Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005393.1 Hibiscus syriacus cultivar Beakdansim tig00012360_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102504
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:4919 original size:21 final size:20
Alignment explanation
Indices: 4894--4932 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4884 AATCAAAGTC
*
4894 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
4915 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
4933 TCCTGCAATG
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:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:10745 original size:2 final size:2
Alignment explanation
Indices: 10738--10770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10728 ATATAAATTA
10738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10771 AGGTAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15986 original size:13 final size:13
Alignment explanation
Indices: 15968--15992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15958 TGTGCATAAG
15968 GCAAGTCTTTATT
1 GCAAGTCTTTATT
15981 GCAAGTCTTTAT
1 GCAAGTCTTTAT
15993 GGTATATGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
GCAAGTCTTTATT
Found at i:22631 original size:4 final size:4
Alignment explanation
Indices: 22617--22675 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
22607 GGACCTGTTT
* *
22617 TAAA AAAA TAAA TAAA TAAA TAAA AATAA TAAA T-AA TAATA TAAA TAATA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA TAA-A TAAA TAA-A
22667 TAAAA TAAA
1 T-AAA TAAA
22676 AACTATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 3 0.07
4 30 0.65
5 11 0.24
6 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:22647 original size:21 final size:21
Alignment explanation
Indices: 22617--22675 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 21
22607 GGACCTGTTT
22617 TAAAAA-AATAAATAAATAAA
1 TAAAAATAATAAATAAATAAA
22637 TAAAAATAATAAAT-AAT-AA
1 TAAAAATAATAAATAAATAAA
* *
22656 TATAAATAATATA-AAATAAA
1 TAAAAATAATAAATAAATAAA
22676 AACTATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.47
20 11 0.32
21 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAAATAATAAATAAATAAA
Found at i:22718 original size:16 final size:16
Alignment explanation
Indices: 22691--22728 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
22681 TATAACATAT
22691 ATTATA-TTTTCAAAA
1 ATTATATTTTTCAAAA
22706 ATTATATTTTTCAAAA
1 ATTATATTTTTCAAAA
22722 ATTATAT
1 ATTATAT
22729 ATTATATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATATTTTTCAAAA
Found at i:22804 original size:23 final size:20
Alignment explanation
Indices: 22750--22804 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 20
22740 TTCCAAAAAT
22750 CGTTTTAAAAAACTATATATA
1 CGTTTT-AAAAACTATATATA
* *
22771 TGTTTTCAAAACTATATTATTTA
1 CGTTTTAAAAACTATA-TA--TA
22794 CGTTTTAAAAA
1 CGTTTTAAAAA
22805 ATTGTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 9 0.33
21 7 0.26
23 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (20 bp):
CGTTTTAAAAACTATATATA
Found at i:22834 original size:38 final size:37
Alignment explanation
Indices: 22770--22894 Score: 150
Period size: 37 Copynumber: 3.4 Consensus size: 37
22760 AACTATATAT
22770 ATGTTTTCAAAACTATAT-TATT-TACGTTTTAAAAA
1 ATGTTTTCAAAACTATATATATTATACGTTTTAAAAA
* *
22805 ATTGTTTTTAAAACTATATATATTATACGTTTTCAAAA
1 A-TGTTTTCAAAACTATATATATTATACGTTTTAAAAA
*
22843 ATGTATTTTCAAAACTATATA-A-TATATGTTTTCAAAAA
1 ATG--TTTTCAAAACTATATATATTATACGTTTT-AAAAA
22881 CATGTTTTCAAAAC
1 -ATGTTTTCAAAAC
22895 CACAGTATGT
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
35 1 0.01
36 16 0.21
37 25 0.32
38 18 0.23
39 18 0.23
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (37 bp):
ATGTTTTCAAAACTATATATATTATACGTTTTAAAAA
Found at i:22874 original size:37 final size:37
Alignment explanation
Indices: 22773--23011 Score: 138
Period size: 37 Copynumber: 6.5 Consensus size: 37
22763 TATATATATG
* * * * *
22773 TTTTCAAAACTATATTATTTACGTTTTAAAAAATTGT-
1 TTTTCAAAACTATATAATATATGTTTTCAAAAA-CGTA
* *
22810 TTTT-AAAACTATATATATTATACGTTTTCAAAAATGTA
1 TTTTCAAAACTATATA-A-TATATGTTTTCAAAAACGTA
* *
22848 TTTTCAAAACTATATAATATATGTTTTCAAAAACATG
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
* * *
22885 TTTTCAAAACCACAGT-ATGTA--TTTTCAAAAACCG-A
1 TTTTCAAAACTATA-TAATATATGTTTTCAAAAA-CGTA
* * * *
22920 TTTTTAAAA-AACTAT-ATATATGCTTTCAAAAA--AA
1 TTTTCAAAACTA-TATAATATATGTTTTCAAAAACGTA
* * * * **
22954 ATCTGAAAACTATATATTATATGTTTTCAAAAAAATA
1 TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
*
22991 TTTTCAAAAACTATATTATAT
1 TTTTC-AAAACTATATAATAT
23012 TATTATATAT
Statistics
Matches: 158, Mismatches: 29, Indels: 29
0.73 0.13 0.13
Matches are distributed among these distances:
34 16 0.10
35 35 0.22
36 20 0.13
37 43 0.27
38 33 0.21
39 11 0.07
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATGTTTTCAAAAACGTA
Found at i:25998 original size:81 final size:81
Alignment explanation
Indices: 25862--26688 Score: 1305
Period size: 81 Copynumber: 10.2 Consensus size: 81
25852 ACAATTTTAA
** * *
25862 CCATTATTCTTTTACTCAAAAGTATCTAACCGTTCATCTAACTGGCATAATTGGTACCTTCCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
25927 CAATTGCATAGTTAGG
66 CAATTGCACAGTTAGG
* * * *
25943 CCATTATTCTGTTACTCAACGGTATTTAACCGTTCATCTAACTGGTATAACTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
26008 CAATTGCACAGTTAGA
66 CAATTGCACAGTTAGG
* * * *
26024 CCATTATTCTTTTACTCAACGATATTTAATCGTTCATCTAACTGGCATAATTAGTACTTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
