273160 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACATATGGT
1 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
* *
273225 GACAAGGCAGGAACGGGCGGTGTAGCATTTGTGTAGGCGT
66 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
*
273265 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTATCCTGGGTTAATCGGCGAGGCACAGATGGT
1 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
273330 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
66 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
* *
273370 GACGGCG-TTTTGTGGCACTGGCTGGGAGACGGTATCCTGGGTTAATCGGCAAGGCACAGATGGT
1 GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
273434 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
66 GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
273474 GACGGCGTTTTTGTGGCAC
1 GACGGCGTTTTTGTGGCAC
273493 AAAAACAAAA
Statistics
Matches: 423, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
104 103 0.24
105 320 0.76
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (105 bp):
GACGGCGTTTTTGTGGCACTGGCTGGGAGACGGTTTCCTGGGTTAATCGGCGAGGCACAGATGGT
GACAAGGCAGGAACGGGCGGTGAAGCATCTGTGTAGGCGT
Found at i:274684 original size:66 final size:66
Alignment explanation
Indices: 274526--274718 Score: 325
Period size: 68 Copynumber: 2.9 Consensus size: 66
274516 TTTCATCATG
*
274526 AAAAAAAAAACATTTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCC
1 AAAAAAAAAA-AATTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCC
274591 AT
65 AT
*
274593 AAAATAAAAAAAATTACGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAA-GATT
1 AAAA-AAAAAAAATT-GGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGA-T
274657 CCAT
63 CCAT
274661 AAAAAAAAAAAATTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAA
1 AAAAAAAAAAAATTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAA
274719 ACAACATTTG
Statistics
Matches: 120, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
66 43 0.36
67 19 0.16
68 58 0.48
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.19
Consensus pattern (66 bp):
AAAAAAAAAAAATTGGGGCGCTCGTGACATACACGTGAAAAAAATTAATCATAAAAAAGGATCCA
T
Found at i:275847 original size:20 final size:22
Alignment explanation
Indices: 275822--275865 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
275812 AATAGCGGGT
275822 TAAATAAAAAATCT-TC-TAAA
1 TAAATAAAAAATCTATCATAAA
*
275842 TAAATATAAAATCTATCATAAA
1 TAAATAAAAAATCTATCATAAA
275864 TA
1 TA
275866 CATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAAAAAATCTATCATAAA
Found at i:279345 original size:44 final size:43
Alignment explanation
Indices: 279283--279455 Score: 186
Period size: 44 Copynumber: 3.9 Consensus size: 43
279273 AAAAATGTGT
*
279283 TTTAATTTTGATATTCTTCTCATTAGCATATTCAGCAAAAGTATG
1 TTTATTTTTG-TATTCTTCTCATTAGCATATTCAGCAAAA-TATG
* *
279328 TTTATTTTTGTATTCTTCTCATTATCATATATTAAGC-AAATATG
1 TTTATTTTTGTATTCTTCTCATTAGC--ATATTCAGCAAAATATG
* * * *
279372 TTTTAATCTTTGTATTCTTCTCATTAACATATTGAGCAAAAATATC
1 -TTT-ATTTTTGTATTCTTCTCATTAGCATATTCAGC-AAAATATG
* * *
279418 TTAATTTTTGCATTCTTCTCTTTAGCATATTCAGCAAA
1 TTTATTTTTGTATTCTTCTCATTAGCATATTCAGCAAA
279456 GATGACGGCC
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 3 0.03
44 54 0.50
45 17 0.16
46 35 0.32
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.47
