Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004898.1 Hibiscus syriacus cultivar Beakdansim tig00011021_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: 125011
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:179 original size:19 final size:19
Alignment explanation
Indices: 155--201 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
145 AATATTTAGG
155 AGTGCATCGATGCATGACT
1 AGTGCATCGATGCATGACT
*
174 AGTGCATCGATGCATGCCT
1 AGTGCATCGATGCATGACT
*
193 TGTGCATCG
1 AGTGCATCG
202 GTACATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCATGACT
Found at i:570 original size:134 final size:135
Alignment explanation
Indices: 410--676 Score: 416
Period size: 136 Copynumber: 2.0 Consensus size: 135
400 TTGGAGTAAT
*
410 ATTTTGATATTCAAATAATTGTATCGAATATACTT-AGAATCATTTGTAAAATCTTAAAATTCAT
1 ATTTTGATATTCAAATAATTATATCGAATATACTTAAGAATCATTTGTAAAATCTTAAAATTCAT
* * *
474 TTATCTTAA-TTGTTATATCGAAACATCAAAAATGTTTTCAATAATCTCCC-C-TTTTTGATATA
66 TTATATTAATTTGTTATATCAAAACAT-AAAAA--TTTTCAACAATCTCCCACTTTTTTGATATA
536 ACAAAACC
128 ACAAAACC
* *
544 ATTTTGATATTCGAATAATTATATCGAATATACTTAGAGAATTATTTGTAAAATCTTAAAATTCA
1 ATTTTGATATTCAAATAATTATATCGAATATACTTA-AGAATCATTTGTAAAATCTTAAAATTCA
609 TTTATATTAATTTGTTATATCAAAACATAAAAATTTTCAACAATCTCCCACTTTTTTGATATAAC
65 TTTATATTAATTTGTTATATCAAAACATAAAAATTTTCAACAATCTCCCACTTTTTTGATATAAC
674 AAA
130 AAA
677 CCTTTGAGTA
Statistics
Matches: 122, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
134 48 0.39
135 1 0.01
136 57 0.47
137 16 0.13
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (135 bp):
ATTTTGATATTCAAATAATTATATCGAATATACTTAAGAATCATTTGTAAAATCTTAAAATTCAT
TTATATTAATTTGTTATATCAAAACATAAAAATTTTCAACAATCTCCCACTTTTTTGATATAACA
AAACC
Found at i:2981 original size:23 final size:23
Alignment explanation
Indices: 2951--3033 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
2941 ATGCATTTAT
2951 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* *
2974 GAGTGCATCGGTGCATC-TTC-AT
1 GAGTGCATCGATGCA-CATTCAAG
* *
2996 GA-TGTATCGATGCACATTTAAG
1 GAGTGCATCGATGCACATTCAAG
3018 G-GATGCATCGATGCAC
1 GAG-TGCATCGATGCAC
3034 TGTCATGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.25
22 5 0.10
23 29 0.60
24 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:3010 original size:44 final size:44
Alignment explanation
Indices: 2931--3052 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 44
2921 AAAACATGAT
* *
2931 GAGTGTATCGATGCAT-TT-ATGAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCATCTTCATGA-TGTATCGATGCACATTCAAG
* *
2974 GAGTGCATCGGTGCATCTTCATGATGTATCGATGCACATTTAAG
1 GAGTGCATCGATGCATCTTCATGATGTATCGATGCACATTCAAG
3018 G-GATGCATCGATGCA-CTGTCATG-TGTATCGATGCA
1 GAG-TGCATCGATGCATCT-TCATGATGTATCGATGCA
3053 TTAATCACAA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
43 29 0.41
44 37 0.53
45 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
GAGTGCATCGATGCATCTTCATGATGTATCGATGCACATTCAAG
Found at i:15970 original size:20 final size:20
Alignment explanation
Indices: 15945--16005 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
15935 TTTTGGTGCA
*
15945 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
15965 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
15986 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
16006 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:16027 original size:21 final size:21
Alignment explanation
Indices: 15988--16027 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15978 CCCCCTTTGA
* *
15988 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACACCCCAC
*
16009 AGGGGAATCGATACACCCC
1 AGGGGAACCGATACACCCC
16028 TGGGTTCTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACACCCCAC
Found at i:21529 original size:3 final size:3
Alignment explanation
Indices: 21521--21555 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
21511 AATTGTATTA
21521 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21556 TTTGTAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:21543 original size:17 final size:17
Alignment explanation
Indices: 21521--21553 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21511 AATTGTATTA
21521 AATAATAATAATAATAT
1 AATAATAATAATAATAT
21538 AATAATAATAATAATA
1 AATAATAATAATAATA
21554 ATTTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:24194 original size:14 final size:14
Alignment explanation
Indices: 24175--24207 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
24165 TTATATATTC
24175 TAAAAATAAAAATA
1 TAAAAATAAAAATA
*
24189 TAAAAATAAAATTA
1 TAAAAATAAAAATA
24203 TAAAA
1 TAAAA
24208 TTGCAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAATAAAAATA
Found at i:24287 original size:42 final size:40
Alignment explanation
