Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004920.1 Hibiscus syriacus cultivar Beakdansim tig00011079_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: 1590857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 4 of 7
Found at i:748511 original size:23 final size:23
Alignment explanation
Indices: 748485--748575 Score: 78
Period size: 23 Copynumber: 3.8 Consensus size: 23
748475 GAATTTTAAA
*
748485 TATAATTAGATTTTTAATTAATT
1 TATAATTATATTTTTAATTAATT
** *
748508 TATAATTATAAATTTAA-TATTT
1 TATAATTATATTTTTAATTAATT
748530 TATAATTTATTATTTTTAAATTAATT
1 TATAA-TTA-TATTTTT-AATTAATT
748556 TAATAA-TATTCATTTTTAAT
1 T-ATAATTA-T-ATTTTTAAT
748576 CGTGCTCATC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
22 9 0.16
23 17 0.31
24 5 0.09
25 9 0.16
26 11 0.20
27 4 0.07
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
TATAATTATATTTTTAATTAATT
Found at i:748538 original size:15 final size:15
Alignment explanation
Indices: 748513--748554 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
748503 TAATTTATAA
748513 TTATAAATTTAATATT
1 TTAT-AATTTAATATT
*
748529 TTATAATTTATTATT
1 TTATAATTTAATATT
*
748544 TT-TAAATTAAT
1 TTATAATTTAAT
748555 TTAATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATAATTTAATATT
Found at i:751001 original size:26 final size:26
Alignment explanation
Indices: 750957--751010 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
750947 TGTGTCTCAC
*
750957 TAAAAATTTTATTATTTTTGTCATTT
1 TAAAAATTTTATTATTTTTGTAATTT
* *
750983 TAAATATTTTA-TATTTTTTTTAATTT
1 TAAAAATTTTATTA-TTTTTGTAATTT
751009 TA
1 TA
751011 TGAATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TAAAAATTTTATTATTTTTGTAATTT
Found at i:755999 original size:29 final size:30
Alignment explanation
Indices: 755944--756029 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 30
755934 CCCGAAGGAC
* *
755944 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
755973 CTATCCAGAGGTC-TAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
756002 CTGTCC--AGGCCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
756030 ACTGTCCATA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 4 0.08
28 21 0.41
29 26 0.51
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:756977 original size:21 final size:21
Alignment explanation
Indices: 756953--756997 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
756943 TTTTGTTCGT
* *
756953 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
756974 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
756995 TTG
1 TTG
756998 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:757040 original size:22 final size:20
Alignment explanation
Indices: 757003--757042 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
756993 CCTTGCCCAG
*
757003 AAATCATATTTTTAGCTCGA
1 AAATCATATTTCTAGCTCGA
757023 AAATCATTCATTTCTAGCTC
1 AAATCA-T-ATTTCTAGCTC
757043 AACACTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (20 bp):
AAATCATATTTCTAGCTCGA
Found at i:758371 original size:28 final size:27
Alignment explanation
Indices: 758332--758393 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
758322 AGACGACAAT
*
758332 AAATT-TATAAAATCTT-AAAGATAAATA
1 AAATTATAAAAAAT-TTAAAAGATAAA-A
758359 AAATTATAAAAAATTTAAAAGATAAAA
1 AAATTATAAAAAATTTAAAAGATAAAA
758386 ACAATTAT
1 A-AATTAT
758394 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (27 bp):
AAATTATAAAAAATTTAAAAGATAAAA
Found at i:762580 original size:29 final size:29
Alignment explanation
Indices: 762533--762589 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
762523 CAAGCATAGG
*
762533 TCGCCAAGTACTCCAGGCGACCTTGTAGA
1 TCGCCAAGCACTCCAGGCGACCTTGTAGA
**
762562 TCGCCAAGCACTCTGGGCGACCTTGTAG
1 TCGCCAAGCACTCCAGGCGACCTTGTAG
762590 GTCACCATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (29 bp):
TCGCCAAGCACTCCAGGCGACCTTGTAGA
Found at i:763181 original size:7 final size:7
Alignment explanation
Indices: 763169--763199 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
763159 AATTAGTTTG
763169 TTAGGGT
1 TTAGGGT
763176 TTAGGGT
1 TTAGGGT
763183 TTAGGGT
1 TTAGGGT
*
763190 TTAAGGT
1 TTAGGGT
763197 TTA
1 TTA
763200 ATTTTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:763235 original size:21 final size:21
Alignment explanation
Indices: 763209--763252 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
763199 AATTTTGTTA
763209 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
763230 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
763251 AT
1 AT
763253 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:763260 original size:28 final size:28
Alignment explanation
Indices: 763229--763282 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
763219 TAGTATAAAT
*
763229 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
763257 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
763283 ATTAGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:763646 original size:14 final size:14
Alignment explanation
Indices: 763627--763653 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
763617 GTAATTTATT
763627 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
763641 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
763654 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:763740 original size:17 final size:17
Alignment explanation
Indices: 763718--763756 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
763708 ATCTATTCCC
763718 GTTTAAAAAAATATT-GT
1 GTTTAAAAAAAT-TTAGT
*
763735 GTTTAAAAATATTTAGT
1 GTTTAAAAAAATTTAGT
763752 GTTTA
1 GTTTA
763757 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (17 bp):
GTTTAAAAAAATTTAGT
Found at i:763777 original size:83 final size:83
Alignment explanation
Indices: 763675--763837 Score: 272
Period size: 83 Copynumber: 2.0 Consensus size: 83
763665 AATTAGTTAG
* *
763675 TTTATATTAGAGTACATAAAATTAATTTGTTTAATCTATTCCCGTTTAAAAAAATATTGTGTTTA
1 TTTATATTAGAGTACATAAAATTAATTTGTTTAATCTATTACAGTTTAAAAAAATATTGTGTTTA
763740 AAAATATTTAGTGTTTAT
66 AAAATATTTAGTGTTTAT
* * * *
763758 TTTATATTAGATTATATAAAATTAATTTGTTTAATTTATTATAGTTTAAAAAAATATTGTGTTTA
1 TTTATATTAGAGTACATAAAATTAATTTGTTTAATCTATTACAGTTTAAAAAAATATTGTGTTTA
763823 AAAATATTTAGTGTT
66 AAAATATTTAGTGTT
763838 GTTTTAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (83 bp):
TTTATATTAGAGTACATAAAATTAATTTGTTTAATCTATTACAGTTTAAAAAAATATTGTGTTTA
AAAATATTTAGTGTTTAT
Found at i:765677 original size:14 final size:14
Alignment explanation
Indices: 765627--765704 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 14
765617 TTTAAATATT
* *
765627 TAATGATTTAATAC
1 TAATGATTTATTAA
*
765641 TAATGATTTAGTAA
1 TAATGATTTATTAA
765655 T--T-A-TTATTAA
1 TAATGATTTATTAA
765665 TAATGATTTATTATTAA
1 TAATGA--T-TTATTAA
*
765682 TAATGATTTATTAT
1 TAATGATTTATTAA
765696 TAAT-ATTTA
1 TAATGATTTA
765705 ATTATTTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 7 0.13
11 1 0.02
12 2 0.04
13 6 0.11
14 23 0.43
15 1 0.02
17 13 0.25
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (14 bp):
TAATGATTTATTAA
Found at i:765677 original size:17 final size:17
Alignment explanation
Indices: 765655--765700 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
765645 GATTTAGTAA
765655 TTATTATTAATAATGAT
1 TTATTATTAATAATGAT
765672 TTATTATTAATAATGAT
1 TTATTATTAATAATGAT
765689 TTATTATTAATA
1 TTATTATTAATA
765701 TTTAATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTATTATTAATAATGAT
Found at i:765701 original size:76 final size:70
Alignment explanation
Indices: 765609--765763 Score: 184
Period size: 76 Copynumber: 2.1 Consensus size: 70
765599 TAGAATTTAT
* * * *
765609 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTAGTAATTATTATTAATAATGATTT
1 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAATAATGA--A
765674 ATTATTAA
64 ATTA-TAA
* * * *
765682 TAATGATTTATTATTAATATTTAATTATTTGATACTAATTATTTACTAATGATTACTAGTAATGA
1 TAATGATTT-TTA--AATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAATAATGA
765747 AATTATAA
63 AATTATAA
765755 TAATGATTT
1 TAATGATTT
765764 GATACTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
73 21 0.30
74 7 0.10
76 43 0.61
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (70 bp):
TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAATAATGAAAT
TATAA
Found at i:765708 original size:14 final size:14
Alignment explanation
Indices: 765658--765710 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
765648 TTAGTAATTA
*
765658 TTATTAATAATGAT
1 TTATTATTAATGAT
765672 TTATTATTAATAATGAT
1 TTATTA-T--TAATGAT
765689 TTATTATTAAT-AT
1 TTATTATTAATGAT
765702 TTAATTATT
1 TT-ATTATT
765711 TGATACTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 4 0.12
14 16 0.47
16 1 0.03
17 13 0.38
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTATTATTAATGAT
Found at i:765709 original size:17 final size:17
Alignment explanation
Indices: 765653--765710 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
765643 ATGATTTAGT
765653 AATTATTATTAATAATG
1 AATTATTATTAATAATG
*
765670 ATTTATTATTAATAATG
1 AATTATTATTAATAATG
* * *
765687 ATTTATTATTAATATTT
1 AATTATTATTAATAATG
765704 AATTATT
1 AATTATT
765711 TGATACTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTATTATTAATAATG
Found at i:768058 original size:11 final size:11
Alignment explanation
Indices: 768044--768082 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
768034 TTAAACTATT
768044 CTTTAATATAA
1 CTTTAATATAA
*
768055 CTTTAACTAT-T
1 CTTTAA-TATAA
768066 CTTTAATATAA
1 CTTTAATATAA
768077 CTTTAA
1 CTTTAA
768083 CTAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:768063 original size:30 final size:30
Alignment explanation
Indices: 768029--768115 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
768019 TTCCTTAAAC
768029 AACTATTAAACTATTCTTT-A-AT-A---T
1 AACTATTAAACTATTCTTTAATATAACTTT
768053 AACT-TT-AACTATTCTTTAATATAACTTT
1 AACTATTAAACTATTCTTTAATATAACTTT
* *
768081 AACTAATAAACTATTCTTTAATATAACTTA
1 AACTATTAAACTATTCTTTAATATAACTTT
768111 AACTA
1 AACTA
768116 AAAAACTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 6 0.11
25 1 0.02
28 5 0.09
29 1 0.02
30 26 0.49
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.44
Consensus pattern (30 bp):
AACTATTAAACTATTCTTTAATATAACTTT
Found at i:768065 original size:22 final size:22
Alignment explanation
Indices: 768037--768085 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
768027 ACAACTATTA
768037 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
768059 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
768081 AACTA
1 AACTA
768086 ATAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:768102 original size:15 final size:16
Alignment explanation
Indices: 768058--768108 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
768048 AATATAACTT
768058 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
768074 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
768089 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
768104 TAACT
1 TAACT
768109 TAAACTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:768116 original size:30 final size:30
Alignment explanation
Indices: 768059--768123 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
768049 ATATAACTTT
* *
768059 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAACTTAAACTAAAA
768089 AACTATTCTTTAATATAACTTAAACTAAAA
1 AACTATTCTTTAATATAACTTAAACTAAAA
768119 AACTA
1 AACTA
768124 ATTAACTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (30 bp):
AACTATTCTTTAATATAACTTAAACTAAAA
Found at i:768130 original size:52 final size:52
Alignment explanation
Indices: 768029--768130 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
768019 TTCCTTAAAC
* * *****
768029 AACTATTAAACTATTCTTTAATATAACTTTAACTATTCTTTAATATAACTTT
1 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
768081 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAAACTAAT-TAACT
1 AACTAATAAACTATTCTTTAATATAACTTAAACT-AAAAACTAATATAACT
768131 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 37 0.88
53 5 0.12
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (52 bp):
AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
Found at i:768234 original size:41 final size:38
Alignment explanation
Indices: 768179--768292 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 38
768169 CTTAACTATT
*
768179 TAACTAAC--ACAAACTAATTAAATACTTTTTTATATA
1 TAACTAACAAACAAACTAATTAAATATTTTTTTATATA
* * *
768215 TAACTAACGACTAACAAACTAACTAATTATTTTTATTAATATG
1 TAACTAAC-A--AACAAACTAATTAAATATTTTT-TT-ATATA
* *
768258 TAACTATCAAACATACTAATTAAATATTTTTTTAT
1 TAACTAACAAACAAACTAATTAAATATTTTTTTAT
768293 TTCTATATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
36 8 0.13
38 2 0.03
39 2 0.03
40 19 0.30
41 18 0.29
42 3 0.05
43 11 0.17
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (38 bp):
TAACTAACAAACAAACTAATTAAATATTTTTTTATATA
Found at i:768546 original size:27 final size:29
Alignment explanation
Indices: 768511--768575 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
768501 AAAATATAAC
*
768511 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
768538 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
768566 TTAATTATTT
1 TTAAATATTT
768576 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:768761 original size:26 final size:25
Alignment explanation
Indices: 768698--768761 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
768688 GATGTTGTGC
* *
768698 TCTCCCTTTCTTCTTCTTCCTCGTT
1 TCTCCCTTTCTTCTCCTTCCTAGTT
** *
768723 TCTCTGTTATCTTCTCCTTTCCTATTT
1 TCTCCCTT-TCTTCTCC-TTCCTAGTT
768750 TCTCCCTTTCTT
1 TCTCCCTTTCTT
768762 TCTCTCTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 6 0.20
26 11 0.37
27 13 0.43
ACGTcount: A:0.03, C:0.36, G:0.03, T:0.58
Consensus pattern (25 bp):
TCTCCCTTTCTTCTCCTTCCTAGTT
Found at i:768887 original size:11 final size:11
Alignment explanation
Indices: 768871--768906 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
768861 TTCACGGGCT
768871 GCAATAATGCA
1 GCAATAATGCA
*
768882 GCAATAAGTGCT
1 GCAATAA-TGCA
768894 GCAATAATGCA
1 GCAATAATGCA
768905 GC
1 GC
768907 TGAATTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (11 bp):
GCAATAATGCA
Found at i:769498 original size:49 final size:49
Alignment explanation
Indices: 769419--769562 Score: 234
Period size: 49 Copynumber: 2.9 Consensus size: 49
769409 TTATTATTAT
*
769419 CAAGGGCGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTCATC
1 CAAGGACGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTCATC
* * ** *
769468 TAGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCTTCATC
1 CAAGGACGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTCATC
769517 CAAGGACGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTC
1 CAAGGACGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTC
769563 CACAAGTGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 86 1.00
ACGTcount: A:0.18, C:0.37, G:0.29, T:0.16
Consensus pattern (49 bp):
CAAGGACGGACCTCCATGGTGCCCGGGGTATCCCAGGCAACCCCTCATC
Found at i:780811 original size:18 final size:16
Alignment explanation
Indices: 780767--780814 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
780757 TTTTTTAAGA
780767 AAATATATAAATATTTT
1 AAATATAT-AATATTTT
*
780784 ACAATTTATAATATTATT
1 A-AATATATAATATT-TT
780802 CAAATATATAATA
1 -AAATATATAATA
780815 AGGACAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 18 0.69
19 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATAATATTTT
Found at i:781852 original size:24 final size:23
Alignment explanation
Indices: 781798--781875 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
781788 TTCATGTTTA
* * *
781798 TTTATTTAGTGTTCGCGAACGTG
1 TTTATTTAATATTCACGAACGTG
**
781821 TTCGTTTATATATTCACGAACGTG
1 TTTATTTA-ATATTCACGAACGTG
* * *
781845 TTTATTTAGTATTCACAAACATG
1 TTTATTTAATATTCACGAACGTG
781868 TTTATTTA
1 TTTATTTA
781876 GTGTTTGTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (23 bp):