Consensus pattern (43 bp):
TTTATTTTTGTATTCTTCTCATTAGCATATTCAGCAAAATATG
Found at i:279433 original size:90 final size:90
Alignment explanation
Indices: 279275--279447 Score: 249
Period size: 90 Copynumber: 1.9 Consensus size: 90
279265 TTTTTTAAAA
* * * * * *
279275 AAATGTGTTTTAATTTTGATATTCTTCTCATTAGCATATTCAGCAAAAGTATGTTTATTTTTGTA
1 AAATATGTTTTAATTTTGATATTCTTCTCATTAACATATTCAGCAAAAATATCTTAATTTTTGCA
*
279340 TTCTTCTCATTATCATATATTAAGC
66 TTCTTCTCATTAGCATATATTAAGC
*
279365 AAATATGTTTTAATCTTTG-TATTCTTCTCATTAACATATTGAGCAAAAATATCTTAATTTTTGC
1 AAATATGTTTTAAT-TTTGATATTCTTCTCATTAACATATTCAGCAAAAATATCTTAATTTTTGC
*
279429 ATTCTTCTCTTTAGCATAT
65 ATTCTTCTCATTAGCATAT
279448 TCAGCAAAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 69 0.95
91 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (90 bp):
AAATATGTTTTAATTTTGATATTCTTCTCATTAACATATTCAGCAAAAATATCTTAATTTTTGCA
TTCTTCTCATTAGCATATATTAAGC
Found at i:279849 original size:21 final size:21
Alignment explanation
Indices: 279820--279926 Score: 115
Period size: 21 Copynumber: 5.1 Consensus size: 21
279810 GCTACACGCT
* * *
279820 CGCTAAACGGTTCACAAGAAA
1 CGCTGAACGGTTTACACGAAA
*
279841 CGCTGAACGGTTTACAGGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
279862 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* *
279883 CGCTAAACGATTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
*
279904 CGCTGAACGGTTTACACCAAA
1 CGCTGAACGGTTTACACGAAA
279925 CG
1 CG
279927 ATTCTCGCAC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:281648 original size:21 final size:22
Alignment explanation
Indices: 281597--281658 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
281587 ACGGTTCTCG
*
281597 CACGCTTTGCTCGAAACGATTTA
1 CACGCTTTGCCCGAAACGA-TTA
*
281620 CACGCTTTGCCCGAAACG-TTG
1 CACGCTTTGCCCGAAACGATTA
*
281641 CGCGCTTTGCCCGAAACG
1 CACGCTTTGCCCGAAACG
281659 CTAAACGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.53
23 17 0.47
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (22 bp):
CACGCTTTGCCCGAAACGATTA
Found at i:281676 original size:21 final size:21
Alignment explanation
Indices: 281652--281742 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
281642 GCGCTTTGCC
281652 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
* ** * *
281673 CGAAATGCTTCACGATTCACA
1 CGAAACGCTAAACGGTTTACA
281694 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
281715 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
281736 CGAAACG
1 CGAAACG
281743 TTTTTCGCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:286562 original size:26 final size:26
Alignment explanation
Indices: 286533--286647 Score: 106
Period size: 26 Copynumber: 4.4 Consensus size: 26
286523 TAAACTTTTT
*
286533 ATCAATTTTTCACTGAATCATTTACC
1 ATCAATTTTTCACTGAATCATATACC
* *
286559 ATCAATTTGTCACTGAA-CTATATACA
1 ATCAATTTTTCACTGAATC-ATATACC
* * *
286585 ATCATTTTTTTTACTGAATCATTTACC
1 ATCA-ATTTTTCACTGAATCATATACC
* * * * *
286612 ATAAATTTGTCACTGTATCATAAAAC
1 ATCAATTTTTCACTGAATCATATACC
286638 ATCAATTTTT
1 ATCAATTTTT
286648 GTCAGAAGCA
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
25 1 0.01
26 48 0.71
27 18 0.26
28 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (26 bp):
ATCAATTTTTCACTGAATCATATACC