Indices: 24221--24313 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 40
24211 CAACTAAATT
* * *
24221 TAAAATAATTTGAGATTAAAATAAATAATTTAAATTTTAAGG
1 TAAAATAATTTGAAAATAAAATAAAT--TTTAAATGTTAAGG
* * * *
24263 TGAAATAATTTGAAAATAATATAAATTTTGAATGTTAGGG
1 TAAAATAATTTGAAAATAAAATAAATTTTAAATGTTAAGG
24303 TAAAATAATTT
1 TAAAATAATTT
24314 TAAATTACAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 21 0.49
42 22 0.51
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (40 bp):
TAAAATAATTTGAAAATAAAATAAATTTTAAATGTTAAGG
Found at i:25320 original size:22 final size:22
Alignment explanation
Indices: 25295--25629 Score: 451
Period size: 22 Copynumber: 15.3 Consensus size: 22
25285 CTATTTTAAA
25295 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
25317 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
25339 ATTTATTTTTAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
25361 A-TTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
25382 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
25404 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
*
25425 ATTTTATTTTAAAATATGGATTA
1 A-TTTATTTTAAAATATGGATTG
***
25448 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
25470 ATTTATTTTAAAATATGGATTC
1 ATTTATTTTAAAATATGGATTG
*
25492 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
25514 ATTTATTTTAAAATGTGGATTG
1 ATTTATTTTAAAATATGGATTG
***
25536 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
25557 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
25580 ATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAAATATGGATTG
*
25602 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
25624 ATTTAT
1 ATTTAT
25630 GTTGAAAACA
Statistics
Matches: 276, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
21 19 0.07
22 252 0.91
23 5 0.02
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:26686 original size:22 final size:22
Alignment explanation
Indices: 26660--26819 Score: 209
Period size: 22 Copynumber: 7.3 Consensus size: 22
26650 AACAACTTAA
26660 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
***
26682 TTT-AAA-ATGCGAAAAATTTTAT
1 TTTAAAATATG-GATTGA-TTTAT
26704 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
*
26726 TTTAAAATATAGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
** *
26748 TTTAAAATATGGA-AAAATTAT
1 TTTAAAATATGGATTGATTTAT
26769 TTTAAAATATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
*
26791 TTTAAATTATGGATTGATTTAT
1 TTTAAAATATGGATTGATTTAT
26813 TTTAAAA
1 TTTAAAA
26820 ACTTTATTAG
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.03
21 24 0.21
22 81 0.69
23 6 0.05
24 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTAAAATATGGATTGATTTAT
Found at i:26784 original size:43 final size:44
Alignment explanation
Indices: 26699--26819 Score: 163
Period size: 43 Copynumber: 2.8 Consensus size: 44
26689 TGCGAAAAAT
** *
26699 TTTATTTTAAAATATGGATTGATTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGGATAAAATTATTTTAAAATATAGATTGA
*
26743 TTTATTTTAAAATATGGA-AAAATTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATAAAATTATTTTAAAATATAGATTGA
* ** *
26786 TTTATTTTAAATTATGGATTGATTTATTTTAAAA
1 TTTATTTTAAAATATGGATAAAATTATTTTAAAA
26820 ACTTTATTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 38 0.56
44 30 0.44
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.50
Consensus pattern (44 bp):
TTTATTTTAAAATATGGATAAAATTATTTTAAAATATAGATTGA
Found at i:26793 original size:65 final size:66
Alignment explanation
Indices: 26660--26820 Score: 265
Period size: 65 Copynumber: 2.5 Consensus size: 66
26650 AACAACTTAA
26660 TTTAAAATATGGATTGATTTATTTT-AAAATGCGAAAAATTTTATTTTAAAATATGGATTGATTT
1 TTTAAAATATGGATTGATTTATTTTAAAAATGCGAAAAA-TTTATTTTAAAATATGGATTGATTT
26724 AT
65 AT
*
26726 TTTAAAATATAGATTGATTTATTTTAAAATATG-GAAAAA-TTATTTTAAAATATGGATTGATTT
1 TTTAAAATATGGATTGATTTATTTTAAAA-ATGCGAAAAATTTATTTTAAAATATGGATTGATTT
26789 AT
65 AT
*
26791 TTTAAATTATGGATTGATTTATTTTAAAAA
1 TTTAAAATATGGATTGATTTATTTTAAAAA
26821 CTTTATTAGT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
64 1 0.01
65 53 0.59
66 24 0.27
67 9 0.10
68 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (66 bp):
TTTAAAATATGGATTGATTTATTTTAAAAATGCGAAAAATTTATTTTAAAATATGGATTGATTTA
T
Found at i:28425 original size:2 final size:2
Alignment explanation
Indices: 28418--28479 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
28408 GTTTTTAAGA
28418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28460 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
28480 GGATGTTACT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29433 original size:17 final size:17
Alignment explanation
Indices: 29411--29447 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