26089 TAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * *
26105 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAATTGTCATAATTGGTATCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26170 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* *
26186 CCATTATTCTTTTACTCAACGTTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
*
26251 CAATTGCACAATTAGG
66 CAATTGCACAGTTAGG
*
26267 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26332 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
** * * * * *
26348 CCATTATT-TTTTACTCAACGGTATTTAATTGTTCATTTAACTAGCATAATCGATACATTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26412 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * ** *
26428 CTATTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGATATAATTTGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26493 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
*
26509 CCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26574 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * *
26590 CCATTATTCTTTTACTCGACGATATTTAACCGTTCATCTAACTAGCATAATTGGTACCTTTCTAC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
26655 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
26671 CCATTATTCTTTTACTCA
1 CCATTATTCTTTTACTCA
26689 TAGGTCCAGT
Statistics
Matches: 683, Mismatches: 62, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
80 73 0.11
81 610 0.89
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGGTACCTTTCTAC
CAATTGCACAGTTAGG
Found at i:27355 original size:20 final size:20
Alignment explanation
Indices: 27330--27402 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 20
27320 CGATATTGTC
27330 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCTTACCA
*
27350 TGGTATCGATACTACCCTT-CTA
1 TGGTATCG--A-TACCCTTACCA
* *
27372 TGGTACCGATACCCCTA-C-
1 TGGTATCGATACCCTTACCA
27390 TGGTATCGATACC
1 TGGTATCGATACC
27403 AAAATTAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.27
19 6 0.14
20 9 0.20
22 10 0.23
23 7 0.16
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
TGGTATCGATACCCTTACCA
Found at i:27381 original size:22 final size:23
Alignment explanation
Indices: 27339--27383 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
27329 CTGGTATCGA
*
27339 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTACCGATAC
*
27362 TACCCTT-CTATGGTACCGATAC
1 TACCCTTACCATGGTACCGATAC
27384 CCCTACTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:27399 original size:94 final size:95
Alignment explanation
Indices: 27275--27460 Score: 259
Period size: 94 Copynumber: 2.0 Consensus size: 95
27265 TACTTCTATA
* * *
27275 CTATAGTACCGATATCCCTTCGGGTATCGATACCAAAACTAGGTTCGATATTGTC-TGGTATCGA
1 CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATTCGATATT-TCTTGGTATCGA
27339 TA-CCCTTACCATGGTATCGATACTACCCTT
65 TACCCCTTACCATGGTATCGATACTACCCTT
* * * * *
27369 CTATGGTACCGATACCCCTACTGGTATCGATACCAAAATTAGATTTGATGTTTCTTGGTATCGAT
1 CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATTCGATATTTCTTGGTATCGAT
* *
27434 ACCCCTTATCATGGTATTGATACTACC
66 ACCCCTTACCATGGTATCGATACTACC
27461 TCATCTGTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 2 0.03
94 55 0.69
95 23 0.29
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (95 bp):
CTATAGTACCGATACCCCTACGGGTATCGATACCAAAACTAGATTCGATATTTCTTGGTATCGAT
ACCCCTTACCATGGTATCGATACTACCCTT
Found at i:39803 original size:38 final size:38
Alignment explanation
Indices: 39749--39986 Score: 182
Period size: 37 Copynumber: 6.4 Consensus size: 38
39739 AATATAAATA
39749 AAAACTATAT-TATATACGTTTTCAAAAATAGT-TTTT-
1 AAAACTATATATATATACGTTTTCAAAAAT-GTGTTTTC
*
39785 AAAATTATATATATTATACGTTTTCAAAAATGTGTTTTC
1 AAAACTATATATA-TATACGTTTTCAAAAATGTGTTTTC
* * *
39824 AAAACTATATA-ATATATGTTTTCGAAAACGTGTTTTC
1 AAAACTATATATATATACGTTTTCAAAAATGTGTTTTC
* *
39861 AAAACCATAT-TATATA--TTTTCAAAAACTGAT-TTTTA
1 AAAACTATATATATATACGTTTTCAAAAA-TG-TGTTTTC
* * *
39897 AAAACTATATAGTATAT--GCTTTCAAAAAACGT-TTTCTA
1 AAAACTATATA-TATATACGTTTTC-AAAAATGTGTTT-TC
* * *
39935 AAAACTATATAGCATAT--GTTTTCAAAAA-ATATTTTC
1 AAAACTATATA-TATATACGTTTTCAAAAATGTGTTTTC
39971 AAAAACTATAT-TATAT
1 -AAAACTATATATATAT
39987 TATTATATAT
Statistics
Matches: 171, Mismatches: 17, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
35 13 0.08
36 25 0.15
37 63 0.37
38 55 0.32
39 15 0.09
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (38 bp):
AAAACTATATATATATACGTTTTCAAAAATGTGTTTTC
Found at i:39845 original size:37 final size:36
Alignment explanation
Indices: 39749--39986 Score: 196
Period size: 38 Copynumber: 6.4 Consensus size: 36
39739 AATATAAATA
* *
39749 AAAACTATATTATATACGTTTTCAAAAATAGTTTTT-
1 AAAACTATATAATATATGTTTTCAAAAAT-GTTTTTC
* *
39785 AAAATTATATATATTATACGTTTTCAAAAATGTGTTTTC
1 AAAACTATATA-A-TATATGTTTTCAAAAATGT-TTTTC
* *
39824 AAAACTATATAATATATGTTTTCGAAAACGTGTTTTC
1 AAAACTATATAATATATGTTTTCAAAAATGT-TTTTC
* * *
39861 AAAACCATAT--TATATATTTTCAAAAACTGATTTTTA
1 AAAACTATATAATATATGTTTTCAAAAA-TG-TTTTTC
* * * *
39897 AAAACTATATAGTATATGCTTTCAAAAAACGTTTTCTA
1 AAAACTATATAATATATGTTTTC-AAAAATGTTTT-TC
** *
39935 AAAACTATATAGCATATGTTTTCAAAAAAT-ATTTTC
1 AAAACTATATAATATATGTTTTC-AAAAATGTTTTTC
*
39971 AAAAACTATATTATAT
1 -AAAACTATATAATAT
39987 TATTATATAT
Statistics
Matches: 168, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
35 14 0.08
36 24 0.14
37 54 0.32
38 61 0.36
39 15 0.09
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.41
Consensus pattern (36 bp):
AAAACTATATAATATATGTTTTCAAAAATGTTTTTC
Found at i:41072 original size:19 final size:19
Alignment explanation