TTTATTTAATATTCACGAACGTG
Found at i:781869 original size:23 final size:23
Alignment explanation
Indices: 781831--781877 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
781821 TTCGTTTATA
* *
781831 TATTCACGAACGTGTTTATTTAG
1 TATTCACAAACATGTTTATTTAG
781854 TATTCACAAACATGTTTATTTAG
1 TATTCACAAACATGTTTATTTAG
781877 T
1 T
781878 GTTTGTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (23 bp):
TATTCACAAACATGTTTATTTAG
Found at i:784064 original size:33 final size:32
Alignment explanation
Indices: 783989--784065 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 32
783979 ATGTATTTAA
*
783989 ATTTATTAA-ACATATTAAAAATAACATAAAT
1 ATTTATTAATATATATTAAAAATAACATAAAT
** * *
784020 ATTTAAAAATATATAATTAAATATAA-ATCAACT
1 ATTTATTAATATAT-ATTAAAAATAACAT-AAAT
784053 ATTTATTAATATA
1 ATTTATTAATATA
784066 AATAATTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
31 7 0.19
32 5 0.14
33 24 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (32 bp):
ATTTATTAATATATATTAAAAATAACATAAAT
Found at i:784619 original size:20 final size:19
Alignment explanation
Indices: 784593--784636 Score: 79
Period size: 20 Copynumber: 2.3 Consensus size: 19
784583 TAGTTTACTT
784593 TTTTATTTAAACATTAATA
1 TTTTATTTAAACATTAATA
784612 TATTTATTTAAACATTAATA
1 T-TTTATTTAAACATTAATA
784632 TTTTA
1 TTTTA
784637 ATATATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTATTTAAACATTAATA
Found at i:784711 original size:20 final size:22
Alignment explanation
Indices: 784683--784722 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
784673 AATAATTCTT
784683 AAATATTAAA-T-TATAATTAC
1 AAATATTAAACTCTATAATTAC
*
784703 AAATCTTAAACTCTATAATT
1 AAATATTAAACTCTATAATT
784723 CTATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTAAACTCTATAATTAC
Found at i:786500 original size:11 final size:11
Alignment explanation
Indices: 786484--786510 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
786474 TTATGTCACA
786484 TTTTTTGTATT
1 TTTTTTGTATT
786495 TTTTTTGTATT
1 TTTTTTGTATT
786506 TTTTT
1 TTTTT
786511 CACCTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTTGTATT
Found at i:809241 original size:31 final size:32
Alignment explanation
Indices: 809203--809273 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
809193 CTAAATTTAA
* * *
809203 AATTAAATAGAACTATAATTA-ATTTAATTTT
1 AATTAAATAAAACTATAATTATATTCAAATTT
*
809234 AATTAAATAAAATTATAATTATATTCAAATTT
1 AATTAAATAAAACTATAATTATATTCAAATTT
*
809266 AATAAAAT
1 AATTAAAT
809274 TATATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (32 bp):
AATTAAATAAAACTATAATTATATTCAAATTT
Found at i:809252 original size:16 final size:16
Alignment explanation
Indices: 809203--809254 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
809193 CTAAATTTAA
* *
809203 AATTAAATAGAACTAT
1 AATTAAATAAAATTAT
** *
809219 AATT-AATTTAATTTT
1 AATTAAATAAAATTAT
809234 AATTAAATAAAATTAT
1 AATTAAATAAAATTAT
809250 AATTA
1 AATTA
809255 TATTCAAATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTAAATAAAATTAT
Found at i:811990 original size:42 final size:42
Alignment explanation
Indices: 811945--812212 Score: 448
Period size: 42 Copynumber: 6.4 Consensus size: 42
811935 GATTAATCCA
* * *
811945 ACACTAAACACAATAAAACATGAGTTAAGCAGAGAGTCAA-C
1 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
*
811986 AACACTAAACACAATAAAACATGAGTTAAGCAGTGAGACAAGC
1 -ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
812029 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
1 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
812071 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
1 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
*
812113 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGTCAAGC
1 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
* * *
812155 ACACTAAACACAATAAAACACGTGTTAAGCAGCGAGTCAAGC
1 ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
812197 ACACTAAACACAATAA
1 ACACTAAACACAATAA
812213 CTTAAGCTAA
Statistics
Matches: 219, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
42 218 1.00
43 1 0.00
ACGTcount: A:0.50, C:0.21, G:0.15, T:0.13
Consensus pattern (42 bp):
ACACTAAACACAATAAAACACGAGTTAAGCAGTGAGACAAGC
Found at i:820252 original size:20 final size:19
Alignment explanation
Indices: 820206--820253 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
820196 ATAACCAACA
*
820206 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCC
820225 AAATCGCAATGCGATCTCC
1 AAATCGCAATGCGATCTCC
820244 AACATCGCAA
1 AA-ATCGCAA
820254 ATCAGTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCC
Found at i:820511 original size:22 final size:22
Alignment explanation
Indices: 820486--820536 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
820476 CTACGGCGAC
*
820486 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCACCGACGAA
*
820508 ATCCGTCCCCATCACCGGCGAA
1 ATCCGTCCCCATCACCGACGAA
820530 ATCCGTC
1 ATCCGTC
820537 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
ATCCGTCCCCATCACCGACGAA
Found at i:820978 original size:20 final size:20
Alignment explanation
Indices: 820953--820999 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
820943 GATTTTCTCG
820953 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCAAATTCGTA
** *
820973 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGTA
820993 TTGCGAT
1 TTGCGAT
821000 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGTA
Found at i:821007 original size:20 final size:20
Alignment explanation
Indices: 820984--821022 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
820974 TGCGATAGTC
820984 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
821004 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
821023 AAGTTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:821029 original size:20 final size:20
Alignment explanation
Indices: 820986--821029 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
820976 CGATAGTCAT
* *
820986 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTTAAG
821006 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
821026 TTTC
1 TTTC
821030 ATAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:822981 original size:20 final size:20
Alignment explanation
Indices: 822941--822989 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
822931 GAAACTTAAA
*
822941 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATAACT
**
822961 ATCGCAACGCGAATTTAACT
1 ATCGCAACGCGAAAATAACT
*
822981 ATCACAACG
1 ATCGCAACG
822990 AGATAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:823078 original size:19 final size:19
Alignment explanation
Indices: 823056--823100 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
823046 AAATCGCAAC
823056 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
823075 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
823094 GC-AATTT
1 GCGAATTT
823101 TTATTTCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:823107 original size:19 final size:19
Alignment explanation
Indices: 823061--823114 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
823051 GCAACGCGAA
*
823061 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGCGTTGCAATT
**
823081 TTGGTTTCGCGTTGCAATT
1 TTTATTTCGCGTTGCAATT
*
823100 TTTATTTCGCATTGC
1 TTTATTTCGCGTTGC
823115 CATTATCCCG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTATTTCGCGTTGCAATT
Found at i:823167 original size:20 final size:20
Alignment explanation
Indices: 823144--823191 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
823134 TCAAATTCGC
*
823144 GTTGCGGTAGTCATTTCCGT
1 GTTGCGATAGTCATTTCCGT
*
823164 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTCCGT
*
823184 ATTGCGAT
1 GTTGCGAT
823192 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.42
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:823201 original size:20 final size:20
Alignment explanation
Indices: 823178--823221 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