29401 GGTAGCATGG
29411 CCGGTTCGCTAACCGGT
1 CCGGTTCGCTAACCGGT
*
29428 CCGGTTCGTTAACCGGT
1 CCGGTTCGCTAACCGGT
29445 CCG
1 CCG
29448 ATTCTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.35, G:0.30, T:0.24
Consensus pattern (17 bp):
CCGGTTCGCTAACCGGT
Found at i:30499 original size:23 final size:24
Alignment explanation
Indices: 30472--30530 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
30462 TAAGCTACCA
30472 AAAGACAGAGAA-AAACGTGCTAC
1 AAAGACAGAGAATAAACGTGCTAC
* * *
30495 AAAGACAGA-AATAAATGTGTTAT
1 AAAGACAGAGAATAAACGTGCTAC
*
30518 AAAGGCAGAGAAT
1 AAAGACAGAGAAT
30531 GTGTCACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 2 0.07
23 25 0.83
24 3 0.10
ACGTcount: A:0.53, C:0.10, G:0.22, T:0.15
Consensus pattern (24 bp):
AAAGACAGAGAATAAACGTGCTAC
Found at i:31738 original size:4 final size:4
Alignment explanation
Indices: 31729--31759 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
31719 CAATACATGT
31729 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
31760 GTTGAACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:31849 original size:3 final size:3
Alignment explanation
Indices: 31841--31891 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
31831 TTTGTTTTAT
* *
31841 TTA TTA TTA TTA AT- TTG TT- TTA TTA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31885 TTA TTA T
1 TTA TTA T
31892 GAAATAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31864 original size:19 final size:20
Alignment explanation
Indices: 31840--31890 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
31830 ATTTGTTTTA
*
31840 TTTATTATTATTAATT-TGT
1 TTTATTATTATTAATTATAT
31859 TTTATTATTATT-ATTATAT
1 TTTATTATTATTAATTATAT
*
31878 TATATTATTATTA
1 TTTATTATTATTA
31891 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTATTATTAATTATAT
Found at i:31869 original size:22 final size:21
Alignment explanation
Indices: 31830--31891 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 21
31820 TTTTTATTTC
31830 ATTTGTTTTATTTATTATTATT
1 ATTTGTTTTA-TTATTATTATT
31852 AATTTGTTTTATTATTATTATT
1 -ATTTGTTTTATTATTATTATT
* *
31874 ATATTATATTATTATTAT
1 AT-TTGTTTTATTATTAT
31892 GAAATAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 2 0.06
22 24 0.67
23 10 0.28
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
ATTTGTTTTATTATTATTATT
Found at i:33828 original size:15 final size:16
Alignment explanation
Indices: 33805--33851 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
33795 TATTTTAAAT
33805 AAATAAATATATTTTA
1 AAATAAATATATTTTA
*
33821 AAAT-AATATGATTATA
1 AAATAAATAT-ATTTTA
*
33837 AATTAAATATATTTT
1 AAATAAATATATTTT
33852 GAATTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
16 16 0.62
17 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAATAAATATATTTTA
Found at i:33856 original size:16 final size:16
Alignment explanation
Indices: 33794--33856 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
33784 TCCTTTTCTG
33794 ATATTTTAAATAAATAAAT
1 ATATTTTAAAT---TAAAT
*
33813 ATATTTTAAAAT-AAT
1 ATATTTTAAATTAAAT
*
33828 ATGATTATAAATTAAAT
1 AT-ATTTTAAATTAAAT
*
33845 ATATTTTGAATT
1 ATATTTTAAATT
33857 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 5 0.14
16 17 0.46
17 5 0.14
19 10 0.27
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
ATATTTTAAATTAAAT
Found at i:34309 original size:13 final size:12
Alignment explanation
Indices: 34293--34344 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
34283 CTTTCAATTT
34293 TTTTTACTTATTA
1 TTTTTA-TTATTA
34306 TTTTTATATATTA
1 TTTTTAT-TATTA
34319 TTATTTATTATT-
1 TT-TTTATTATTA
34331 TTATTTATT-TTA
1 TT-TTTATTATTA
34343 TT
1 TT
34345 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.06
12 12 0.33
13 17 0.47
14 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:34310 original size:16 final size:16
Alignment explanation
Indices: 34300--34341 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
34290 TTTTTTTTAC
34300 TTATTATTTTTATATA
1 TTATTATTTTTATATA
34316 TTATTATTTATTAT-T-
1 TTATTATTT-TTATATA
34331 TTATTTATTTT
1 TTA-TTATTTT
34342 ATTCAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTATTTTTATATA
Found at i:35000 original size:18 final size:18
Alignment explanation
Indices: 34965--35002 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34955 CACCAATTTA
*
34965 TTTATTTTCTTTCTCATT
1 TTTATTTTCTTTATCATT
34983 TTTATTTT-TTTATACATT
1 TTTATTTTCTTTAT-CATT
35001 TT
1 TT
35003 GGTTTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTCTTTATCATT
Found at i:35973 original size:14 final size:14
Alignment explanation
Indices: 35935--35988 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
35925 ATTTTAAATA
*
35935 ATTTACATTTACA-
1 ATTTACATTTGCAT
35948 ATTTTACATTTGCAT