Found at i:286647 original size:53 final size:53
Alignment explanation
Indices: 286533--286647 Score: 146
Period size: 53 Copynumber: 2.2 Consensus size: 53
286523 TAAACTTTTT
* *
286533 ATCAA-TTTTTCACTGAATCATTTACCATCAATTTGTCACTGAACTATATACA
1 ATCAATTTTTTCACTGAATCATTTACCATAAATTTGTCACTGAACTATAAACA
* * *
286585 ATCATTTTTTTTACTGAATCATTTACCATAAATTTGTCACTGTA-TCATAAA-A
1 ATCAATTTTTTCACTGAATCATTTACCATAAATTTGTCACTGAACT-ATAAACA
286637 CATCAATTTTT
1 -ATCAATTTTT
286648 GTCAGAAGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
52 6 0.11
53 48 0.89
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (53 bp):
ATCAATTTTTTCACTGAATCATTTACCATAAATTTGTCACTGAACTATAAACA
Found at i:294378 original size:21 final size:20
Alignment explanation
Indices: 294354--294415 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
294344 CGATAAACCT
294354 GATAGGAGTAACGCACGATAG
1 GATAGGA-TAACGCACGATAG
*
294375 GATAGGATTAACGCACAATAG
1 GATAGGA-TAACGCACGATAG
* *
294396 GACAGTATACACGCACGATA
1 GATAGGATA-ACGCACGATA
294416 CAAAAGGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (20 bp):
GATAGGATAACGCACGATAG
Found at i:296078 original size:44 final size:43
Alignment explanation
Indices: 296000--296181 Score: 152
Period size: 44 Copynumber: 4.1 Consensus size: 43
295990 TTGATTTTTA
* *
296000 AACAAAATGTGTTTTAATTTTGATATTCTTCTCATTAGCATATTC
1 AACAAAA-GTATTTTATTTTTG-TATTCTTCTCATTAGCATATTC
* * *
296045 AACAAAAGTATGTTTATTTTTGTATTTTTCTCATCA-TATATT-
1 AACAAAAGTAT-TTTATTTTTGTATTCTTCTCATTAGCATATTC
* * * * * *
296087 AAGCAAATGTGTTTTAATTTCTGTATTCTCCTCATTAACATATTG
1 AA-CAAAAGTATTTT-ATTTTTGTATTCTTCTCATTAGCATATTC
* * * *
296132 AGCAAAAATATCTTAATTTTTGCATTCTTCTCATTAGCATATTC
1 AACAAAAGTAT-TTTATTTTTGTATTCTTCTCATTAGCATATTC
*
296176 AGCAAA
1 AACAAA
296182 GATGACAGCC
Statistics
Matches: 109, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
42 5 0.05
43 29 0.27
44 56 0.51
45 19 0.17
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (43 bp):
AACAAAAGTATTTTATTTTTGTATTCTTCTCATTAGCATATTC
Found at i:296102 original size:87 final size:87
Alignment explanation
Indices: 296004--296165 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
295994 TTTTTAAACA
* * * * * *
296004 AAATGTGTTTTAATTT-TGATATTCTTCTCATTAGCATATTCAACAAAAGTATGTTTATTTTTGT
1 AAATGTGTTTTAATTTCTG-TATTCTCCTCATTAACATATTCAACAAAAATATCTTAATTTTTGC
*
296068 ATTTTTCTCATCATATATTAAGC
65 ATTCTTCTCATCATATATTAAGC
* *
296091 AAATGTGTTTTAATTTCTGTATTCTCCTCATTAACATATTGAGCAAAAATATCTTAATTTTTGCA
1 AAATGTGTTTTAATTTCTGTATTCTCCTCATTAACATATTCAACAAAAATATCTTAATTTTTGCA
296156 TTCTTCTCAT
66 TTCTTCTCAT
296166 TAGCATATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 63 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (87 bp):
AAATGTGTTTTAATTTCTGTATTCTCCTCATTAACATATTCAACAAAAATATCTTAATTTTTGCA
TTCTTCTCATCATATATTAAGC
Found at i:296569 original size:21 final size:21
Alignment explanation
Indices: 296545--296630 Score: 109
Period size: 21 Copynumber: 4.1 Consensus size: 21
296535 GTTACACGCT
* *
296545 CGCTAAACGGTTCACAAGAAA
1 CGCTAAACGGTTTACACGAAA
*
296566 CGCTGAACGGTTTACACGAAA
1 CGCTAAACGGTTTACACGAAA
*
296587 CGCTAAACGATTTACACGAAA
1 CGCTAAACGGTTTACACGAAA
* * *
296608 CGCTGAACGGTTAACACCAAA
1 CGCTAAACGGTTTACACGAAA
296629 CG
1 CG