823168 CGATAGTCAT
823178 TTTCGTATTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
*
823198 TTTCGTGTTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
823218 TTTC
1 TTTC
823222 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:823767 original size:42 final size:42
Alignment explanation
Indices: 823704--823797 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
823694 CACCTATTAT
*
823704 CGTTCAAGAGGCCCCTATCATCCCTT-AAGA-GTCCTCTCCCAC
1 CGTTCAAGAGGCCCCTATCAT-CATTGAAGAGGTCC-CTCCCAC
*
823746 CGTTCAAGAGGCCCCTGTCATCATTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTGAAGAGGTCCCTCCCAC
*
823788 CATTCAAGAG
1 CGTTCAAGAG
823798 CCTGATTCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 3 0.06
42 40 0.85
43 4 0.09
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCATTGAAGAGGTCCCTCCCAC
Found at i:823791 original size:21 final size:21
Alignment explanation
Indices: 823730--823797 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
823720 ATCATCCCTT
*
823730 AAGA-GTCCTCTCCCACCGTTC
1 AAGAGGTCC-CTCCCACCATTC
* ** * *
823751 AAGAGGCCCCTGTCATCATTG
1 AAGAGGTCCCTCCCACCATTC
823772 AAGAGGTCCCTCCCACCATTC
1 AAGAGGTCCCTCCCACCATTC
823793 AAGAG
1 AAGAG
823798 CCTGATTCAC
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGAGGTCCCTCCCACCATTC
Found at i:825186 original size:14 final size:14
Alignment explanation
Indices: 825167--825203 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
825157 GCTTGTTTAA
825167 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
825181 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
825195 TTGATTTGT
1 TTGATTTGT
825204 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:825448 original size:20 final size:20
Alignment explanation
Indices: 825419--825535 Score: 153
Period size: 20 Copynumber: 5.8 Consensus size: 20
825409 GTGATTTTCT
*
825419 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
825439 CGTTGTGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
825459 CGTTAAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
825479 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
825499 TGTTGCGATAATAAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
825519 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
825536 GAATGTGTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:827799 original size:12 final size:14
Alignment explanation
Indices: 827765--827792 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
827755 CTCTCGTGGC
827765 ATTTTCTTCGGGGA
1 ATTTTCTTCGGGGA
827779 ATTTTCTTCGGGGA
1 ATTTTCTTCGGGGA
827793 TTTCTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (14 bp):
ATTTTCTTCGGGGA
Found at i:828834 original size:20 final size:20
Alignment explanation
Indices: 828809--828915 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
828799 GAAATTCAGT
828809 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
828829 GTTGCGATAGTTAGAATCGC
1 GTTGCGATAGTCAGAATCGC
828849 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * *
828869 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* *
828889 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
828909 GTTGCGA
1 GTTGCGA
828916 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 73 0.97
21 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:829541 original size:59 final size:60
Alignment explanation
Indices: 829390--829546 Score: 153
Period size: 59 Copynumber: 2.6 Consensus size: 60
829380 GTCAAGGTTA
* * * * **
829390 AAATTAGAATATTTAAAAGTTTGGGAT-TAATATAGAATGAGGGTTATAGTTTGAAGATG
1 AAATTATAATATTTAAAAGTTTGGGATCTAATTTAAAATAAAAGTTATAGTTTGAAGATG
* *
829449 -AATT-TAGTATGTTCAAAAGTTTTGGGA-CTAATTTAAAATAAAAG-TATAGTTTGAGGATG
1 AAATTATAATAT-TT-AAAAG-TTTGGGATCTAATTTAAAATAAAAGTTATAGTTTGAAGATG
* * *
829508 AAATTATAATATTTAAAAGTTTAGGATCCAATTTGAAAT
1 AAATTATAATATTTAAAAGTTTGGGATCTAATTTAAAAT
829547 GAGGATCATA
Statistics
Matches: 79, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
57 4 0.05
58 12 0.15
59 34 0.43
60 24 0.30
61 5 0.06
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (60 bp):
AAATTATAATATTTAAAAGTTTGGGATCTAATTTAAAATAAAAGTTATAGTTTGAAGATG
Found at i:833411 original size:28 final size:28
Alignment explanation
Indices: 833379--833437 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
833369 TCTCAAAATA
833379 AAAAAC-CTAAAAT-TCTTAATTTCTTAAG
1 AAAAACTCTAAAATCT-TTAATTTC-TAAG
*
833407 AAAAACTCTAAAATCTTTAGTTTCTAAG
1 AAAAACTCTAAAATCTTTAATTTCTAAG
833435 AAA
1 AAA
833438 CCTCCTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 13 0.46
29 14 0.50
30 1 0.04
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAACTCTAAAATCTTTAATTTCTAAG
Found at i:836542 original size:6 final size:6
Alignment explanation
Indices: 836533--836572 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
836523 AATTATTCTT
* * *
836533 ATAATA ATAACA ATAACA ATAACA ACAACA ATAATA ATAA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAA
836573 ATTATATTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (6 bp):
ATAACA
Found at i:853266 original size:59 final size:58
Alignment explanation
Indices: 853145--853279 Score: 139
Period size: 59 Copynumber: 2.3 Consensus size: 58
853135 ATTATAATCT
* * * * *
853145 TCATTTTAAATAGGTTTTTAAAATTTTAAATAATTTACTTTCATCTCCAAATTAGTCTC
1 TCATTTTAAATA-GTCTTTAAAATTTTAAATAATTTAATTTCATCTCCAAAATAGACCC
* *
853204 TCATTTTAAATTAGTCTTTAAACTTTTAAAT-ATTCTAATTTTATC-CCAAAATATGACCC
1 TCATTTTAAA-TAGTCTTTAAAATTTTAAATAATT-TAATTTCATCTCCAAAATA-GACCC
*
853263 TCATTCTAAACTAGTCT
1 TCATTTTAAA-TAGTCT
853280 AAATTTTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 10 0.16
59 52 0.81
60 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.45
Consensus pattern (58 bp):
TCATTTTAAATAGTCTTTAAAATTTTAAATAATTTAATTTCATCTCCAAAATAGACCC
Found at i:853523 original size:60 final size:57
Alignment explanation
Indices: 853431--853620 Score: 179
Period size: 60 Copynumber: 3.2 Consensus size: 57
853421 GCATATATTG
* * ** *
853431 ATAGTTTGAG-ATGAAATTGAAATGTAAAAAAGTTTAGAGACCAATTTAGAATGAGGGTC
1 ATAGTTTAAGAATGAAATTGAAATATTCAAAAGTTTA-AGACTAATTTAGAATGA--GTC
* * *
853490 ATAGTTTGAGAATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGTT
1 ATAGTTTAAGAATGAAATTGAAATATTCAAAAGTTTAA-GACTAATTTAGAATGAGTC
* * * *
853548 ATAATTTAAGGAT-AAATT-AGAATATTCAAAAGTTTATACACTAATTTAGAATGATAATC
1 ATAGTTTAAGAATGAAATTGA-AATATTCAAAAGTTTA-AGACTAATTTAGAATG--AGTC
853607 ATAGTTTAAGAATG
1 ATAGTTTAAGAATG
853621 TATATTATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 34 0.31
58 13 0.12
59 24 0.22
60 37 0.34
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (57 bp):
ATAGTTTAAGAATGAAATTGAAATATTCAAAAGTTTAAGACTAATTTAGAATGAGTC
Found at i:853542 original size:29 final size:28
Alignment explanation
Indices: 853504--853583 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
853494 TTTGAGAATG
*
853504 AAATTGAAATATTCAAAAGTTTAAGGACT
1 AAATTAAAATATTCAAAAGTTTAAGGA-T
* *
853533 AATTTAAAATGAGTT-ATAA-TTTAAGGAT
1 AAATTAAAAT-A-TTCAAAAGTTTAAGGAT
*
853561 AAATTAGAATATTCAAAAGTTTA
1 AAATTAAAATATTCAAAAGTTTA
853584 TACACTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 13 0.32
29 16 0.39
30 4 0.10
31 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (28 bp):
AAATTAAAATATTCAAAAGTTTAAGGAT
Found at i:853943 original size:31 final size:32
Alignment explanation
Indices: 853908--853967 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
853898 TAAACGAGTT
853908 GAGCTCGACTCGACTCGAAAACTC-TGAAATA
1 GAGCTCGACTCGACTCGAAAACTCATGAAATA
* *
853939 GAGCTCGACTTGACTTGAAAACTCATGAA
1 GAGCTCGACTCGACTCGAAAACTCATGAA
853968 TCGAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (32 bp):
GAGCTCGACTCGACTCGAAAACTCATGAAATA
Found at i:861167 original size:21 final size:21
Alignment explanation
Indices: 861116--861168 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
861106 ATTATGACTA
861116 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