1 A-TTTACATTTGCAT
35963 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
35978 CTTTGCATTTG
1 ATTTACATTTG
35989 TATTGCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 1 0.03
14 21 0.60
15 13 0.37
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:35977 original size:15 final size:15
Alignment explanation
Indices: 35950--35988 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35940 CATTTACAAT
35950 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
35964 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
35979 TTTGCATTTG
1 TTTACATTTG
35989 TATTGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:38938 original size:2 final size:2
Alignment explanation
Indices: 38931--38978 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
38921 TTATCCTTTA
38931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38973 AT AT AT
1 AT AT AT
38979 CCTTTGTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41753 original size:114 final size:114
Alignment explanation
Indices: 41545--41770 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
41535 AAGTGCCATG
* *
41545 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* * *
41610 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGATTCGGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
*
41659 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* * *
41724 TGATTCGGTATGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGATTCGGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
41771 CTGCATGATC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTATGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:43980 original size:54 final size:54
Alignment explanation
Indices: 43891--44096 Score: 228
Period size: 54 Copynumber: 3.9 Consensus size: 54
43881 AGAAATTTTG
* * * *
43891 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* **
43945 GCAAAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGA
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
* *
43999 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAGTG-TTT-T--ACATCTCGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCT-GA
* * *
44050 -CAGAAACCACAGGAAAAGATGAATGTATTGTCAAATGTTTTATGAAC
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAAC
44097 CAGTGATTAT
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
50 36 0.28
51 6 0.05
52 1 0.01
53 5 0.04
54 78 0.61
55 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (54 bp):
GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTATGAACATCTGA
Found at i:44492 original size:22 final size:22
Alignment explanation
Indices: 44463--44517 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
44453 ATCTACACTC
*
44463 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
44485 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
44507 TTCAAAGATGA
1 TTCAAAGATGA
44518 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:45132 original size:113 final size:113
Alignment explanation
Indices: 44926--45469 Score: 893
Period size: 113 Copynumber: 4.8 Consensus size: 113
44916 GATTCAAATC
* * *
44926 CATCATTCGATGGATCAGCATTGTTAGGTC-AATTCATAATGAGAAGAACTCATTTGAAGAAAG-
1 CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
44989 TGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
**
45037 CATCATTCGATGGATCAACATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
*
45102 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* **
45150 CATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
45215 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
*
45263 CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATTTGAAGAAAG-
1 CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
* *
45327 TGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* *
45375 CATCACTCGATGGATCAAC-TTGTTAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAG-AAG
1 CATCATTCGATGGATCAACATTGTTAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
45437 AAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
65 -AAGAAGAAGTTCATAATGAGAAGAACTTGTTC
45470 GTTCATAATT
Statistics
Matches: 409, Mismatches: 19, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
110 3 0.01
111 63 0.15
112 126 0.31
113 217 0.53
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAACATTGTTAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:45473 original size:24 final size:24
Alignment explanation
Indices: 45446--45492 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
45436 GAAAGAAGAA
45446 GTTCATAATGAGAAGAACTTGTTC
1 GTTCATAATGAGAAGAACTTGTTC
*
45470 GTTCATAATTAGAAGAACTTGTT
1 GTTCATAATGAGAAGAACTTGTT
45493 TAATCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (24 bp):
GTTCATAATGAGAAGAACTTGTTC