Indices: 41045--41094 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
41035 TGTAAAGGTT
41045 AATTCTTAAATT-ATTATTTA
1 AATT-TTAAATTGATT-TTTA
41065 AATTTTAAATTGATTTTTA
1 AATTTTAAATTGATTTTTA
* *
41084 AGTTTAAAATT
1 AATTTTAAATT
41095 TTGTAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTTTAAATTGATTTTTA
Found at i:41994 original size:22 final size:22
Alignment explanation
Indices: 41966--42014 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
41956 GACGATACGG
* *
41966 GGACGGTCGGGGTACGTATCGT
1 GGACGGTCGAGGTACGTACCGT
41988 GGACGGTCGAGGTACGTACCGT
1 GGACGGTCGAGGTACGTACCGT
42010 GGACG
1 GGACG
42015 AGCCACTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18
Consensus pattern (22 bp):
GGACGGTCGAGGTACGTACCGT
Found at i:43162 original size:75 final size:75
Alignment explanation
Indices: 43074--43230 Score: 172
Period size: 75 Copynumber: 2.1 Consensus size: 75
43064 CAGTCTTAAT
* * ** * *
43074 ATTTGATACTTTAATATTATGGTTTGA-TTATGGATTTTATTACTCTAGAGTTAATATTGTGATT
1 ATTTGACACTTTAATATTATGATTT-ATTTATAAATTTTATTACTCTAAACTTAATATTGTGATT
43138 TGAATCTTGAG
65 TGAATCTTGAG
* * ** * *
43149 ATTTGACATTTTAATATTGTGATTTATTTATAAATTTTATTGTTTTAAACTTAATATTGTGGTTT
1 ATTTGACACTTTAATATTATGATTTATTTATAAATTTTATTACTCTAAACTTAATATTGTGATTT
* *
43214 GAGTCTTGAT
66 GAATCTTGAG
43224 ATTTGAC
1 ATTTGAC
43231 TTTATTTATA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 1 0.01
75 66 0.99
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.52
Consensus pattern (75 bp):
ATTTGACACTTTAATATTATGATTTATTTATAAATTTTATTACTCTAAACTTAATATTGTGATTT
GAATCTTGAG
Found at i:43246 original size:19 final size:20
Alignment explanation
Indices: 43222--43262 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43212 TTGAGTCTTG
*
43222 ATATTTGAC-TTTATTTATA
1 ATATTTGACATCTATTTATA
*
43241 ATATTTTACATCTATTTATA
1 ATATTTGACATCTATTTATA
43261 AT
1 AT
43263 TTTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTTGACATCTATTTATA
Found at i:43274 original size:18 final size:19
Alignment explanation
Indices: 43232--43275 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
43222 ATATTTGACT
* *
43232 TTATTTATAATATTTTACA
1 TTATTTATAATATTTAAAA
43251 TCTATTTATAAT-TTTAAAA
1 T-TATTTATAATATTTAAAA
43270 TTATTT
1 TTATTT
43276 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 10 0.45
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTATAATATTTAAAA
Found at i:43354 original size:12 final size:12
Alignment explanation
Indices: 43337--43361 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43327 TTTCCTGTCC
43337 CCGTCCCCGTAT
1 CCGTCCCCGTAT
43349 CCGTCCCCGTAT
1 CCGTCCCCGTAT
43361 C
1 C
43362 GGTGCAACAT
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:0.08, C:0.52, G:0.16, T:0.24
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:44683 original size:16 final size:17
Alignment explanation
Indices: 44644--44692 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 17
44634 GTTGCCTTGA
*
44644 GATGATGACTGTGTGGT
1 GATGATGGCTGTGTGGT
**
44661 GGCGATGGCT-TGTGGT
1 GATGATGGCTGTGTGGT
44677 GATGATGG-TG-GTGGT
1 GATGATGGCTGTGTGGT
44692 G
1 G
44693 GTGGTGGTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.12, C:0.06, G:0.49, T:0.33
Consensus pattern (17 bp):
GATGATGGCTGTGTGGT
Found at i:44688 original size:3 final size:3
Alignment explanation
Indices: 44672--44705 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
44662 GCGATGGCTT
* *
44672 GTG GTG ATG ATG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
44706 CGGCGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.06, C:0.00, G:0.62, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:45380 original size:3 final size:3
Alignment explanation
Indices: 45372--45462 Score: 94
Period size: 3 Copynumber: 29.7 Consensus size: 3
45362 TTCATTTAAA
* * *
45372 TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT TACT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * *
45421 AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
45463 CAAACGGGCC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.03
3 63 0.86
4 8 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:45439 original size:19 final size:19
Alignment explanation
Indices: 45370--45456 Score: 78
Period size: 19 Copynumber: 4.9 Consensus size: 19
45360 TTTTCATTTA
45370 AATATTATTATT-ATTA-T
1 AATATTATTATTAATTACT
* *
45387 --TATTATAATT-ATTATT
1 AATATTATTATTAATTACT
* *
45403 ATTATAATTA-TAATTACT
1 AATATTATTATTAATTACT
* *
45421 AATTTTATTATTTATTACT
1 AATATTATTATTAATTACT
45440 AATATTATTATTAATTA
1 AATATTATTATTAATTA
45457 TTATTACAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
15 13 0.24
16 1 0.02
17 1 0.02
18 18 0.33
19 22 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTATTATTAATTACT
Found at i:46786 original size:13 final size:13
Alignment explanation
Indices: 46758--46792 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
46748 TTTTATTATA
46758 TTATTAAATA-TT
1 TTATTAAATATTT
46770 TTATTAAATATTT
1 TTATTAAATATTT
46783 TTA-TAAATAT
1 TTATTAAATAT
46793 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:47490 original size:15 final size:13
Alignment explanation
Indices: 47481--47525 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
47471 TTTTTATTAC
47481 TTATTATT-TTTT
1 TTATTATTATTTT
*
47493 ATATTATTATTTT
1 TTATTATTATTTT
47506 TTATT-TTATTTAT
1 TTATTATTATTT-T
47519 TTATTAT
1 TTATTAT
47526 ATTCAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 13 0.46
13 14 0.50
14 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:47502 original size:18 final size:17
Alignment explanation