861137 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
861158 TCGCAATGCGA
1 TCGCAATGCGA
861169 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:861183 original size:20 final size:21
Alignment explanation
Indices: 861158--861209 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
861148 TTTTCCCAAT
*
861158 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
861178 TCGCAATGCAAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
861199 TCGCAATGCGA
1 TCGCAATGCGA
861210 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:861223 original size:20 final size:20
Alignment explanation
Indices: 861198--861292 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
861188 AATTTGGAAA
*
861198 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
861218 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
861239 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
861259 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
861279 ATCGCAACGAGATA
1 ATCGCAACGCGATA
861293 ATACAGAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.69
21 15 0.24
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:861465 original size:12 final size:12
Alignment explanation
Indices: 861446--861479 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
861436 CTCTCCGGCG
861446 ACATCCGTTCCT
1 ACATCCGTTCCT
*
861458 ATATCCGTTCCT
1 ACATCCGTTCCT
861470 ACATCC-TTCC
1 ACATCCGTTCC
861480 CCACCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:862080 original size:24 final size:24
Alignment explanation
Indices: 862020--862087 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
862010 GTGAGTACTA
* * *
862020 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATATTG
* *
862044 GTCAATACCCGGACTTTGATATTG
1 GTCAATACTCGGAATTTGATATTG
*
862068 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
862088 GTTGTTTCAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATATTG
Found at i:862279 original size:12 final size:12
Alignment explanation
Indices: 862262--862286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
862252 ATATAATCCT
862262 GAAGAAGAAAAA
1 GAAGAAGAAAAA
862274 GAAGAAGAAAAA
1 GAAGAAGAAAAA
862286 G
1 G
862287 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:864627 original size:19 final size:20
Alignment explanation
Indices: 864546--864639 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
864536 GGCAATCATT
*
864546 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
864566 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
864587 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
864607 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
864626 TGAAAATCGCAACG
1 TGACTATCGCAACG
864640 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:864649 original size:14 final size:14
Alignment explanation
Indices: 864630--864684 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
864620 GCGAAATGAA
864630 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
864644 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
864663 AATCGCAACGAGAG
1 AATCGCAACGAGAG
864677 AATCGCAA
1 AATCGCAA
864685 AGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:864657 original size:33 final size:33
Alignment explanation
Indices: 864612--864703 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
864602 GGAAATGACT
*
864612 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
*
864645 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
*
864678 ATCGCAAAGCGAAATGAAAAACGCAA
1 ATCGCAAAGCGAAATGAAAATCGCAA
864704 TGCGAATCGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
ATCGCAAAGCGAAATGAAAATCGCAACGAGAGA
Found at i:864668 original size:19 final size:18
Alignment explanation
Indices: 864592--864709 Score: 81
Period size: 19 Copynumber: 6.7 Consensus size: 18
864582 CTTAATGTCT
**
864592 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
864612 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
864631 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
864645 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
864664 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
864678 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
*
864697 AACGCAATGCGAA
1 ATCGCAA-GCGAA
864710 TCGTTGCGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
14 18 0.23
15 4 0.05
16 4 0.05
17 4 0.05
18 4 0.05
19 36 0.46
20 9 0.11
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:864737 original size:19 final size:19
Alignment explanation
Indices: 864713--864771 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
864703 ATGCGAATCG
864713 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
864732 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
864746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
864765 TTGCGAT
1 TTGCGAT
864772 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:864779 original size:19 final size:17
Alignment explanation
Indices: 864721--864771 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
864711 CGTTGCGATT
864721 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
864738 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
864752 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
864771 T
1 T
864772 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:864897 original size:14 final size:14
Alignment explanation
Indices: 864878--864914 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
864868 CATCAATTAA
864878 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
864892 ACAAATCATCTTTT
1 ACAAATCAACTTTT
864906 ACAAATCAA
1 ACAAATCAA
864915 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:866329 original size:21 final size:21
Alignment explanation
Indices: 866263--866329 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
866253 GTGAATCGGG
*
866263 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
866283 CCTCTTCAACGATGATAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
866305 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
866326 CTCT
1 CTCT
866330 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:866340 original size:42 final size:41
Alignment explanation
Indices: 866263--866381 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 41
866253 GTGAATCGGG
* * *
866263 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATA-GTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATATG-GGC
866305 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATATGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATATGGGC
* * * * *
866347 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
866382 CAGGCGAGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
41 4 0.06
42 54 0.83
43 7 0.11
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATATGGGC
Found at i:868381 original size:40 final size:38
Alignment explanation
Indices: 868337--868482 Score: 141
Period size: 33 Copynumber: 4.1 Consensus size: 38
868327 TCTTTTGGTT
**
868337 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAACGC
1 GAAATGACTATCGCAACGAGA-AATGAAAATCGCAACGC
868376 GGAAATGACTATCGCAACGAG--A-G--AATCGCAACGC
1 -GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* *
868410 GAAATGACTATCGCAACGCGAAATGAAAATCGTAA--C
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
* * *
868446 GAGA-GA--ATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
868481 GA
1 GA
868483 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 6, Indels: 19
0.79 0.05 0.16
Matches are distributed among these distances:
33 44 0.47
34 11 0.12
35 6 0.06
36 6 0.06
37 1 0.01
38 7 0.08
40 18 0.19
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (38 bp):
GAAATGACTATCGCAACGAGAAATGAAAATCGCAACGC
Found at i:868424 original size:19 final size:19
Alignment explanation
Indices: 868346--868435 Score: 91
Period size: 20 Copynumber: 4.9 Consensus size: 19
868336 TGAAATGAAA
* **
868346 ATCGCAACGAGATAATGAAA
1 ATCGCAACGCGA-AATGACT
