Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold163
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: 1788591
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.32
Warning! 179834 characters in sequence are not A, C, G, or T
File 5 of 13
Found at i:446130 original size:2 final size:2
Alignment explanation
Indices: 446123--446153 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
446113 TCCCAATTAC
446123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
446154 GAAAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:447048 original size:19 final size:20
Alignment explanation
Indices: 447015--447053 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
447005 AAGAAACTGT
447015 TTTAAATTCAATTGAGTTTA
1 TTTAAATTCAATTGAGTTTA
*
447035 TTTAAATT-AATTGATTTTA
1 TTTAAATTCAATTGAGTTTA
447054 GATCAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTAAATTCAATTGAGTTTA
Found at i:447530 original size:13 final size:13
Alignment explanation
Indices: 447508--447551 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
447498 AATTCAGATA
447508 TTAA-TATTTAAT
1 TTAATTATTTAAT
*
447520 TAAATTATTTAAT
1 TTAATTATTTAAT
*
447533 TTAATTAATTAAT
1 TTAATTATTTAAT
447546 TTAATT
1 TTAATT
447552 TAATAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 3 0.11
13 25 0.89
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAATTATTTAAT
Found at i:447536 original size:18 final size:18
Alignment explanation
Indices: 447513--447555 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
447503 AGATATTAAT
447513 ATTTAATTAAATT-ATTTA
1 ATTTAATT-AATTAATTTA
447531 ATTTAATTAATTAATTTA
1 ATTTAATTAATTAATTTA
447549 ATTTAAT
1 ATTTAAT
447556 AATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAATTAATTAATTTA
Found at i:447570 original size:18 final size:20
Alignment explanation
Indices: 447494--447570 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 20
447484 AAACTAAAAA
*
447494 AATTAATTCAGATA-TTAA-T
1 AATTAATT-AAATATTTAATT
*
447513 ATTTAATTAAATTATTTAATTT
1 AATTAATTAAA-TATTTAA-TT
*
447535 AATTAATTAATTTAATTTAA-T
1 AATTAATTAA-AT-ATTTAATT
447556 AA-TAATTAAATATTT
1 AATTAATTAAATATTT
447571 TCGATTTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
18 6 0.13
19 10 0.21
20 11 0.23
21 3 0.06
22 11 0.23
23 6 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (20 bp):
AATTAATTAAATATTTAATT
Found at i:447900 original size:2 final size:2
Alignment explanation
Indices: 447893--447926 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
447883 TAAGTGTTAG
447893 TA TA TA TA TA TA 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
447927 GACTAATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:447984 original size:16 final size:17
Alignment explanation
Indices: 447963--448002 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
447953 TCAAAAATGG
447963 CATAAAATAAAAAATAA
1 CATAAAATAAAAAATAA
* *
447980 C-TAAAATATAAGATAA
1 CATAAAATAAAAAATAA
447996 CATAAAA
1 CATAAAA
448003 AATAACATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (17 bp):
CATAAAATAAAAAATAA
Found at i:448031 original size:29 final size:30
Alignment explanation
Indices: 447985--448044 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
447975 AATAACTAAA
447985 ATATAAGATAACATAAAAAATAACA-TCATT
1 ATATAAGATAACATAAAAAATAA-ATTCATT
*
448015 ATATAA-ATATACA-AAAATATAAATTCATT
1 ATATAAGATA-ACATAAAAAATAAATTCATT
448044 A
1 A
448045 AAAATGAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 1 0.04
29 17 0.63
30 9 0.33
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (30 bp):
ATATAAGATAACATAAAAAATAAATTCATT
Found at i:448582 original size:2 final size:2
Alignment explanation