Indices: 47470--47520 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
47460 TTCTTTCAAA
47470 TTTTTTATTACTTATTAT
1 TTTTTTATTACTTATT-T
47488 TTTTTATATTA-TTATTT
1 TTTTT-TATTACTTATTT
* *
47505 TTTATT-TTATTTATTT
1 TTTTTTATTACTTATTT
47521 ATTATATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 5 0.17
18 10 0.33
19 5 0.17
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTATTACTTATTT
Found at i:47525 original size:7 final size:7
Alignment explanation
Indices: 47473--47525 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
47463 TTTCAAATTT
47473 TTTATTA
1 TTTATTA
*
47480 CTTATTA
1 TTTATTA
*
47487 TTTTTTA
1 TTTATTA
47494 TATTATTA
1 T-TTATTA
*
47502 TTTTTTA
1 TTTATTA
47509 TTTTATTTA
1 -TTTA-TTA
47518 TTTATTA
1 TTTATTA
47525 T
1 T
47526 ATTCAAGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.57
8 13 0.35
9 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTA
Found at i:49030 original size:8 final size:7
Alignment explanation
Indices: 49006--49047 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
48996 TTTTCATACA
49006 TGCA-TT
1 TGCATTT
49012 TGCATTT
1 TGCATTT
49019 TGCATCTT
1 TGCAT-TT
49027 TGCATTT
1 TGCATTT
* *
49034 TTCATTG
1 TGCATTT
49041 TGCATTT
1 TGCATTT
49048 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:49030 original size:15 final size:14
Alignment explanation
Indices: 49006--49047 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
48996 TTTTCATACA
49006 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
49019 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
49034 TTCATTGTGCATTT
1 TGCATTTTGCATTT
49048 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:49136 original size:26 final size:26
Alignment explanation
Indices: 49107--49165 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
49097 CATTCACATA
*
49107 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
49133 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
49159 TTTACAT
1 TTTACAT
49166 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:51125 original size:15 final size:15
Alignment explanation
Indices: 51105--51157 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
51095 TCCAGCAAAG
51105 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
*
51120 AAAGAAGAAGAAAAA
1 AAAGAAGAAGAAGAA
* *
51135 AAAAAAGAAAAAGGAA
1 AAAGAAGAAGAA-GAA
51151 AATAGAA
1 AA-AGAA
51158 TAAAGATGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 24 0.77
16 4 0.13
17 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAGAAGAAGAAGAA
Found at i:51147 original size:6 final size:6
Alignment explanation
Indices: 51101--51163 Score: 63
Period size: 6 Copynumber: 9.8 Consensus size: 6
51091 CTCATCCAGC
* * *
51101 AAAGAA AGAAGAA GAAGAA AAAGAA GAAGAA AAAAAA AAAGAA AAAGGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA
51151 AATAGAA TAAAGA
1 AA-AGAA -AAAGA
51164 TGGGTGATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
6 28 0.60
7 16 0.34
8 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:53484 original size:83 final size:83
Alignment explanation
Indices: 53383--53730 Score: 581
Period size: 83 Copynumber: 4.2 Consensus size: 83
53373 AATGGAACAA
* *
53383 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAATC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
53448 AATCATTGAATTTGGAAG
66 AATCATTGAATTTAGAAG
*
53466 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
53531 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * *
53549 ATGAATTTGTTCATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
53614 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* * *
53632 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
*
53696 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTAGAAG
53715 ATGAATTTGCTCATAG
1 ATGAATTTGCTCATAG
53731 TAGAAATAAG
Statistics
Matches: 252, Mismatches: 12, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
82 4 0.02
83 248 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTAGAAG
Found at i:55059 original size:74 final size:74
Alignment explanation
Indices: 54907--55068 Score: 202
Period size: 74 Copynumber: 2.2 Consensus size: 74
54897 AAGCAAATAT
* * *
54907 TGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
54972 GCAAAATGC
66 GCAAAATGC
* * ** *
54981 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
55046 TAGC-CAATG-
64 CAGCAAAATGC
55055 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
55069 GGCCTATATC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
74 64 0.84
75 6 0.08
76 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Found at i:56386 original size:22 final size:22
Alignment explanation
Indices: 56360--56411 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
56350 TACACTCTTC
* *
56360 AAAGATGATAGATTCTCTTTTA
1 AAAGATGACAAATTCTCTTTTA
*
56382 AAAGATGACAAATTCTCTTTTC
1 AAAGATGACAAATTCTCTTTTA
56404 AAAGATGA
1 AAAGATGA
56412 AAACTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
AAAGATGACAAATTCTCTTTTA
Found at i:56987 original size:112 final size:112
Alignment explanation
Indices: 56815--58293 Score: 1203
Period size: 113 Copynumber: 13.0 Consensus size: 112
56805 CAAAGATATA
* * * * ** *
56815 AATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAA-CTCATCTGAAG
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAAG
* *
56879 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCC-CTG
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTC-G
* * *** *
56927 AATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAACCTATCTGAAGA
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCTATCTGAAGA
* *
56992 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
*
57039 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCTATCTGAAGA
* *
57104 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
*
57151 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACATATCTGAAGA
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCTATCTGAAGA
* * *
57216 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * *
57263 AATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAATAA-CTCATCTGAAG
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAAG
* * * *
57327 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCA
65 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * *
57376 AATCCATCA-TTCGATGGATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAA-CTCATCTGAA
1 AATTCATCACTT-GATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAA
* ** **
57439 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
64 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * * * *
57489 AATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCTATCTGAAGA
* * ******
57554 GGAAGAAGAAATTCATAATGAGAAGAACTCAT-TTGAA----GAAGAAG
66 GGAAGAAGAAGTTCATAATGAGAAGAACT--TGTTCAACCTTTTCCTCG
** * * * * ** * * * * *
57598 AACTTGTTCAACTT-TTTGCTTAA-ATTCATCACCCG-G-TGGATCAGCAGTGTCAGTTAG-A-G
1 AA-TTCATC-ACTTGATGGATTAACATT--T--CCAGAGAAAGTTCA-TAATG--AG-AAGAACC
** * * * * * *** **
57657 T-TCAT-AATGA-GAAGAACTCA-TCTGA-AGAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
56 TATC-TGAA-GAGGAAGAA-GAAGT-TCATA-ATG-AGAAGAACTT-GT--T--CAACCTTTTCC
57717 TC-
110 TCG
* * * * *** *
57719 AACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGA
1 AA----TT-CAT-CA--CTTGA--TG--G-ATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
* * *
57784 ACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
53 ACCTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
*
57844 AATTCATCACTTGATGGATTAACACTTCCAGAGAAAGTTCATAATGAGAAGAA-CTCATCTGAAG
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAAG
* * * *
57908 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
65 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * *
57957 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAA-CTCATCTGAAG
1 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAAG
* * * *
58021 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * *
58070 AATCCATCA-TTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA-CTCATCTGAA
1 AATTCATCACTT-GATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCT-ATCTGAA
* * *
58133 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
64 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
* * * * *
58183 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCTTCATCTA
1 AATTCATCACTTGATGGATTAACATTTCCAGAG-AAAGTTCATAATGAGAAGAAC-C-T-ATCTG
* * *
58247 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
62 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
58294 GCATAATTCT
Statistics
Matches: 1141, Mismatches: 159, Indels: 130
0.80 0.11 0.09
Matches are distributed among these distances:
109 4 0.00
110 8 0.01
111 10 0.01
112 453 0.40
113 508 0.45
114 18 0.02
115 5 0.00
116 50 0.04
117 3 0.00
118 3 0.00
119 1 0.00
120 2 0.00
121 4 0.00
124 10 0.01
125 4 0.00
126 1 0.00
127 2 0.00
128 3 0.00
129 12 0.01
130 13 0.01
131 16 0.01
132 6 0.01
133 3 0.00
134 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACCTATCTGAAGA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTCCTCG
Found at i:57416 original size:113 final size:111
Alignment explanation
Indices: 56815--57580 Score: 998
Period size: 112 Copynumber: 6.8 Consensus size: 111
56805 CAAAGATATA
* * ** *
56815 AATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
56880 GGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-CCCTG
65 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC-G
* * * *** *
56927 AATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAAC-CTATCTGAAG
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTC-ATCTGAAG
* *
56991 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
64 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* *
57039 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
57104 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
65 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
*
57151 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACAT-ATCTGAAG
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAAC-TCATCTGAAG
* * *
57215 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
64 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* * * * *
57263 AATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAATAACTCATCTGAAGA
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-
* * *
57328 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCA
64 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* * *
57376 AATCCATCATTCGATGGATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATT-GATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-
* * * **
57441 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
64 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
* * * *
57489 AATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATTCATCA-TTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
57554 GGAAGAAGAAATTCATAATGAGAAGAA
65 GGAAGAAGAAGTTCATAATGAGAAGAA
57581 CTCATTTGAA
Statistics
Matches: 594, Mismatches: 52, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
111 2 0.00
112 392 0.66
113 198 0.33