296631 ATTCTCGCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (21 bp):
CGCTAAACGGTTTACACGAAA
Found at i:296594 original size:42 final size:42
Alignment explanation
Indices: 296545--296630 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
296535 GTTACACGCT
* * *
296545 CGCTAAACGGTTCACAAGAAACGCTGAACGGTTTACACGAAA
1 CGCTAAACGATTCACAAGAAACGCTGAACGGTTAACACCAAA
* *
296587 CGCTAAACGATTTACACGAAACGCTGAACGGTTAACACCAAA
1 CGCTAAACGATTCACAAGAAACGCTGAACGGTTAACACCAAA
296629 CG
1 CG
296631 ATTCTCGCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (42 bp):
CGCTAAACGATTCACAAGAAACGCTGAACGGTTAACACCAAA
Found at i:298376 original size:21 final size:21
Alignment explanation
Indices: 298352--298418 Score: 125
Period size: 21 Copynumber: 3.2 Consensus size: 21
298342 GCGCTTTGCC
298352 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
*
298373 CGAAACGCTAAGCGGTTTACA
1 CGAAACGCTAAACGGTTTACA
298394 CGAAACGCTAAACGGTTTACA
1 CGAAACGCTAAACGGTTTACA
298415 CGAA
1 CGAA
298419 CGTTTTTCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (21 bp):
CGAAACGCTAAACGGTTTACA
Found at i:299619 original size:2 final size:2
Alignment explanation
Indices: 299612--299673 Score: 115
Period size: 2 Copynumber: 30.5 Consensus size: 2
299602 TCGTCATAAA
299612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG NAG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG
299655 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
299674 ATACTGGTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 57 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:300016 original size:2 final size:2
Alignment explanation
Indices: 300009--300059 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
299999 CGCTGTAAAA
*
300009 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
300051 TC TC TC TC T
1 TC TC TC TC T
300060 GTACTTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:304423 original size:11 final size:11
Alignment explanation
Indices: 304407--304432 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
304397 ATTTTTAATT
304407 AAACTGGTACA
1 AAACTGGTACA
304418 AAACTGGTACA
1 AAACTGGTACA
304429 AAAC
1 AAAC
304433 AGTGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (11 bp):
AAACTGGTACA
Found at i:308093 original size:19 final size:20
Alignment explanation
Indices: 308069--308113 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
308059 GTAACGATAT
*
308069 CCACGGAGTAACACA-GTGG
1 CCACGGAGTAACACAGGCGG
*
308088 CCACGGAGTTACACAGGCGG
1 CCACGGAGTAACACAGGCGG
308108 CCACGG
1 CCACGG
308114 TGCGACACGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09
Consensus pattern (20 bp):
CCACGGAGTAACACAGGCGG
Found at i:308344 original size:10 final size:10
Alignment explanation
Indices: 308329--308357 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
308319 CAGTAGAAAT
308329 GTACAGTGGG
1 GTACAGTGGG
308339 GTACAGTGGG
1 GTACAGTGGG
308349 GTACAGTGG
1 GTACAGTGG
308358 ATGTCAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.48, T:0.21
Consensus pattern (10 bp):
GTACAGTGGG
Found at i:308365 original size:43 final size:42
Alignment explanation
Indices: 308291--308407 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 42
308281 ACTGGACTCT
* * * *