Indices: 448575--448604 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
448565 ATATGCATCC
448575 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
448605 TAACTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449023 original size:2 final size:2
Alignment explanation
Indices: 449016--449047 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
449006 TAGAAAAAGT
449016 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
449048 TGGGATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:449772 original size:2 final size:2
Alignment explanation
Indices: 449765--449794 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
449755 TTAACATGTG
*
449765 TA TA TA TA TA CA 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
449795 CACACACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:456945 original size:36 final size:37
Alignment explanation
Indices: 456864--456946 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 37
456854 AAATAAGTAA
* * *
456864 TTTAATTTAA-ATTATTTTTTATAATTAAAATAAAAT
1 TTTAATTTAATATTATTTTTAAAAAATAAAATAAAAT
* * * *
456900 TATATTTTAATATTA-TTTTAAAAAATAATATAAATT
1 TTTAATTTAATATTATTTTTAAAAAATAAAATAAAAT
456936 TTTAATTTAAT
1 TTTAATTTAAT
456947 TTTAACTTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
36 33 0.89
37 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
TTTAATTTAATATTATTTTTAAAAAATAAAATAAAAT
Found at i:457310 original size:21 final size:21
Alignment explanation
Indices: 457286--457344 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
457276 TACTCTACTA
457286 ATTTTATTTTTTAAATTTATT
1 ATTTTATTTTTTAAATTTATT
* *
457307 ATTTTATCTTTTAAA-ATATT
1 ATTTTATTTTTTAAATTTATT
*
457327 -TTTTATATTTTTATATTT
1 ATTTTAT-TTTTTAAATTT
457345 TTAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 6 0.19
20 10 0.32
21 15 0.48
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTATTTTTTAAATTTATT
Found at i:457895 original size:21 final size:22
Alignment explanation
Indices: 457871--457928 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
457861 AATTATTATG
*
457871 ATTATAAATATAATAAAT-TAA
1 ATTATTAATATAATAAATATAA
457892 ATTATTAAT-T-ATAAAATATAA
1 ATTATTAATATAAT-AAATATAA
457913 ATTATTAATATTAATA
1 ATTATTAATA-TAATA
457929 TAAACAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 20 0.65
23 2 0.06
24 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTATTAATATAATAAATATAA
Found at i:457979 original size:51 final size:50
Alignment explanation
Indices: 457860--457979 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 50
457850 TATTATATTA
*
457860 TAATTATTATGATTATAA-ATATAATAAATTAAATTATTAATTATAAAATAT
1 TAATTATTAT-ATTATAATATATAACAAATTAAATTATTAA-TATAAAATAT
*
457911 AAATTATTA-A-TATTAATATA-AACAAATTTAAAATTATTAA-ATAACAATAT
1 TAATTATTATATTA-TAATATATAACAAA-TT-AAATTATTAATATAA-AATAT
*
457961 TAATTTTTATATTATAATA
1 TAATTATTATATTATAATA
457980 ATTATTTAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
48 2 0.03
49 13 0.22
50 17 0.29
51 24 0.41
52 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (50 bp):
TAATTATTATATTATAATATATAACAAATTAAATTATTAATATAAAATAT
Found at i:458004 original size:13 final size:12
Alignment explanation
Indices: 457969--458034 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
457959 ATTAATTTTT
457969 ATATTATAATAA
1 ATATTATAATAA
*
457981 TTATT-T-A-AA
1 ATATTATAATAA
457990 ATATTAATAATAA
1 ATATT-ATAATAA
*
458003 ATATTATTATAA
1 ATATTATAATAA
*
458015 TTAATTATAATAAA
1 AT-ATTATAAT-AA
458029 ATATTA
1 ATATTA
458035 ATCAAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
9 6 0.14
10 1 0.02
11 2 0.05
12 12 0.29
13 18 0.43
14 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTATAATAA
Found at i:458066 original size:41 final size:39
Alignment explanation
Indices: 457970--458067 Score: 130
Period size: 39 Copynumber: 2.5 Consensus size: 39
457960 TTAATTTTTA
*
457970 TATTATAA-TAATTAT-TTAAAATATTAATAATAAATAT
1 TATTATAATTAATTATAATAAAATATTAATAATAAATAT
458007 TATTATAATTAATTATAATAAAATATTAATCAA-AAATTAT
1 TATTATAATTAATTATAATAAAATATTAAT-AATAAA-TAT
*
458047 TATTTTAAATTAATTATAATA
1 TATTAT-AATTAATTATAATA
458068 TTATATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
37 8 0.15
38 7 0.13
39 15 0.28
40 10 0.19
41 14 0.26
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTATAATTAATTATAATAAAATATTAATAATAAATAT
Found at i:458227 original size:26 final size:26
Alignment explanation
Indices: 458196--458267 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
458186 ATGTATTCGT
458196 ATTTATGTTATTTTTTATAT-TTAA-A
1 ATTTAT-TTATTTTTTATATATTAATA
458221 A--TA-TTATATTTTTATATATTAATA
1 ATTTATTTAT-TTTTTATATATTAATA
*
458245 ATTTATTTTATTTTATATATATT
1 ATTTA-TTTATTTTTTATATATT
458268 TTTATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
21 4 0.10
22 9 0.23
23 6 0.15
24 2 0.05
25 1 0.03
26 2 0.05
27 11 0.28
28 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
ATTTATTTATTTTTTATATATTAATA
Found at i:458235 original size:22 final size:22
Alignment explanation
Indices: 458203--458262 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
458193 CGTATTTATG
458203 TTATTTTTTATAT-TTAA-AAT
1 TTATTTTTTATATATTAATAAT
458223 ATTATATTTTTATATATTAATAAT
1 -TTAT-TTTTTATATATTAATAAT
*
458247 TTATTTTATTTTATAT
1 TTATTTT-TTATATAT
458263 ATATTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 4 0.12
22 12 0.35
23 15 0.44
24 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTTTTATATATTAATAAT
Found at i:458242 original size:23 final size:25
Alignment explanation
Indices: 458203--458267 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
458193 CGTATTTATG
458203 TTAT-TTTTTATAT-TTAA-AA-TA
1 TTATATTTTTATATATTAATAATTA
458224 TTATATTTTTATATATTAATAATTTA
1 TTATATTTTTATATATTAATAA-TTA
*
458250 TTTTATTTTATATATATT
1 TTATATTTT-TATATATT
458268 TTTATATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 4 0.11
22 9 0.24
23 4 0.11
24 2 0.05
26 10 0.27
27 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATATTTTTATATATTAATAATTA
Found at i:459141 original size:8 final size:8
Alignment explanation
Indices: 459096--459206 Score: 57
Period size: 8 Copynumber: 13.5 Consensus size: 8
459086 ATTTATATAA
459096 ATATTTAT
1 ATATTTAT
* *
459104 ACATTAAT
1 ATATTTAT
459112 A-ATTTATT
1 ATATTTA-T
* * *
459120 TTATATAG
1 ATATTTAT
459128 ATATTTAT
1 ATATTTAT
459136 ATATTTAT
1 ATATTTAT
*
459144 ATAATTATT
1 ATATTTA-T
* *
459153 AATATATAA
1 -ATATTTAT
*
459162 ATGTTTAT
1 ATATTTAT
459170 ATATTTAT
1 ATATTTAT
459178 ATTATCTTTAT
1 A-TA--TTTAT
*
459189 TTATTT-T
1 ATATTTAT
459196 ATATTT-T
1 ATATTTAT
459203 ATAT
1 ATAT
459207 AAATTTTTAA
Statistics
Matches: 77, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
7 15 0.19
8 43 0.56
9 7 0.09
10 7 0.09
11 5 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:459142 original size:20 final size:20
Alignment explanation
Indices: 459096--459159 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
459086 ATTTATATAA
* *
459096 ATATTTATA-CATTAATAAT
1 ATATTTATATAATTATTAAT
* *
459115 TTATTTTATATAGA-TATTTAT
1 ATA-TTTATATA-ATTATTAAT
459136 ATATTTATATAATTATTAAT
1 ATATTTATATAATTATTAAT
459156 ATAT
1 ATAT
459160 AAATGTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.09
20 24 0.69
21 7 0.20
22 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTTATATAATTATTAAT
Found at i:459159 original size:34 final size:34
Alignment explanation