Found at i:45823 original size:3 final size:3
Alignment explanation
Indices: 45817--45897 Score: 57
Period size: 3 Copynumber: 28.3 Consensus size: 3
45807 CTAGTTTTTT
* * * *
45817 TTA TTA TTA TTT TTA TT- TCA TT- TGTT TTA TTTA TTA TTA TTA AT-
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA
*
45861 TTG TT- TTA TTA TTA TTA TTA -TA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45898 GAAATAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
2 9 0.14
3 50 0.79
4 4 0.06
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45870 original size:19 final size:20
Alignment explanation
Indices: 45846--45896 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
45836 ATTTGTTTTA
*
45846 TTTATTATTATTAATT-TGT
1 TTTATTATTATTAATTATAT
45865 TTTATTATTATT-ATTATAT
1 TTTATTATTATTAATTATAT
*
45884 TATATTATTATTA
1 TTTATTATTATTA
45897 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTATTATTAATTATAT
Found at i:45875 original size:22 final size:21
Alignment explanation
Indices: 45820--45897 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 21
45810 GTTTTTTTTA
*
45820 TTATTATTTTTATTTCATTTGTT
1 TTATTATTATTA-TT-ATTTGTT
45843 TTATTTATTATTATTAATTTGTT
1 TTA-TTATTATTATT-ATTTGTT
* *
45866 TTATTATTATTATTATATTATA
1 TTATTATTATTATTAT-TTGTT
45888 TTATTATTAT
1 TTATTATTAT
45898 GAAATAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.04
22 24 0.49
23 15 0.31
24 8 0.16
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (21 bp):
TTATTATTATTATTATTTGTT
Found at i:46419 original size:19 final size:18
Alignment explanation
Indices: 46380--46416 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
46370 AGAGACAGAG
*
46380 ACAGAGAACGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
46398 ACAGAGAAAGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
46416 A
1 A
46417 ACAAATATAC
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:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (18 bp):
ACAGAGAAAGAAAAAAAA
Found at i:47322 original size:20 final size:21
Alignment explanation
Indices: 47285--47325 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
47275 GATATTTTTA
**
47285 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
47306 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
47326 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:51878 original size:25 final size:24
Alignment explanation
Indices: 51840--51888 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
51830 AGAAAGTTAA
*
51840 ATTTATATATAATCAGAACTAAAC
1 ATTTATATATAATCAAAACTAAAC
*
51864 ATTTCATATTTAATCAAAACTAAAC
1 ATTT-ATATATAATCAAAACTAAAC
51889 GTTATATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (24 bp):
ATTTATATATAATCAAAACTAAAC
Found at i:55169 original size:19 final size:20
Alignment explanation
Indices: 55128--55166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55118 GATCAATCAT
*
55128 TTTCTCTAAAGGATCGATCC
1 TTTCTCCAAAGGATCGATCC
*
55148 TTTCTCCAAGGGATCGATC
1 TTTCTCCAAAGGATCGATC
55167 TTTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (20 bp):
TTTCTCCAAAGGATCGATCC
Found at i:55202 original size:20 final size:20
Alignment explanation
Indices: 55158--55206 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55148 TTTCTCCAAG
* *
55158 GGATCGATCTTTTTGAAAAT
1 GGATTGATCTTTTCGAAAAT
55178 GGATTGATCTTTTCGAAAA-
1 GGATTGATCTTTTCGAAAAT
55197 GTGATTGATC
1 G-GATTGATC
55207 CTTTGCTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (20 bp):
GGATTGATCTTTTCGAAAAT
Found at i:61374 original size:69 final size:69
Alignment explanation
Indices: 61263--61423 Score: 173
Period size: 69 Copynumber: 2.3 Consensus size: 69
61253 GTCTGCTAAT
* * * * ** *
61263 TAGGTACAATTATATCCTTGTATAATTCATACTCTGACACTACAAGTTGTTCGAAAC-ATGTCCT
1 TAGGTACAACTATATCC-TATAAAATTCATACCCTGACACTACAAGTTACTC-AAACTATGCCCT
61327 ACTCAG
64 ACTCAG
* *
61333 TAGGTACAACTATATCCTATAAAATTTATACCCT-AGCACTACAAGTTACTCAAACTATGCCCTG
1 TAGGTACAACTATATCCTATAAAATTCATACCCTGA-CACTACAAGTTACTCAAACTATGCCCTA
*
61397 CTCAT
65 CTCAG
*
61402 TAGATACAACTATATCCCTATA
1 TAGGTACAACTATAT-CCTATA
61424 GTTTCATACT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
68 5 0.06
69 50 0.65
70 22 0.29
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (69 bp):
TAGGTACAACTATATCCTATAAAATTCATACCCTGACACTACAAGTTACTCAAACTATGCCCTAC
TCAG
Found at i:65394 original size:10 final size:10
Alignment explanation
Indices: 65379--65423 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
65369 TTAGTACACA
65379 TTTTTTTCTT
1 TTTTTTTCTT
65389 TTTTTTTCTT
1 TTTTTTTCTT
*
65399 TTTTTTTCACT
1 TTTTTTTC-TT
*
65410 TTTTTTACTT
1 TTTTTTTCTT
65420 TTTT
1 TTTT
65424 ATGCTGCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:74420 original size:18 final size:19