308291 GTGGTGTACTGTGGGATACAGT-GCTGTTCAGTAGAAATGTACA
1 GTGGGGTACAGTGGGGTACAGTGGATG-TCAGT-GAAATGTACA
308334 GTGGGGTACAGTGGGGTACAGTGGATGTCAGTGAAATGTACA
1 GTGGGGTACAGTGGGGTACAGTGGATGTCAGTGAAATGTACA
* ***
308376 GTGAGGTACAGTCAATGTACAGTGGATGTCAG
1 GTGGGGTACAGT-GGGGTACAGTGGATGTCAG
308408 ACAATGTCAG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 21 0.33
43 40 0.62
44 3 0.05
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.26
Consensus pattern (42 bp):
GTGGGGTACAGTGGGGTACAGTGGATGTCAGTGAAATGTACA
Found at i:308377 original size:22 final size:21
Alignment explanation
Indices: 308349--308407 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
308339 GTACAGTGGG
308349 GTACAGTGGATGTCAGTGAAAT
1 GTACAGTGGATGTCAGT-AAAT
* *
308371 GTACAGT-GAGGTACAGTCAAT
1 GTACAGTGGATGT-CAGTAAAT
308392 GTACAGTGGATGTCAG
1 GTACAGTGGATGTCAG
308408 ACAATGTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.31, C:0.12, G:0.32, T:0.25
Consensus pattern (21 bp):
GTACAGTGGATGTCAGTAAAT
Found at i:308412 original size:21 final size:21
Alignment explanation
Indices: 308349--308418 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
308339 GTACAGTGGG
308349 GTACAGTGGATGTCAGTGA-AAT
1 GTACAGTGGATGTCA--GACAAT
* *
308371 GTACAGT-GAGGTACAGTCAAT
1 GTACAGTGGATGT-CAGACAAT
308392 GTACAGTGGATGTCAGACAAT
1 GTACAGTGGATGTCAGACAAT
308413 GT-CAGT
1 GTACAGT
308419 CAATATTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.12
21 23 0.56
22 13 0.32
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (21 bp):
GTACAGTGGATGTCAGACAAT
Found at i:308414 original size:42 final size:41
Alignment explanation
Indices: 308324--308407 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
308314 CTGTTCAGTA
* **
308324 GAAATGTACAGTGGGGTACAGTGGGGTACAGTGGATGTCAG
1 GAAATGTACAGTGAGGTACAGTAAGGTACAGTGGATGTCAG
*
308365 TGAAATGTACAGTGAGGTACAGTCAATGTACAGTGGATGTCAG
1 -GAAATGTACAGTGAGGTACAGT-AAGGTACAGTGGATGTCAG
308408 ACAATGTCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.24
Consensus pattern (41 bp):
GAAATGTACAGTGAGGTACAGTAAGGTACAGTGGATGTCAG
Found at i:317830 original size:8 final size:8
Alignment explanation
Indices: 317774--317833 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
317764 AACTGAAGTG
317774 GGACAGAC
1 GGACAGAC
*
317782 AGACAGAC
1 GGACAGAC
*
317790 GGACGGAC
1 GGACAGAC
* * *
317798 AGTCGGAC
1 GGACAGAC
*
317806 AGACAGAC
1 GGACAGAC
*
317814 GGACGGAC
1 GGACAGAC
317822 GGACAGAC
1 GGACAGAC
317830 GGAC
1 GGAC
317834 GCAGAGGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.35, C:0.25, G:0.38, T:0.02
Consensus pattern (8 bp):
GGACAGAC
Found at i:317834 original size:4 final size:4
Alignment explanation
Indices: 317787--317834 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
317777 CAGACAGACA
* * * * *
317787 GACG GACG GACA GTCG GACA GACA GACG GACG GACG GACA GACG GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
317835 CAGAGGAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.42, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:317834 original size:12 final size:12
Alignment explanation
Indices: 317783--317833 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
317773 GGGACAGACA
317783 GACAGACGGACG
1 GACAGACGGACG
* *
317795 GACAGTCGGACA
1 GACAGACGGACG