114 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (111 bp):
AATTCATCATTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAG
GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCG
Found at i:57575 original size:39 final size:39
Alignment explanation
Indices: 57518--57599 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
57508 CAGCTTTTCC
* *
57518 AGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
*
57557 AGAAGAAA-TTCATAATGAGAAGAACTCATTTGAAGAAGA
1 AGAA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
57596 AGAA
1 AGAA
57600 CTTGTTCAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 36 0.92
40 3 0.08
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (39 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:57599 original size:131 final size:131
Alignment explanation
Indices: 57462--57711 Score: 385
Period size: 131 Copynumber: 1.9 Consensus size: 131
57452 GTTCATAATG
* *** * *
57462 AGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAGC-TTTTCCAGAAAAAG
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGATGGATCAGCAGTGT-CAGAAAAAG
*
57526 TTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAA
65 TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAA
57591 GA
130 GA
* ** *
57593 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGTCAGTTAGAGT
1 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGATGGATCAGCAGTGTCAGAAAAAGT
57658 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA
66 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA
57712 TTTGTTCAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
131 105 0.98
132 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (131 bp):
AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGATGGATCAGCAGTGTCAGAAAAAGT
TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAAG
A
Found at i:58115 original size:581 final size:582
Alignment explanation
Indices: 57074--58162 Score: 1824
Period size: 581 Copynumber: 1.9 Consensus size: 582
57064 TTCCAGAGAA
* * *
57074 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *
57139 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
*
57204 CATATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCA
131 CATATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCA
* * *
57269 TCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAATAACTCATCTGAAGAAGGAAG
196 TCACTTGATGGATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
57334 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCAGC
261 AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCAAC
* *
57399 ATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
326 ATTGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
* * * * *
57464 AAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTC
391 AAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAAAAAGTTC
*
57529 ATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAAGA
456 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAAGA
57593 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGTCAGTTAG
521 AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGTCAGTTAG
*
57655 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *** *
57720 ACCTTTTCC-CTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
*
57784 ACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTC
130 ACATATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTC
57849 ATCACTTGATGGATTAACACTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
195 ATCACTTGATGGATTAACA-TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** * *
57913 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCA
259 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCA
* *
57978 ACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
324 ACATTGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* *
58043 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAGAAAGT
389 AGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAAAAAGT
*
58108 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
454 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
58163 TTTGTTCAAC
Statistics
Matches: 470, Mismatches: 35, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
580 1 0.00
581 440 0.94
582 29 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (582 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CATATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCA
TCACTTGATGGATTAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCAAC
ATTGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAG
AAGAACTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCTTTTCCAGAAAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAAGA
AGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGTCAGTTAG
Found at i:58190 original size:226 final size:226
Alignment explanation
Indices: 56815--58295 Score: 1774
Period size: 224 Copynumber: 6.5 Consensus size: 226
56805 CAAAGATATA
* *
56815 AATTCATCATTTGATGGATCATCATTACCAGTTAG-A-GTTCATAATGAGAAGAACTCATCTGAA
1 AATTCATCATTTGATGGATCAACATTGCCAG--AGAAGGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
56878 G-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-CCCTGAATTCATTACTT-G
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC-AAATTCATCA-TTCG
* * *** * *
56940 ATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGAAC-CTATCTGAAG-AGGAAGAAGAAG
127 ATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTC-ATCTGAAGAAGGAAGAAGAAA
* * *
57003 TTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCG
191 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * * *
57039 AATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-
1 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
57103 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTT-GATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTCGATG
* * *
57167 GATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAACAT-ATCTGAAG-AGGAAGAAGAAGTTC
130 GATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAATTC
* *
57230 ATAATGAGAAGAACTTGTTTAACCTTTTGCTTG
194 ATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * *
57263 AATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAATAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
57328 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCATTCGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGG
* *
57393 ATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
* * * *
57458 AATGAGAAGAACTTGTTCAACTTTTTGTTTA
196 AATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * * * *
57489 AATTCATCATTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAG-
1 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* *
57553 AGGAAGAAGAAATTCATAATGAGAAGAACTCATTTGAAGAAGAAGAACTTGTTCAACTTTTTGCT
66 AGGAAGAAGAAGTTC---AT-------A---A--T---G-AGAAGAACTTGTTCAACCTTTTGCT
* ** * * ** *
57618 TAAATTCATCACCCGGTGGATCAGCAGTGT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
112 CAAATTCATCATTCGATGGATCAGCA-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
57682 AG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTG
176 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
* * * * *** * *
57732 AATTCATTACTTGATGAATTATTTTTTCCAGAGGAA-GTTCATAATGAGAAGAACTTATCTGAAG
1 AATTCATCATTTGATGGATCAACATTGCCAGA-GAAGGTTCATAATGAGAAGAACTCATCTGAAG
* *
57796 -AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTT-GAT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCA-TTCGAT
* * *
57859 GGATTAACACTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
129 GGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTC
57924 ATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
194 ATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
57957 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
58022 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGG
* *
58087 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
58152 AATGAGAAGAATTTGTTCAACCTTTTGCTTG
196 AATGAGAAGAATTTGTTCAACCTTTTGCTTG
* *
58183 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCTTCATCTA
1 AATTCATCATTTGATGGATCAACATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTG
* * *
58247 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGC
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
58296 ATAATTCTAT
Statistics
Matches: 1104, Mismatches: 113, Indels: 75
0.85 0.09 0.06
Matches are distributed among these distances:
222 2 0.00
223 2 0.00
224 337 0.31
225 218 0.20
226 295 0.27
228 4 0.00
229 50 0.05
230 1 0.00
233 1 0.00
235 1 0.00
238 1 0.00
240 3 0.00
243 110 0.10
244 77 0.07
245 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (226 bp):
AATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCATTCGATGG
ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCTTG
Found at i:58694 original size:3 final size:3
Alignment explanation
Indices: 58686--58785 Score: 103
Period size: 3 Copynumber: 32.7 Consensus size: 3
58676 TTCATTTAAA
* * *
58686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAA AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
58734 TAT AAT TACT AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT
58781 TAT TA
1 TAT TA
58786 CAAACGGGCC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 70 0.88
4 8 0.10
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:60103 original size:13 final size:13
Alignment explanation
Indices: 60075--60109 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
60065 TTTTATTATA
60075 TTATTAAATA-TT
1 TTATTAAATATTT
60087 TTATTAAATATTT
1 TTATTAAATATTT
60100 TTA-TAAATAT
1 TTATTAAATAT
60110 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:61847 original size:3 final size:3
Alignment explanation
Indices: 61839--61888 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
61829 ACATTAGTTA
*
61839 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TA- TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61885 TAT T
1 TAT T
61889 TTTTATTTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:74860 original size:9 final size:8
Alignment explanation
Indices: 74843--74872 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
74833 AGAAAAATGG
74843 GAAAAAAA
1 GAAAAAAA
74851 GAAAACAAA
1 GAAAA-AAA
74860 GAAAAAAA
1 GAAAAAAA
74868 GAAAA
1 GAAAA
74873 TGAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:77846 original size:13 final size:15
Alignment explanation
Indices: 77806--77835 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
77796 AATTTTTTTA
*
77806 ATATATTTAATATAT
1 ATATATATAATATAT
77821 ATATATATAATATAT
1 ATATATATAATATAT
77836 TATCTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATATAATATAT
Found at i:80043 original size:177 final size:178
Alignment explanation
Indices: 79744--80100 Score: 565
Period size: 177 Copynumber: 2.0 Consensus size: 178
79734 TGTCGTTAAA
*
79744 TATTAATGGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
1 TATTAATAGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
*
79809 ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTTAATCATCAATCCGA
66 ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCCGA
* *