868366 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
868386 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
868400 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
868419 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
868436 AAATCGTAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
14 7 0.12
16 6 0.10
17 5 0.08
18 1 0.02
19 17 0.29
20 21 0.36
21 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:868441 original size:19 final size:19
Alignment explanation
Indices: 868337--868482 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
868327 TCTTTTGGTT
*
868337 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
868356 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
868376 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
868394 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
868410 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
868429 GAAATGAAAATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
868446 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
868462 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
868481 GA
1 GA
868483 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 41 0.41
20 28 0.28
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:868451 original size:52 final size:52
Alignment explanation
Indices: 868345--868482 Score: 195
Period size: 52 Copynumber: 2.6 Consensus size: 52
868335 TTGAAATGAA
* **
868345 AATCGCAACGAGATAATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
** *
868399 AATCGCAACGCGAAATGACTATCGCAACGCGAAATGAAAATCGTAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
868451 AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
868483 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
52 48 0.64
53 15 0.20
54 12 0.16
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:868532 original size:19 final size:20
Alignment explanation
Indices: 868508--868562 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
868498 GCGATTATCT
868508 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
**
868527 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
868547 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
868563 CTCGAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:868550 original size:20 final size:19
Alignment explanation
Indices: 868508--868555 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
868498 GCGATTATCT
**
868508 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
868527 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
868547 CGTTGCGAT
1 CGTTGCGAT
868556 TTTCATTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:869129 original size:20 final size:20
Alignment explanation
Indices: 869106--869199 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
869096 CGATAGTCAG
869106 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
869126 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
869146 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
869167 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
869187 ATTTGAATTGCGA
1 ATTCGCATTGCGA
869200 ATTATGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:869222 original size:21 final size:21
Alignment explanation
Indices: 869196--869252 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
869186 TATTTGAATT
*
869196 GCGAATTATGAAAATCACAAC
1 GCGAATTACGAAAATCACAAC
* * *
869217 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCACAAC
*
869237 GCGAATTAGGAAAATC
1 GCGAATTACGAAAATC
869253 TCATTGCGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (21 bp):
GCGAATTACGAAAATCACAAC
Found at i:869260 original size:21 final size:21
Alignment explanation
Indices: 869195--869261 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
869185 GTATTTGAAT
*
869195 TGCGAATTATGAAAATCACAA
1 TGCGAATTACGAAAATCACAA
* * *
869216 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCACAA
* * *
869236 TGCGAATTAGGAAAATCTCAT
1 TGCGAATTACGAAAATCACAA
869257 TGCGA
1 TGCGA
869262 TAGTCATAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCACAA
Found at i:872276 original size:55 final size:59
Alignment explanation
Indices: 872118--872281 Score: 167
Period size: 55 Copynumber: 2.8 Consensus size: 59
872108 TTTTGATGAC
* * * *
872118 TTTAGGGATGAAATTGGAATATTCCAAAGCTTAGGGGCCAATTTAGAAATAGGGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGATTAGGGACCAATTTAGAAATAGGG-CATAG
* * * * * **
872178 TTTAGGGTTGAAATTAAAATTTTCAAAAGTTTAAGGATTAATTTAG-AAT-GGG-A-AG
1 TTTAGGGATGAAATTAGAATATTCAAAAGATTAGGGACCAATTTAGAAATAGGGCATAG
* *
872233 TTTAAGGATGAAATTAGAATATTCAAAAAATTAGGGACCAATTT-GAAAT
1 TTTAGGGATGAAATTAGAATATTCAAAAGATTAGGGACCAATTTAGAAAT
872282 GAGATTCATA
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
54 1 0.01
55 40 0.48
56 1 0.01
58 3 0.04
59 3 0.04
60 36 0.43
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGATTAGGGACCAATTTAGAAATAGGGCATAG
Found at i:872753 original size:13 final size:12
Alignment explanation
Indices: 872688--872747 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
872678 TTTTTTAATT
*
872688 TTTTAATAAAATA
1 TTTTAATATAA-A
* *
872701 TTTTATTCACAAA
1 TTTTAAT-ATAAA
872714 TTTTAATATAAAA
1 TTTTAATAT-AAA
*
872727 TCTTAATATAAA
1 TTTTAATATAAA
872739 TTTTAATAT
1 TTTTAATAT
872748 CGAATTCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 12 0.31
13 24 0.62
14 3 0.08
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTTAATATAAA
Found at i:874826 original size:60 final size:60
Alignment explanation
Indices: 874759--874877 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
874749 CTATAATCGT
* ** * * *
874759 TCGACTATAGGATA-TTGTTTTGTTGAGTCTCTTGGCTATTAAAAGTTATAAAATGATCAA
1 TCGACTATAAGA-AGTTGTTTTGTTGAGTCAATTGACTATTAAAAGTTACAAAATAATCAA
874819 TCGACTATAAGAAGTTGTTTTGTTGAGTCAATTGACTATTAAAAGTTACAAAATAATCA
1 TCGACTATAAGAAGTTGTTTTGTTGAGTCAATTGACTATTAAAAGTTACAAAATAATCA
874878 CCCGATTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (60 bp):
TCGACTATAAGAAGTTGTTTTGTTGAGTCAATTGACTATTAAAAGTTACAAAATAATCAA
Found at i:875204 original size:60 final size:60
Alignment explanation
Indices: 875093--875206 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
875083 ATAGTCAGAT
* * * *
875093 GACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGTAATTCCCTATAGTCGGGA
1 GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAATTCCCTATAGTCGGGA
* *
875153 GACCATTTTATAACTTTTAATAGTCAAGGGACTTAATAAAATAATAT-CCTATAG
1 GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAAT-TCCCTATAG
875207 ACAGGGGACT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAATTCCCTATAGTCGGGA
Found at i:875229 original size:60 final size:60
Alignment explanation
Indices: 875093--875229 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
875083 ATAGTCAGAT
* * * *
875093 GACCATTT-TGTAACTTTTAATAGTCGATGGACTCAACAAAGTAATTCCCTATAGTCGGGA
1 GACCATTTATGT-ACTTTTAATAGTCAAGGGACTCAACAAAATAATTCCCTATAGACGGGA
* * *
875153 GACCATTTTAT-AACTTTTAATAGTCAAGGGACTTAATAAAATAATAT-CCTATAGACAGGG-
1 GACCA-TTTATGTACTTTTAATAGTCAAGGGACTCAACAAAATAAT-TCCCTATAGAC-GGGA
*
875213 GACTATTTATGTACTTT
1 GACCATTTATGTACTTT
875230 ACCCTTTTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
59 5 0.08
60 50 0.79
61 7 0.11
62 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Consensus pattern (60 bp):
GACCATTTATGTACTTTTAATAGTCAAGGGACTCAACAAAATAATTCCCTATAGACGGGA
Found at i:881988 original size:60 final size:57
Alignment explanation
Indices: 881872--882001 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 57
881862 TATGTTTATC
* * * * *
881872 ATTTTTTAATTTTTAATAGAGGGACTCAACAAAGCAATACCCTATAGTTGGAGGACT
1 ATTTTATAACTTTTAATAGAGGGACTCAACAAAGCAACACCCTATAATCGGAGGACT
*
881929 ATTTTATAACTTTTAATAGACGATGGACTCAACAAAGTAACACCCTATAATC-GAGGGACT
1 ATTTTATAACTTTTAATAGA-G--GGACTCAACAAAGCAACACCCTATAATCGGA-GGACT
881989 A-TTTATATACTTT
1 ATTTTATA-ACTTT
882002 ACCCTTAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