317807 GACAGACGGACG
1 GACAGACGGACG
* *
317819 GACGGACAGACG
1 GACAGACGGACG
317831 GAC
1 GAC
317834 GCAGAGGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.33, C:0.25, G:0.39, T:0.02
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:335859 original size:21 final size:21
Alignment explanation
Indices: 335834--335883 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
335824 CATGAAGGTA
*
335834 AAATTAAACACAGCATTGATG
1 AAATTAAACACACCATTGATG
* *
335855 AAATTAAACAGACCATTGTTG
1 AAATTAAACACACCATTGATG
*
335876 ATATTAAA
1 AAATTAAA
335884 AAGATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (21 bp):
AAATTAAACACACCATTGATG
Found at i:347358 original size:496 final size:495
Alignment explanation
Indices: 346419--347415 Score: 1949
Period size: 496 Copynumber: 2.0 Consensus size: 495
346409 TTAAGAACTT
*
346419 TGAGACAAATGTAGAAAGTCGGGTTAGCGACTATCAGTTAAGATTGAGTTATTTGATTCAATATT
1 TGAGAAAAATGTAGAAAGTCGGGTTAGCGACTATCAGTTAAGATTGAGTTATTTGATTCAATATT
346484 GTAAAGATGAGGCAAAATCCTCAATTGAGGACTGTGTACTTTTAGAGCCAAAAGAAGGGTATCTT
66 GTAAAGATGAGGCAAAATCCTCAATTGAGGACTGTGTACTTTTAGAGCCAAAAGAAGGGTATCTT
346549 AAAGCAAGAGAAATATTATTCTCACGATATGGCAAGTCACATTTAGTTGCAAGATCATTTATTGA
131 AAAGCAAGAGAAATATTATTCTCACGATATGGCAAGTCACATTTAGTTGCAAGATCATTTATTGA
346614 GAAAATTGTTAATGGCAGTGAAATCAAAGCATCCAATGTCAATGAATTGTCAAAACTTGCTTTAG
196 GAAAATTGTTAATGGCAGTGAAATCAAAGCATCCAATGTCAATGAATTGTCAAAACTTGCTTTAG
346679 AAATGCAAAAGTGTGAAATTACATTGTCACAATTAGGGTTTAAGTCAAATATTGACAACTCGGAC
261 AAATGCAAAAGTGTGAAATTACATTGTCACAATTAGGGTTTAAGTCAAATATTGACAACTCGGAC
346744 AACTTGACACGCATTGTTAGAAGATTACCTACTCATCTGAGGACCAGGTGGGTGGATGTTGCTCA
326 AACTTGACACGCATTGTTAGAAGATTACCTACTCATCTGAGGACCAGGTGGGTGGATGTTGCTCA
346809 CTCAAACACAGAGTCCGGTAGAGAGCCGCGGTTCTCGGATTTGACAAAGTTTGTTGATGAACGGG
391 CTCAAACACAGAGTCCGGTAGAGAGCCGCGGTTCTCGGATTTGACAAAGTTTGTTGATGAACGGG
346874 CAAGAATTTCCTCTTCTATGTTCGGCCTCGACCTTGTACG
456 CAAGAATTTCCTCTTCTATGTTCGGCCTCGACCTTGTACG
346914 TGAGAANAAATGTAGAAAGTCGGGTTAGCGACTATCAGTTAAGATTGAGTTATTTGATTCAATAT
1 TGAGAA-AAATGTAGAAAGTCGGGTTAGCGACTATCAGTTAAGATTGAGTTATTTGATTCAATAT
346979 TGTAAAGATGAGGCAAAATCCTCAATTGAGGACTGTGTACTTTTAGAGCCAAAAGAAGGGTATCT
65 TGTAAAGATGAGGCAAAATCCTCAATTGAGGACTGTGTACTTTTAGAGCCAAAAGAAGGGTATCT
347044 TAAAGCAAGAGAAATATTATTCTCACGATATGGCAAGTCACATTTAGTTGCAAGATCATTTATTG
130 TAAAGCAAGAGAAATATTATTCTCACGATATGGCAAGTCACATTTAGTTGCAAGATCATTTATTG
347109 AGAAAATTGTTAATGGCAGTGAAATCAAAGCATCCAATGTCAATGAATTGTCAAAACTTGCTTTA
195 AGAAAATTGTTAATGGCAGTGAAATCAAAGCATCCAATGTCAATGAATTGTCAAAACTTGCTTTA
*
347174 GAAATGCAAAAGTGTGAAATTACATTGTCACAATTAGGGTTTAAGTCAGATATTGACAACTCGGA
260 GAAATGCAAAAGTGTGAAATTACATTGTCACAATTAGGGTTTAAGTCAAATATTGACAACTCGGA
*
347239 CAACTTGAGACGCATTGTTAGAAGATTACCTACTCATCTGAGGACCAGGTGGGTGGATGTTGCTC
325 CAACTTGACACGCATTGTTAGAAGATTACCTACTCATCTGAGGACCAGGTGGGTGGATGTTGCTC
*
347304 ACTCAATCACAGAGTCCGGTAGAGAGCCGCGGTTCTCGGATTTGACAAAGTTTGTTGATGAACGG
390 ACTCAAACACAGAGTCCGGTAGAGAGCCGCGGTTCTCGGATTTGACAAAGTTTGTTGATGAACGG
347369 GCAAGAATTTCCTCTTCTATGTTCGGCCTCGACCTTGTACG
455 GCAAGAATTTCCTCTTCTATGTTCGGCCTCGACCTTGTACG
347410 TGAGAA
1 TGAGAA
347416 TAACCCAAGG
Statistics
Matches: 497, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
495 5 0.01
496 492 0.99