79874 TGGTGATATATATCACTATTTGATTAGA-TTTTTTAATATTGTTTATT
131 TGGTGACATATATCACTATGTGATTAGATTTTTTTAATATTGTTTATT
* *
79921 TATTAATAGAGGAGATGATGTAGCAA-TTAATAAAATTTATATACTTACACATTTAGTCCTCATT
1 TATTAATAGAGGAGAAGATGTAG-AAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATT
* * * *
79985 ACTTACACATTTTATTAATTTGGTCCTAACTTTTATTTAATTCAATAAATTGAATCATCAATCTG
65 AATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCCG
* * * *
80050 ATGGTGACATGTATCACTGTGTGATTGGATTTTTTTAATATTTTTTATT
130 ATGGTGACATATATCACTATGTGATTAGATTTTTTTAATATTGTTTATT
80099 TA
1 TA
80101 ATAAATTTTC
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
177 142 0.87
178 22 0.13
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (178 bp):
TATTAATAGAGGAGAAGATGTAGAAGTTAATAAAATTTATATAATTACACATTTAGTCCTCATTA
ATTACACATTTTATTAATTTGGTCCTAACATGTATTTAATTCAATAAATTGAATCATCAATCCGA
TGGTGACATATATCACTATGTGATTAGATTTTTTTAATATTGTTTATT
Found at i:80363 original size:2 final size:2
Alignment explanation
Indices: 80350--80385 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
80340 AATAGTATGA
*
80350 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80386 CATAATTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:81485 original size:15 final size:15
Alignment explanation
Indices: 81462--81495 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
81452 CCCTAAAAAC
*
81462 TAATATTTTATAATT
1 TAATATTTTATAAAT
*
81477 TAATGTTTTATAAAT
1 TAATATTTTATAAAT
81492 TAAT
1 TAAT
81496 TTAATGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TAATATTTTATAAAT
Found at i:89788 original size:60 final size:60
Alignment explanation
Indices: 89667--89791 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
89657 AGATTCCTTA
* **
89667 ACTATAGGACATTACTTTGTTAAGTCTATCAACTATTAAAAGATACAATATGACCTTCTG
1 ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGATACAATATGACCAGCTG
* * * * * *
89727 ACTATATGACATTACTTTGTTAAATTTTTCGACTATTAAAAGTTATCAA-ATGATCAGCTG
1 ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGATA-CAATATGACCAGCTG
89787 ACTAT
1 ACTAT
89792 TTTATATTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 52 0.95
61 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (60 bp):
ACTATAGGACATTACTTTGTTAAATCTATCAACTATTAAAAGATACAATATGACCAGCTG
Found at i:91250 original size:26 final size:26
Alignment explanation
Indices: 91215--91264 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
91205 GAATTTTTTT
91215 AAAAAAATTCAAAGGAACTCGTCACA
1 AAAAAAATTCAAAGGAACTCGTCACA
91241 AAAAAAATTCAAAGGAACTCGTCA
1 AAAAAAATTCAAAGGAACTCGTCA
91265 TGTCGGTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (26 bp):
AAAAAAATTCAAAGGAACTCGTCACA
Found at i:93068 original size:15 final size:14
Alignment explanation
Indices: 93045--93081 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
93035 TGTTTTACTT
93045 TCATTTTATTTTGG
1 TCATTTTATTTTGG
*
93059 TCACTTTTATTTTTG
1 TCA-TTTTATTTTGG
93074 TCATTTTA
1 TCATTTTA
93082 CTATGATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.65
Consensus pattern (14 bp):
TCATTTTATTTTGG
Found at i:94052 original size:139 final size:138
Alignment explanation
Indices: 93888--94186 Score: 406
Period size: 139 Copynumber: 2.1 Consensus size: 138
93878 TTTTAAGTTT
* *
93888 AGTCTAATAGTTGATTAAAATTGACTAGGTTAATAATTAAAGCTTCC-AT-TTTAGGTTTAATTT
1 AGTC-AATAATTGATTAAAATTGACTAGGTTAATAATT--AG-ATCCTATGTTTAGGTTTAATTT
* * * * *
93951 CAAACTTAGTCTTTAAATTTAGGGGAATTTTTAATTTGTTCCTCACTTTTGCTCGATGTTTCA-T
62 CAAACTTACTCCTTAAATTTAGGGGAATTTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATT
94015 TTTAATTATTCG
127 TTTAATTATTCG
* *
94027 AGTCAAATGATTGATTAAAATTGACTAGGTTAATGATTAGATCCTATGGTTTAGGTTTAATTTCA
1 AGTC-AATAATTGATTAAAATTGACTAGGTTAATAATTAGATCCTAT-GTTTAGGTTTAATTTCA
* *
94092 AACTTACTCCTTAAATTTAGGGGAATTTTTAATTTGGTACTCGCTTTTGCTTGATGTTCCATTTT
64 AACTTACTCCTTAAATTTAGGGGAATTTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATTTT
94157 TAATTATTCG
129 TAATTATTCG
* *
94167 ATTCAATAATTTATTAAAAT
1 AGTCAATAATTGATTAAAAT
94187 GGTTTGGATT
Statistics
Matches: 141, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
136 3 0.02
137 4 0.03
139 118 0.84
140 16 0.11
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (138 bp):
AGTCAATAATTGATTAAAATTGACTAGGTTAATAATTAGATCCTATGTTTAGGTTTAATTTCAAA
CTTACTCCTTAAATTTAGGGGAATTTTTAATTTGGTACTCACTTTTGCTCGATGTTCCATTTTTA
ATTATTCG
Found at i:96800 original size:33 final size:33
Alignment explanation
Indices: 96761--96826 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
96751 TAGTACGGAT
96761 GGTGGACACGACCTTATGTGTCATACGGATTAG
1 GGTGGACACGACCTTATGTGTCATACGGATTAG
96794 GGTGGACACGACCTTATGTGTCATACGGATTAG
1 GGTGGACACGACCTTATGTGTCATACGGATTAG
96827 CACTATGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (33 bp):
GGTGGACACGACCTTATGTGTCATACGGATTAG
Found at i:98506 original size:18 final size:18
Alignment explanation
Indices: 98480--98516 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
98470 ATGTTTAATG
98480 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
98498 AAAAGGATACCAATTGTT
1 AAAAAGATACCAATTGTT
98516 A
1 A
98517 CCAATGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:98527 original size:28 final size:28
Alignment explanation
Indices: 98487--98549 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
98477 ATGAAAAAGA
* * *
98487 TACCAATTGTTAAAAGGATACCAATTGT
1 TACCAATGGTTAAAAAGAAACCAATTGT
98515 TACCAATGGTTAAAAAGAAACCAATTGT
1 TACCAATGGTTAAAAAGAAACCAATTGT
98543 TACCAAT
1 TACCAAT
98550 TGTTGGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (28 bp):
TACCAATGGTTAAAAAGAAACCAATTGT
Done.