57 18 0.29
58 1 0.02
59 8 0.13
60 35 0.56
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (57 bp):
ATTTTATAACTTTTAATAGAGGGACTCAACAAAGCAACACCCTATAATCGGAGGACT
Found at i:893385 original size:11 final size:11
Alignment explanation
Indices: 893369--893393 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
893359 TTTAGCTGCT
893369 TTTCTTCTTTG
1 TTTCTTCTTTG
893380 TTTCTTCTTTG
1 TTTCTTCTTTG
893391 TTT
1 TTT
893394 GTTATGTGAT
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:0.16, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTCTTCTTTG
Found at i:896089 original size:24 final size:24
Alignment explanation
Indices: 896060--896109 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
896050 ATAATATAAA
*
896060 CATGTAGTTCATCTCCTAAAACAT
1 CATGTAGTTCAACTCCTAAAACAT
*
896084 CATGTAGTTCAACTCGTAAAACAT
1 CATGTAGTTCAACTCCTAAAACAT
896108 CA
1 CA
896110 CTCGATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (24 bp):
CATGTAGTTCAACTCCTAAAACAT
Found at i:899541 original size:21 final size:21
Alignment explanation
Indices: 899497--899544 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
899487 GTTAGGGGAA
* **
899497 TTACGTTATGAGGTCGGTGTT
1 TTACGTCATGAGGTCGGTACT
*
899518 TTACGTCATGAGGTTGGTACT
1 TTACGTCATGAGGTCGGTACT
899539 TTACGT
1 TTACGT
899545 GAAGATAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.42
Consensus pattern (21 bp):
TTACGTCATGAGGTCGGTACT
Found at i:902036 original size:18 final size:18
Alignment explanation
Indices: 902015--902050 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
902005 AAGCCGGTTG
*
902015 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
902033 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
902051 CTTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:904345 original size:24 final size:24
Alignment explanation
Indices: 904308--904361 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
904298 CCATCACATC
904308 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
904332 ATCAAAGTCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
904356 ATCAAA
1 ATCAAA
904362 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:904375 original size:24 final size:24
Alignment explanation
Indices: 904326--904375 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
904316 CCGAGTATTA
* *
904326 ACCAAGATCAAAGTCTGAGTATTG
1 ACCAAGATCAAAGTCTGAATACTG
*
904350 ACCAAGATCAAA-TTTCGAATACTG
1 ACCAAGATCAAAGTCT-GAATACTG
904374 AC
1 AC
904376 TAGTACTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
ACCAAGATCAAAGTCTGAATACTG
Found at i:904508 original size:12 final size:12
Alignment explanation
Indices: 904487--904520 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
904477 GGTTGTGGGT
*
904487 TTTGAGATTGTG
1 TTTGATATTGTG
904499 TTTGATATTGTG
1 TTTGATATTGTG
*
904511 TTTGGTATTG
1 TTTGATATTG
904521 GAAATTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:905109 original size:14 final size:15
Alignment explanation
Indices: 905073--905110 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
905063 GAGATCATTG
905073 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
905088 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
905103 AAAAATTA
1 AAAAATTA
905111 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:905303 original size:20 final size:20
Alignment explanation
Indices: 905278--905332 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
905268 TTGTGAAATT
905278 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
905298 AAATTC-AGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
**
905317 ACTTTCGCGTTGCGAA
1 AAATTCGCGTTGCGAA
905333 ATTGGAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:915898 original size:33 final size:33
Alignment explanation
Indices: 915860--916138 Score: 161
Period size: 32 Copynumber: 8.2 Consensus size: 33
915850 TCGAAAATTT
*
915860 ATATATTATATAGTTTTTGAAAATATTTTTAAA
1 ATATATTATATAGTTTTTGAAAACATTTTTAAA
* **
915893 ATATATATAATATA-TAGTTTTGAAAACATTTTCATTT
1 ATATAT-T-ATATAGT--TTTTGAAAACATTTTTA-AA
915930 ATATATTATATAGTTTTT-AAAACA-TTTTAAA
1 ATATATTATATAGTTTTTGAAAACATTTTTAAA
* *
915961 ACTTATATAATATATAATTTTTTAAAACATTTTTGAAAAA
1 A--TATAT--TATATAGTTTTTGAAAACATTTTT---AAA
*
916001 ATATATAATATATAG-TTTTAAAAACATTTTTTTGAAA
1 ATATAT--TATATAGTTTTTGAAAACA--TTTTT-AAA
*
916038 ACT-TA-TATAATA-TTTTT-AAAACATTTTGAAA
1 A-TATATTAT-ATAGTTTTTGAAAACATTTTTAAA
916069 ACTATA-TATATAG-TTTTGAAAAC-TTCTTTAAAA
1 A-TATATTATATAGTTTTTGAAAACATT-TTT-AAA
* * * *
916102 ATATAATATATAG--TTTAAAAATATTTTTGAA
1 ATATATTATATAGTTTTTGAAAACATTTTTAAA
916133 ATATAT
1 ATATAT
916139 ATACTATATA
Statistics
Matches: 202, Mismatches: 17, Indels: 56
0.73 0.06 0.20
Matches are distributed among these distances:
31 23 0.11
32 34 0.17
33 30 0.15
34 15 0.07
35 28 0.14
36 23 0.11
37 26 0.13
38 14 0.07
39 5 0.02
40 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (33 bp):
ATATATTATATAGTTTTTGAAAACATTTTTAAA
Found at i:915898 original size:35 final size:35
Alignment explanation
Indices: 915781--916140 Score: 187
Period size: 35 Copynumber: 10.2 Consensus size: 35
915771 TTATATATAT
* * *
915781 ATATATAGTAATATAGTTTGTGAAAATGTTTTTGACAA
1 ATATATA-TTATATAGTTTTTGAAAATATTTTT-A-AA
* * * *
915819 A-ATATAATATATAATTTTTAGAAAACGATTTTCGAAA
1 ATATATATTATATAGTTTTT-GAAAA-TATTTT-TAAA
915856 ATTTATATATTATATAGTTTTTGAAAATATTTTTAAA
1 A--TATATATTATATAGTTTTTGAAAATATTTTTAAA
* * *
915893 ATATATATAATATATAG-TTTTGAAAACA-TTTTCAT
1 ATATATAT--TATATAGTTTTTGAAAATATTTTTAAA
* *
915928 TTATATATTATATAGTTTTT-AAAACA-TTTTAAA
1 ATATATATTATATAGTTTTTGAAAATATTTTTAAA
* * * *
915961 ACTTATATAATATATAATTTTTTAAAACATTTTTGAAAAA
1 A--TATATATTATATAGTTTTTGAAAATATTTTT---AAA
* ** *
916001 ATATATAATATATAGTTTTAAAAACATTTTTTTGAAA
1 ATATATATTATATAGTTTTTGAAA-ATATTTTT-AAA
* *
916038 ACT-TATA-TA-ATA-TTTTT-AAAACATTTTGAAA
1 A-TATATATTATATAGTTTTTGAAAATATTTTTAAA
* *
916069 A-CTATA-TATATAG-TTTTGAAAACT-TCTTTAAA
1 ATATATATTATATAGTTTTTGAAAA-TATTTTTAAA
* * *
916101 A-ATATAATATATAG--TTTAAAAATATTTTTGAA
1 ATATATATTATATAGTTTTTGAAAATATTTTTAAA
916133 ATATATAT
1 ATATATAT
916141 ACTATATAAT
Statistics
Matches: 258, Mismatches: 38, Indels: 57
0.73 0.11 0.16
Matches are distributed among these distances:
30 6 0.02
31 12 0.05
32 34 0.13
33 33 0.13
34 8 0.03
35 39 0.15
36 27 0.10
37 36 0.14
38 32 0.12
39 11 0.04
40 20 0.08
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATATATTATATAGTTTTTGAAAATATTTTTAAA
Found at i:915939 original size:77 final size:79
Alignment explanation
Indices: 915773--915943 Score: 187
Period size: 76 Copynumber: 2.2 Consensus size: 79
915763 TATTTTGTTT
* * *
915773 ATATATATATATATAGTAATATAGTTTGTGAAAATGTTTTTGACAAAATATAATATATAATTTTT
1 ATATATAT-TATATAGTAATATAGTTTGTGAAAATATTTTTGAAAAAATATAATATATAAGTTTT
915838 AGAAAACGATTTTCG
65 AGAAAACGATTTTCG
* * *
915853 A-AAAT-TTATATA-TTATATAGTTTTTGAAAATATTTTT-AAAATATATATAATATAT-AGTTT
1 ATATATATTATATAGTAATATAGTTTGTGAAAATATTTTTGAAAA-A-ATATAATATATAAGTTT
915913 T-GAAAAC-ATTTTC-
64 TAGAAAACGATTTTCG
915926 ATTTATATATTATATAGT
1 A--TATATATTATATAGT
915944 TTTTAAAACA
Statistics
Matches: 77, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
73 1 0.01
74 6 0.08
75 9 0.12
76 31 0.40
77 24 0.31
78 2 0.03
79 3 0.04
80 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (79 bp):
ATATATATTATATAGTAATATAGTTTGTGAAAATATTTTTGAAAAAATATAATATATAAGTTTTA
GAAAACGATTTTCG
Found at i:916139 original size:33 final size:34
Alignment explanation
Indices: 915781--916148 Score: 202
Period size: 33 Copynumber: 10.4 Consensus size: 34
915771 TTATATATAT
* * **
915781 ATATATAGTAATATAGTTTGTGAAAATGTTTTTGACA
1 ATATATAAT-ATATAGTTT-TAAAAACATTTTTGA-A
* * *
915818 AAATATAATATATAATTTTTAGAAAACGATTTTCGAAA
1 ATATATAATATAT-AGTTTTA-AAAAC-ATTTTTG-AA
* * * *
915856 ATTTATATATTATATAGTTTTTGAAAATATTTTTAAAA
1 A--TATATAATATATAG-TTTTAAAAACATTTTT-GAA
* * *
915894 TATATATAATATATAGTTTTGAAAACA-TTTTCAT
1 -ATATATAATATATAGTTTTAAAAACATTTTTGAA
* * * *