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (495 bp):
TGAGAAAAATGTAGAAAGTCGGGTTAGCGACTATCAGTTAAGATTGAGTTATTTGATTCAATATT
GTAAAGATGAGGCAAAATCCTCAATTGAGGACTGTGTACTTTTAGAGCCAAAAGAAGGGTATCTT
AAAGCAAGAGAAATATTATTCTCACGATATGGCAAGTCACATTTAGTTGCAAGATCATTTATTGA
GAAAATTGTTAATGGCAGTGAAATCAAAGCATCCAATGTCAATGAATTGTCAAAACTTGCTTTAG
AAATGCAAAAGTGTGAAATTACATTGTCACAATTAGGGTTTAAGTCAAATATTGACAACTCGGAC
AACTTGACACGCATTGTTAGAAGATTACCTACTCATCTGAGGACCAGGTGGGTGGATGTTGCTCA
CTCAAACACAGAGTCCGGTAGAGAGCCGCGGTTCTCGGATTTGACAAAGTTTGTTGATGAACGGG
CAAGAATTTCCTCTTCTATGTTCGGCCTCGACCTTGTACG
Found at i:352696 original size:24 final size:24
Alignment explanation
Indices: 352609--352688 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
352599 TTCACACTGG
*
352609 CCATCACTTGAATTTCCCTCTTTT
1 CCATCACTTGAATTTCCCACTTTT
*
352633 CCATCACTTGAATTTCCCCCTTTT
1 CCATCACTTGAATTTCCCACTTTT
*
352657 CCATCACTTAAATTTCCCACTTTT
1 CCATCACTTGAATTTCCCACTTTT
352681 -CATCACTT
1 CCATCACTT
352689 AGATTTTCTG
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 8 0.15
24 45 0.85
ACGTcount: A:0.20, C:0.35, G:0.03, T:0.42
Consensus pattern (24 bp):
CCATCACTTGAATTTCCCACTTTT
Found at i:380147 original size:22 final size:22
Alignment explanation
Indices: 380097--380147 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
380087 CGTCTCGGCT
* *
380097 TTACTTTGTGTTTACTCAGGAT
1 TTACTTTGGGTTTACTCAGGAA
*
380119 TTACTTTGGGTTTACTCGGGAA
1 TTACTTTGGGTTTACTCAGGAA
*
380141 TTGCTTT
1 TTACTTT
380148 TGGGGTCAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.22, T:0.49
Consensus pattern (22 bp):
TTACTTTGGGTTTACTCAGGAA
Found at i:381006 original size:17 final size:18
Alignment explanation
Indices: 380984--381031 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
380974 TTCTTTATAA
*
380984 ATATCCCATTTGG-TATT
1 ATATCCCATTTGGCTATC
***
381001 ATATCCCAAAGGGCTATC
1 ATATCCCATTTGGCTATC
381019 ATATCCCATTTGG
1 ATATCCCATTTGG
381032 GTGATTGGCA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (18 bp):
ATATCCCATTTGGCTATC
Found at i:381181 original size:4 final size:4
Alignment explanation
Indices: 381172--381234 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
381162 TAACAAAGAT
381172 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
381220 ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA
381235 NNNNNNNNNN
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:384346 original size:21 final size:21
Alignment explanation
Indices: 384333--384404 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
384323 TTGTTTGTAC
* *
384333 TCACTGTCAACTTGTTC-CTGC
1 TCACTGTCAACTTGTTCAGT-A
384354 TCACTGTCAACTTGTTCAGGT-
1 TCACTGTCAACTTGTTCA-GTA
384375 TCACTGTCAACTTGTTCAGTA
1 TCACTGTCAACTTGTTCAGTA
384396 TCACTGTCA
1 TCACTGTCA
384405 TGATGTTCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
23 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (21 bp):
TCACTGTCAACTTGTTCAGTA
Found at i:389908 original size:16 final size:16
Alignment explanation
Indices: 389887--389919 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
389877 AGGACTTTTG
389887 GTCCCCAAGATGTTTA
1 GTCCCCAAGATGTTTA
389903 GTCCCCAAGATGTTTA
1 GTCCCCAAGATGTTTA
389919 G
1 G
389920 GCACCTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (16 bp):