Indices: 459089--459179 Score: 116
Period size: 34 Copynumber: 2.7 Consensus size: 34
459079 ATTTTAAATT
* *
459089 TATATAAATATTTATACA-TTA-ATAATTTATTT
1 TATATAAATATTTATATATTTATATAATTTATTA
*
459121 TATATAGATATTTATATATTTATATAA-TTATTAA
1 TATATAAATATTTATATATTTATATAATTTATT-A
*
459155 TATATAAATGTTTATATATTTATAT
1 TATATAAATATTTATATATTTATAT
459180 TATCTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 16 0.31
33 8 0.16
34 27 0.53
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
TATATAAATATTTATATATTTATATAATTTATTA
Found at i:459178 original size:20 final size:19
Alignment explanation
Indices: 459119--459207 Score: 52
Period size: 19 Copynumber: 5.0 Consensus size: 19
459109 AATAATTTAT
*
459119 TTTATATAGATATTTATATA
1 TTTATATAAAT-TTTATATA
459139 TTTATAT-AA--TTAT-TA
1 TTTATATAAATTTTATATA
*
459154 -ATATATAAATGTTTATATA
1 TTTATATAAAT-TTTATATA
* *
459173 TTTATAT-TATCTTTATTTA
1 TTTATATAAAT-TTTATATA
459192 TTT-TAT--ATTTTATATA
1 TTTATATAAATTTTATATA
459208 AATTTTTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
14 5 0.09
15 4 0.07
16 11 0.20
17 2 0.04
18 7 0.12
19 15 0.27
20 12 0.21
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTATATAAATTTTATATA
Found at i:459257 original size:42 final size:43
Alignment explanation
Indices: 459184--459282 Score: 114
Period size: 42 Copynumber: 2.3 Consensus size: 43
459174 TTATATTATC
** *
459184 TTTATTTATTTTATATTTTATATAAATTTTTAAATAATTA-AA-
1 TTTATTTATTAAATATTTTAAATAAATTTTT-AATAATTATAAT
*
459226 TTTATTTATTAAATATTTTAAAATAAA-TTTTATTAATTATAAT
1 TTTATTTATTAAATATTTT-AAATAAATTTTTAATAATTATAAT
459269 TTTATTTAATTAAA
1 TTTATTT-ATTAAA
459283 AAATTTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 7 0.14
42 23 0.47
43 13 0.27
44 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (43 bp):
TTTATTTATTAAATATTTTAAATAAATTTTTAATAATTATAAT
Found at i:459277 original size:16 final size:15
Alignment explanation
Indices: 459251--459280 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
459241 TTTTAAAATA
459251 AATTTTATTAATTAT
1 AATTTTATTAATTAT
459266 AATTTTATTTAATTA
1 AATTTTA-TTAATTA
459281 AAAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTTATTAATTAT
Found at i:460114 original size:17 final size:16
Alignment explanation
Indices: 460094--460136 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
460084 TTTAACAAAT
460094 TTTTTAAATAAATTTTA
1 TTTTTAAAT-AATTTTA
**
460111 TTTTTATCTAATTTTA
1 TTTTTAAATAATTTTA
460127 TTTGTTAAAT
1 TTT-TTAAAT
460137 TACTATTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTTAAATAATTTTA
Found at i:462191 original size:24 final size:24
Alignment explanation
Indices: 462164--462212 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
462154 TACATAGTTG
462164 TTGCATGTGAATAACATTGGAGAT
1 TTGCATGTGAATAACATTGGAGAT
462188 TTGCATGTGAATAACATTGGAGAT
1 TTGCATGTGAATAACATTGGAGAT
462212 T
1 T
462213 AACTTCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (24 bp):
TTGCATGTGAATAACATTGGAGAT
Found at i:466090 original size:67 final size:67
Alignment explanation
Indices: 466019--466144 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 67
466009 AATATTTATT
*
466019 TTTTAAAATAA-TTATTTAATATATTTTATT-AAATAATTATTTTAATTTTATATAAAATAAAAA
1 TTTTAAAA-AATTTATTTAATATATTTTATTAAAATAATTAATTTAATTTTA-ATAAAATAAAAA
466082 ATTA
64 ATTA
*
466086 TTTTAAAAAATTTATTTAATATTTTTTATTAAAATAATTAATTTAATTTTAATAAAATA
1 TTTTAAAAAATTTATTTAATATATTTTATTAAAATAATTAATTTAATTTTAATAAAATA
466145 TAATTAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
66 2 0.04
67 34 0.62
68 19 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (67 bp):
TTTTAAAAAATTTATTTAATATATTTTATTAAAATAATTAATTTAATTTTAATAAAATAAAAAAT
TA