915928 TTATATATTATATAGTTTTTAAAACA-TTTTAAA
1 ATATATAATATATAGTTTTAAAAACATTTTTGAA
* *
915961 ACTTATATAATATATAATTTTTTAAAACATTTTTGAAAAA
1 A--TATATAATATAT-AGTTTTAAAAACATTTTTG---AA
916001 ATATATAATATATAGTTTTAAAAACATTTTTTTGAA
1 ATATATAATATATAGTTTTAAAAACA--TTTTTGAA
*
916037 A-ACT-T-ATATAATA-TTTTTAAAACA-TTTTGAA
1 ATA-TATAATAT-ATAGTTTTAAAAACATTTTTGAA
*
916068 A-ACTAT-ATATATAGTTTTGAAAAC-TTCTTT-AA
1 ATA-TATAATATATAGTTTTAAAAACATT-TTTGAA
* *
916100 AAATATAATATATAG-TTTAAAAATATTTTTGAA
1 ATATATAATATATAGTTTTAAAAACATTTTTGAA
916133 ATATATATACTATATA
1 ATATATA-A-TATATA
916149 ATTTATATTA
Statistics
Matches: 267, Mismatches: 34, Indels: 62
0.74 0.09 0.17
Matches are distributed among these distances:
31 14 0.05
32 31 0.12
33 50 0.19
34 16 0.06
35 26 0.10
36 31 0.12
37 43 0.16
38 26 0.10
39 13 0.05
40 17 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
ATATATAATATATAGTTTTAAAAACATTTTTGAA
Found at i:916205 original size:20 final size:20
Alignment explanation
Indices: 916164--916204 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
916154 TATTATATTA
916164 TTATTATTATTCTATTTGTT
1 TTATTATTATTCTATTTGTT
916184 TTATTAATTATT-T-TTTGTT
1 TTATT-ATTATTCTATTTGTT
916203 TT
1 TT
916205 TTGTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (20 bp):
TTATTATTATTCTATTTGTT
Found at i:917068 original size:3 final size:3
Alignment explanation
Indices: 917060--917148 Score: 80
Period size: 3 Copynumber: 29.7 Consensus size: 3
917050 TTTATTTCGT
*
917060 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTCA TTC TCT- TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T-TA TTA TTA
*
917104 TTA TGT- TTA TTA TTA TTA TTA TTTA TGTA TT- TCA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TT
917149 TTTTACATAT
Statistics
Matches: 74, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
2 7 0.09
3 57 0.77
4 10 0.14
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:917159 original size:25 final size:25
Alignment explanation
Indices: 917112--917159 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
917102 TATTATGTTT
**
917112 ATTATTATTATTATTTATGTATTTC
1 ATTATTATTATTATTTACATATTTC
*
917137 ATTATTATTATTTTTTACATATT
1 ATTATTATTATTATTTACATATT
917160 GTTTTCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTATTATTATTATTTACATATTTC
Found at i:920184 original size:23 final size:23
Alignment explanation
Indices: 920158--920235 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
920148 CACCACAGCT
920158 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
920181 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
920204 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
920227 TATAATAAT
1 CAT-ATAAT
920236 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:921857 original size:22 final size:21
Alignment explanation
Indices: 921832--921891 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
921822 TTCGCTTGAG
*
921832 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
921854 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
921874 GAGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
921892 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:925476 original size:23 final size:23
Alignment explanation
Indices: 925450--925527 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
925440 CACTACAGCT
* *
925450 CATATAATTACACTGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
925473 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
925496 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
925519 TATAATAAT
1 CAT-ATAAT
925528 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:925750 original size:103 final size:103
Alignment explanation
Indices: 925526--925751 Score: 364
Period size: 103 Copynumber: 2.2 Consensus size: 103
925516 CCATATAATA
** *
925526 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATATTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
*
925590 GTCTCACCAGACTTCACACATGTTCCAAAGAATATATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
* * *
925629 ATGTCCCGAATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
925694 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
925732 ATGTCCCAAAGGATCACATA
1 ATGTCCCAAAGGACCACATA
925752 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 110 0.98
104 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:927146 original size:22 final size:21
Alignment explanation
Indices: 927121--927180 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
927111 TTCGCTTGAG
*
927121 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
927143 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
927163 GAGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
927181 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:930748 original size:23 final size:23
Alignment explanation
Indices: 930722--930799 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
930712 CACTACAACT
930722 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
930745 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
930768 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
930791 TATAATAAT
1 CAT-ATAAT
930800 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:930989 original size:103 final size:101
Alignment explanation
Indices: 930809--931021 Score: 345
Period size: 103 Copynumber: 2.1 Consensus size: 101
930799 TGTCCATAAG
* * *
930809 GACCACATATCATTCCTTAAGAATCATATATATATTAGGGATCAAGTATGTGTCTCACCAAACTT
1 GACCACATATCATTCCTTAAGAATCATATACATATCAAGGATCAAGTATGTGTCTCACCAAACTT
*
930874 CACACACGTTCCAAAGAATATATATATGTCCCGAAT
66 CACACACGTTCCAAAGAATACATATATGTCCCGAAT
* *
930910 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCATCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATAT--CAAGGATCAAGTATGTGTCTCACCAAAC
*
930975 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
64 TTCACACACGTTCCAAAGAATACATATATGTCCCGAAT
931013 GACCACATA
1 GACCACATA
931022 GACCCTCGAC
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 34 0.33
103 69 0.67
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (101 bp):
GACCACATATCATTCCTTAAGAATCATATACATATCAAGGATCAAGTATGTGTCTCACCAAACTT
CACACACGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:932399 original size:22 final size:21
Alignment explanation
Indices: 932374--932433 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
932364 TTCGCTTGAG
*
932374 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
932396 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
932416 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
932434 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:935193 original size:24 final size:24
Alignment explanation
Indices: 935142--935196 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
935132 AAAGACAATT
* *
935142 GGTGACAGACAATGATTAGCTATC
1 GGTGACAGACAATGATTAGATATA
* *
935166 GGTGACAGACAATGGTTAGATGTA
1 GGTGACAGACAATGATTAGATATA
935190 GGTGACA
1 GGTGACA
935197 TCCAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.24
Consensus pattern (24 bp):
GGTGACAGACAATGATTAGATATA
Found at i:936820 original size:21 final size:20
Alignment explanation
Indices: 936774--936821 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
936764 GATTCTGACT
936774 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
936794 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
936816 ATCGCA
1 ATCGCA
936822 ACGCGATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:937158 original size:27 final size:26
Alignment explanation
Indices: 937101--937152 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
937091 CATCGCCGAC
*
937101 GAAATCCCTCACAACCATTCACGGACA
1 GAAATCCCTCACAACCATTCAC-GAAA
*
937128 GAAATCCCTCACAATCATTCA-GAAA
1 GAAATCCCTCACAACCATTCACGAAA
937153 TGGAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
27 20 0.87
ACGTcount: A:0.40, C:0.33, G:0.10, T:0.17
Consensus pattern (26 bp):
GAAATCCCTCACAACCATTCACGAAA
Done.