Alignment explanation
Indices: 74381--74436 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 19
74371 TAATAAATTA
*
74381 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
* *
74399 ATTTATTA-AAAATATTAG
1 ATTTATAATAAAATAATAG
74417 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
74436 A
1 A
74437 AAGTTTAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:74947 original size:2 final size:2
Alignment explanation
Indices: 74942--74984 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
74932 TATCAATTAT
*
74942 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74984 T
1 T
74985 TTAATTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:75680 original size:21 final size:21
Alignment explanation
Indices: 75619--75680 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
75609 AAGTTAAAGC
* * * *
75619 GAGAGAATCAGAACGAGAAAT
1 GAGAGAAACACAAAGAGAAGT
* *
75640 GAGAGAAACATAGAGAGAAGT
1 GAGAGAAACACAAAGAGAAGT
75661 GAGAGAAACACAAAGAGAAG
1 GAGAGAAACACAAAGAGAAG
75681 CTAGAAAAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.55, C:0.08, G:0.31, T:0.06
Consensus pattern (21 bp):
GAGAGAAACACAAAGAGAAGT
Found at i:75896 original size:28 final size:29
Alignment explanation
Indices: 75854--75925 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 29
75844 TTATTCTAGT
* * *
75854 TGTTAAACTATATTACATTTCACTT-GAA
1 TGTTGAACTACATTACATTTCACTTAAAA
*
75882 TGTTGAACTACATTATATTTCACTTAAAA
1 TGTTGAACTACATTACATTTCACTTAAAA
75911 T-TTGAACTACATTAC
1 TGTTGAACTACATTAC
75926 TTTAATGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (29 bp):
TGTTGAACTACATTACATTTCACTTAAAA
Found at i:76278 original size:43 final size:43
Alignment explanation
Indices: 76227--76334 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
76217 TAAAAACGAT
** *
76227 GCTAAATGTCCTAACCTATTGTGGTGTTTG-TAAAAGAAACACC
1 GCTAAATGTCCTAACCTATTGCAGTATTTGTTAAAA-AAACACC
* * * **
76270 GCTAAATGTCCTAACATGTTGCAGTATTTGTTAACAAAACGTC
1 GCTAAATGTCCTAACCTATTGCAGTATTTGTTAAAAAAACACC
*
76313 GCTAAAGGTCCTAACCTATTGC
1 GCTAAATGTCCTAACCTATTGC
76335 GGCGTTTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
43 49 0.92
44 4 0.08
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (43 bp):
GCTAAATGTCCTAACCTATTGCAGTATTTGTTAAAAAAACACC
Found at i:77039 original size:13 final size:14
Alignment explanation
Indices: 77002--77039 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
76992 TTTGCATAAA
77002 AATATTATTTTTGT
1 AATATTATTTTTGT
77016 AAT-TTATTTTT-T
1 AATATTATTTTTGT
77028 AATATTAATTTT
1 AATATT-ATTTT
77040 AGAATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 10 0.45
14 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
AATATTATTTTTGT
Found at i:79317 original size:29 final size:29
Alignment explanation
Indices: 79258--79314 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
79248 TTTATATTAA
* **
79258 TTTAAAATTTTAATAATTATTTTTTCAAT
1 TTTAAAATTTTAATAATTAATTAATCAAT
*
79287 TTTAAAATTTTAATTATTAAATTAATCA
1 TTTAAAATTTTAATAATT-AATTAATCA
79315 TTTGAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAAAATTTTAATAATTAATTAATCAAT
Found at i:89815 original size:3 final size:3
Alignment explanation
Indices: 89807--89857 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
89797 TTAAATCAAC
89807 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
89855 ATA
1 ATA
89858 CTTGATGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:92507 original size:38 final size:39
Alignment explanation
Indices: 92452--92554 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 39
92442 CATGTACTTC
* * *
92452 TAGAGTCTTCTCCATTTGTTTGAAGATGTCATGCAGTCG
1 TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAATCG
* **
92491 T-GGGTCTTCTCTATTTGCCTGAAGATGTCATACAATCG
1 TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAATCG
*
92529 TAGAGTCTT-TATATTTGATTTGAAGA
1 TAGAGTCTTCTCTATTTG-TTTGAAGA
92555 CACACAGAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 39 0.75
39 13 0.25
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (39 bp):
TAGAGTCTTCTCTATTTGTTTGAAGATGTCATACAATCG
Found at i:93254 original size:6 final size:7
Alignment explanation
Indices: 93235--93260 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
93225 GTCGAGCTTC
93235 AATTTTT
1 AATTTTT
93242 AATTTTT
1 AATTTTT
93249 AATTTTT
1 AATTTTT
93256 AATTT
1 AATTT
93261 GAGTTGAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:99357 original size:286 final size:286
Alignment explanation
Indices: 98845--99417 Score: 1119
Period size: 286 Copynumber: 2.0 Consensus size: 286
98835 GGAATTAATC
98845 TCCCGCAAGTATGCTCAGGGGGTGAATATTGGTGATTCTCGAAATACGTCGACATTCTTTTCAAA
1 TCCCGCAAGTATGCTCAGGGGGTGAATATTGGTGATTCTCGAAATACGTCGACATTCTTTTCAAA
*