GTCCCCAAGATGTTTA
Found at i:392317 original size:172 final size:171
Alignment explanation
Indices: 392031--392373 Score: 677
Period size: 172 Copynumber: 2.0 Consensus size: 171
392021 AATAATTAAA
392031 AAATAATATATAAATAAAATTATATATACAAGTATATACCTACATGTAACATGCAATATCTTAAT
1 AAATAATATATAAATAAAATTATATATACAAGTATATACCTACATGTAACATGCAATATCTTAAT
392096 ATGGATATAAATATTTTATATCAATTTGTGTAAGATTTGATTATGTACATGTTTATACTAGTCAT
66 ATGGATATAAATATTTTATATCAATTTGTGTAAGATTTGATTATGTACATGTTTATACTAGTCAT
392161 TCACAATTTTAGGGGAGAAGATCGGCGGAAGTGCCTCCACT
131 TCACAATTTTAGGGGAGAAGATCGGCGGAAGTGCCTCCACT
392202 NAAATAATATATAAATAAAATTATATATACAAGTATATACCTACATGTAACATGCAATATCTTAA
1 -AAATAATATATAAATAAAATTATATATACAAGTATATACCTACATGTAACATGCAATATCTTAA
392267 TATGGATATAAATATTTTATATCAATTTGTGTAAGATTTGATTATGTACATGTTTATACTAGTCA
65 TATGGATATAAATATTTTATATCAATTTGTGTAAGATTTGATTATGTACATGTTTATACTAGTCA
392332 TTCACAATTTTAGGGGAGAAGATCGGCGGAAGTGCCTCCACT
130 TTCACAATTTTAGGGGAGAAGATCGGCGGAAGTGCCTCCACT
392374 GATGTCACAG
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 171 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
AAATAATATATAAATAAAATTATATATACAAGTATATACCTACATGTAACATGCAATATCTTAAT
ATGGATATAAATATTTTATATCAATTTGTGTAAGATTTGATTATGTACATGTTTATACTAGTCAT
TCACAATTTTAGGGGAGAAGATCGGCGGAAGTGCCTCCACT
Found at i:411090 original size:21 final size:21
Alignment explanation
Indices: 411066--411117 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
411056 ATGAATATTG
411066 ACATAAATATA-TTGCATGTTA
1 ACATAAATA-ACTTGCATGTTA
*
411087 ACATAAATAACTTGCATGTTC
1 ACATAAATAACTTGCATGTTA
*
411108 ACATACATAA
1 ACATAAATAA
411118 GTCGCATACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (21 bp):
ACATAAATAACTTGCATGTTA
Found at i:411124 original size:21 final size:21
Alignment explanation
Indices: 411066--411124 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
411056 ATGAATATTG
*
411066 ACATAAATATA-TTGCATGTTA
1 ACATAAATA-ACTCGCATGTTA
* *
411087 ACATAAATAACTTGCATGTTC
1 ACATAAATAACTCGCATGTTA
* *
411108 ACATACATAAGTCGCAT
1 ACATAAATAACTCGCAT
411125 ACCAACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (21 bp):
ACATAAATAACTCGCATGTTA
Found at i:414609 original size:2 final size:2
Alignment explanation
Indices: 414602--414639 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
414592 AAAAAGTTCA
414602 CT CT CT 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 CT CT CT
414640 GTTGTATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:415010 original size:12 final size:12
Alignment explanation
Indices: 414984--415025 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
414974 TACTTTACTC
*
414984 ATGTAATG-GCA
1 ATGTAATGTACA
414995 ATGTAATGTACA
1 ATGTAATGTACA
* *
415007 ATGTAGTTTACA
1 ATGTAATGTACA
415019 ATGTAAT
1 ATGTAAT
415026 TCGCCCCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (12 bp):
ATGTAATGTACA
Found at i:419421 original size:16 final size:15
Alignment explanation
Indices: 419385--419421 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
419375 CTGGCGGATG
419385 CTGGAGAAGTCGTAT
1 CTGGAGAAGTCGTAT
419400 CATGGAGAAGTCGTACT
1 C-TGGAGAAGTCGTA-T
419417 CTGGA
1 CTGGA
419422 AATATCATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (15 bp):
CTGGAGAAGTCGTAT
Done.