98910 AACTGCATCATGATTTTCTAAAATTAAGACAATGTCCGGTTATTAGGCACAATAGCTGATCTCCC
66 AACTGCATCATGATTTTCTAAAATTAAGACAATGCCCGGTTATTAGGCACAATAGCTGATCTCCC
*
98975 GCATTCATGCTAAGGACAAATGCTATTGTCCTCAATAAACGACTACCCTTTTCAACTTTTTGCAT
131 GCATTCATGCTAAGGACAAATGATATTGTCCTCAATAAACGACTACCCTTTTCAACTTTTTGCAT
99040 CTGTAATTATTTTCAAATTAAATAAAGATTGAACTTAAAATTTCCAATTTTAAATATAGGGTAAT
196 CTGTAATTATTTTCAAATTAAATAAAGATTGAACTTAAAATTTCCAATTTTAAATATAGGGTAAT
99105 CAACTAGGTATCAATTTTTGGACGCT
261 CAACTAGGTATCAATTTTTGGACGCT
99131 TCCCGCAAGTATGCTCAGGGGGTGAATATTGGTGATTCTCGAAATACGTCGACATTCTTTTCAAA
1 TCCCGCAAGTATGCTCAGGGGGTGAATATTGGTGATTCTCGAAATACGTCGACATTCTTTTCAAA
*
99196 AACTGCATCATGATTTTCTAAAATTATGACAATGCCCGGTTATTAGGCACAATAGCTGATCTCCC
66 AACTGCATCATGATTTTCTAAAATTAAGACAATGCCCGGTTATTAGGCACAATAGCTGATCTCCC
99261 GCATTCATGCTAAGGACAAATGATATTGTCCTCAATAAACGACTACCCTTTTCAACTTTTTGCAT
131 GCATTCATGCTAAGGACAAATGATATTGTCCTCAATAAACGACTACCCTTTTCAACTTTTTGCAT
99326 CTGTAATTATTTTCAAATTAAATAAAGATTGAACTTAAAATTTCCAATTTTAAATATAGGGTAAT
196 CTGTAATTATTTTCAAATTAAATAAAGATTGAACTTAAAATTTCCAATTTTAAATATAGGGTAAT
99391 CAACTAGGTATCAATTTTTGGACGCT
261 CAACTAGGTATCAATTTTTGGACGCT
99417 T
1 T
99418 ATGGGGTGCT
Statistics
Matches: 284, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 284 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (286 bp):
TCCCGCAAGTATGCTCAGGGGGTGAATATTGGTGATTCTCGAAATACGTCGACATTCTTTTCAAA
AACTGCATCATGATTTTCTAAAATTAAGACAATGCCCGGTTATTAGGCACAATAGCTGATCTCCC
GCATTCATGCTAAGGACAAATGATATTGTCCTCAATAAACGACTACCCTTTTCAACTTTTTGCAT
CTGTAATTATTTTCAAATTAAATAAAGATTGAACTTAAAATTTCCAATTTTAAATATAGGGTAAT
CAACTAGGTATCAATTTTTGGACGCT
Found at i:101471 original size:20 final size:20
Alignment explanation
Indices: 101425--101471 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
101415 GCGATTCCCA
* *
101425 CTTC-CTTCTTTTTCTTGTT
1 CTTCTCTTCTTATTCTTATT
101444 CTTCTCTTCTTATTCTTCATT
1 CTTCTCTTCTTATTCTT-ATT
101465 CTT-TCTT
1 CTTCTCTT
101472 TGGAGCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 15 0.62
21 5 0.21
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (20 bp):
CTTCTCTTCTTATTCTTATT
Found at i:107833 original size:18 final size:18
Alignment explanation
Indices: 107810--107844 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
107800 GGAGGCACGG
*
107810 GAGAACCGTTGACGATGA
1 GAGAACCGTTAACGATGA
*
107828 GAGAACTGTTAACGATG
1 GAGAACCGTTAACGATG
107845 GCATCCCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.20
Consensus pattern (18 bp):
GAGAACCGTTAACGATGA
Found at i:109588 original size:40 final size:40
Alignment explanation
Indices: 109524--109619 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
109514 GGTTACGTAG
*
109524 TACCGATAATGTTCTTACATTATCGATACTGCATGAACAA
1 TACCGATATTGTTCTTACATTATCGATACTGCATGAACAA
* * *
109564 TACTGATATTGTTCTTACATTATCGATATTGCATGAATAA
1 TACCGATATTGTTCTTACATTATCGATACTGCATGAACAA
109604 TACCGATATTGTTCTT
1 TACCGATATTGTTCTT
109620 GTGGTACCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (40 bp):
TACCGATATTGTTCTTACATTATCGATACTGCATGAACAA
Found at i:111079 original size:19 final size:20
Alignment explanation
Indices: 111043--111080 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
111033 TGAAAATGAT
* *
111043 TTGATTTTTTAAAGAAAAAG
1 TTGATTTTTGAAAAAAAAAG
111063 TTGA-TTTTGAAAAAAAAA
1 TTGATTTTTGAAAAAAAAA
111081 ATGAAACTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TTGATTTTTGAAAAAAAAAG
Found at i:111080 original size:20 final size:20
Alignment explanation
Indices: 111043--111081 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
111033 TGAAAATGAT
** *
111043 TTGATTTTTTAAAGAAAAAG
1 TTGATTTTGAAAAAAAAAAG
111063 TTGATTTTGAAAAAAAAAA
1 TTGATTTTGAAAAAAAAAA
111082 TGAAACTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
TTGATTTTGAAAAAAAAAAG
Found at i:111472 original size:14 final size:14
Alignment explanation
Indices: 111453--111524 Score: 80
Period size: 14 Copynumber: 5.4 Consensus size: 14
111443 CATTCAGTAA
111453 TATGTTCGTTCATT
1 TATGTTCGTTCATT
111467 TATGTTCG----TT
1 TATGTTCGTTCATT
*
111477 TATGTTCATTCATT
1 TATGTTCGTTCATT
*
111491 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
* *
111505 TATGTGCGTACATT
1 TATGTTCGTTCATT
111519 TATGTT
1 TATGTT
111525 TAGCCAATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 9 0.19
14 38 0.81
ACGTcount: A:0.15, C:0.12, G:0.17, T:0.56
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:111482 original size:24 final size:24
Alignment explanation
Indices: 111453--111500 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
111443 CATTCAGTAA
*
111453 TATGTTCGTTCATTTATGTTCGTT
1 TATGTTCATTCATTTATGTTCGTT
111477 TATGTTCATTCATTTATGTTCGTT
1 TATGTTCATTCATTTATGTTCGTT
111501 CGTTTATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (24 bp):
TATGTTCATTCATTTATGTTCGTT
Found at i:111810 original size:24 final size:24
Alignment explanation
Indices: 111778--111838 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
111768 CGTTTATTGT
111778 GTTCATTTATGTTCGTTTACATCC
1 GTTCATTTATGTTCGTTTACATCC
* *
111802 GTTCGTTTATGTTCGTTTACATTC
1 GTTCATTTATGTTCGTTTACATCC
111826 GTTCATTTATGTT
1 GTTCATTTATGTT
111839 TGTTCATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.15, T:0.54
Consensus pattern (24 bp):
GTTCATTTATGTTCGTTTACATCC
Found at i:111815 original size:10 final size:10
Alignment explanation
Indices: 111744--111820 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 10
111734 CGTTTACGTT
*
111744 TGTTCGTTTG
1 TGTTCGTTTA
111754 TGTTCGTTTA
1 TGTTCGTTTA
**
111764 CATTCGTTTA
1 TGTTCGTTTA
*
111774 TTGTGTTCATTTA
1 ---TGTTCGTTTA
111787 TGTTCGTTTACA
1 TGTTCGTTT--A
111799 TCCGTTCGTTTA
1 T--GTTCGTTTA
111811 TGTTCGTTTA
1 TGTTCGTTTA
111821 CATTCGTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
10 34 0.64
12 4 0.08
13 7 0.13
14 8 0.15
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.56
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:111853 original size:24 final size:23
Alignment explanation
Indices: 111726--111859 Score: 92
Period size: 24 Copynumber: 5.7 Consensus size: 23
111716 ATGTATATTT
* *
111726 ATTGTGTTCGTTTACGTTTGTTC
1 ATTGTGTTCGTTTATGTTCGTTC
* ** *
111749 GTTTGTGTTCGTTTACATTCGTTT
1 -ATTGTGTTCGTTTATGTTCGTTC
*
111773 ATTGTGTTCATTTATGTTCGTTTAC
1 ATTGTGTTCGTTTATGTTCG-TT-C
**
111798 A-TCCGTTCGTTTATGTTCGTTTAC
1 ATTGTGTTCGTTTATGTTCG-TT-C
* * *
111822 ATT-CGTTCATTTATGTTTGTTC
1 ATTGTGTTCGTTTATGTTCGTTC
111844 ATTTGTGTTCGTTTAT
1 A-TTGTGTTCGTTTAT
111860 CATTTAAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.02
23 20 0.22
24 65 0.73
25 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (23 bp):
ATTGTGTTCGTTTATGTTCGTTC
Found at i:115641 original size:4 final size:4
Alignment explanation
Indices: 115632--115748 Score: 76
Period size: 4 Copynumber: 28.2 Consensus size: 4
115622 AATCCAGAAG
** * *
115632 TATT TATT TATT TATTT TATT TGGT TATG TATT TATT TATTT TTTT TATT
1 TATT TATT TATT TA-TT TATT TATT TATT TATT TATT TA-TT TATT TATT
** * * *
115682 CGTT TATT TATTT TATT T-TGT CAGT TATT TATT TATT TCCTT TATT TAATT
1 TATT TATT TA-TT TATT TAT-T TATT TATT TATT TATT T-ATT TATT T-ATT
*
115733 GA-T TATT TATT TATT T
1 TATT TATT TATT TATT T
115749 TTTTCGGTTA
Statistics
Matches: 85, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
3 3 0.04
4 65 0.76
5 17 0.20
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (4 bp):
TATT
Found at i:115664 original size:29 final size:29
Alignment explanation
Indices: 115631--115699 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
115621 AAATCCAGAA
*
115631 GTATTTATTTATTTATTTTATTTGGTTAT
1 GTATTTATTTATTTATTTTATTCGGTTAT
* *
115660 GTATTTATTTATTTTTTTTATTCGTTTAT
1 GTATTTATTTATTTATTTTATTCGGTTAT
*
115689 TTATTTTATTT
1 GTA-TTTATTT
115700 TGTCAGTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 28 0.80
30 7 0.20
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.72
Consensus pattern (29 bp):
GTATTTATTTATTTATTTTATTCGGTTAT
Found at i:115680 original size:21 final size:22
Alignment explanation
Indices: 115637--115715 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 22
115627 AGAAGTATTT
115637 ATTTATTTATTTTATTTGGTTATGT-
1 ATTTATTTA-TTT-TTT--TTATGTC
115662 ATTTATTTATTTTTTTTAT-TC
1 ATTTATTTATTTTTTTTATGTC
* *
115683 GTTTATTTATTTTATTT-TGTC
1 ATTTATTTATTTTTTTTATGTC
*
115704 AGTTATTTATTT
1 ATTTATTTATTT
115716 ATTTCCTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.04
21 31 0.65
23 3 0.06
24 3 0.06
25 9 0.19
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.71
Consensus pattern (22 bp):
ATTTATTTATTTTTTTTATGTC
Found at i:115726 original size:46 final size:46
Alignment explanation
Indices: 115638--115727 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
115628 GAAGTATTTA
* **
115638 TTTATTTATTTTATTTGGTTATGTATTTATTTATTTTTTTTATTCG
1 TTTATTTATTTTATTTGGTCATGTATTTATTTATTTCCTTTATTCG
*
115684 TTTATTTATTTTATTTTGTCA-GTTATTTATTTATTTCCTTTATT
1 TTTATTTATTTTATTTGGTCATG-TATTTATTTATTTCCTTTATT
115728 TAATTGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.18, C:0.04, G:0.07, T:0.71
Consensus pattern (46 bp):
TTTATTTATTTTATTTGGTCATGTATTTATTTATTTCCTTTATTCG
Found at i:123963 original size:20 final size:20
Alignment explanation
Indices: 123930--123969 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
123920 GAGCTTATTT
*
123930 TCATTTTTCAATTTGAAACA
1 TCATTTTTCAATTTAAAACA
123950 TCATTTTT-ATATTTAAAACA
1 TCATTTTTCA-ATTTAAAACA
123970 ATTTCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TCATTTTTCAATTTAAAACA
Done.