Found at i:466162 original size:67 final size:66
Alignment explanation
Indices: 466022--466167 Score: 174
Period size: 67 Copynumber: 2.2 Consensus size: 66
466012 ATTTATTTTT
*
466022 TAAAATAA-TTATTTAATATATTTTATTAAATAATTATTTTAATTTTATATAAAATAAAAAATTA
1 TAAAA-AATTTATTTAATATATTTTATTAAATAATTAATTTAATTTTATATAAAATAAAAAA-TA
**
466086 TTT
64 TAA
*
466089 TAAAAAATTTATTTAATATTTTTTATTAAAATAATTAATTTAATTTTA-ATAAAATATAATTAAA
1 TAAAAAATTTATTTAATATATTTTATT-AAATAATTAATTTAATTTTATATAAAATA-AA--AAA
466153 -ATAA
62 TATAA
466157 T-AAAAATTTAT
1 TAAAAAATTTAT
466168 AAATATAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
66 2 0.03
67 41 0.59
68 24 0.34
70 3 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (66 bp):
TAAAAAATTTATTTAATATATTTTATTAAATAATTAATTTAATTTTATATAAAATAAAAAATATA
A
Found at i:466616 original size:23 final size:23
Alignment explanation
Indices: 466590--466670 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
466580 CAAGTAGAGA
*
466590 AAAAAATATAATTAAATTTAAAT
1 AAAAATTATAATTAAATTTAAAT
* * *
466613 AAAATTTCATAA-TAAGTCTAAAT
1 AAAAATT-ATAATTAAATTTAAAT
**
466636 AATATTTTATAATTAAATTTAAAT
1 AA-AAATTATAATTAAATTTAAAT
466660 AAAAATTATAA
1 AAAAATTATAA
466671 AAAATATAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 27 0.59
24 19 0.41
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (23 bp):
AAAAATTATAATTAAATTTAAAT
Found at i:466685 original size:26 final size:24
Alignment explanation
Indices: 466654--466705 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
466644 ATAATTAAAT
466654 TTAAATAAAAATTATAAAAAATATAA
1 TTAAATAAAAATTAT--AAAATATAA
**
466680 TTAAATTTAAATTATAAAATATAA
1 TTAAATAAAAATTATAAAATATAA
466704 TT
1 TT
466706 TGAACTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAATAAAAATTATAAAATATAA
Found at i:467198 original size:24 final size:24
Alignment explanation
Indices: 467171--467217 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
467161 TTTAAAAATT
*
467171 ATATTTAAAAAATTTAA-TAAATAA
1 ATATGTAAAAAA-TTAAGTAAATAA
467195 ATATGTAAAAAATTAAGTAAATA
1 ATATGTAAAAAATTAAGTAAATA
467218 TTTTTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATGTAAAAAATTAAGTAAATAA
Found at i:467290 original size:17 final size:17
Alignment explanation
Indices: 467270--467321 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
467260 AAAATTGAGT
467270 AATTTTTAATAATAAAA
1 AATTTTTAATAATAAAA
*
467287 AA-TTTTAA-AAAAATAA
1 AATTTTTAATAATAA-AA
*
467303 ATATTTTTAATTATAAAA
1 A-ATTTTTAATAATAAAA
467321 A
1 A
467322 TATGTGAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 3 0.11
18 9 0.32
19 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTTTAATAATAAAA
Found at i:467322 original size:18 final size:18
Alignment explanation
Indices: 467271--467324 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
467261 AAATTGAGTA
467271 ATTTTTAATAATAAAAA-
1 ATTTTTAATAATAAAAAT
*
467288 A-TTTTAA-AAAAATAAAT
1 ATTTTTAATAATAA-AAAT
*
467305 ATTTTTAATTATAAAAAT
1 ATTTTTAATAATAAAAAT
467323 AT
1 AT
467325 GTGAAAGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.13
16 9 0.30
17 2 0.07
18 12 0.40
19 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTTTAATAATAAAAAT
Found at i:467605 original size:17 final size:17
Alignment explanation
Indices: 467583--467632 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
467573 CTTTTATTAT
467583 ATATAAAATAA-ATATAA
1 ATAT-AAATAATATATAA
*
467600 ATATAAATAATATATAT
1 ATATAAATAATATATAA
* *
467617 AGATAAATATTATATA
1 ATATAAATAATATATA
467633 GGTATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 6 0.21
17 23 0.79
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATATAAATAATATATAA
Found at i:472443 original size:21 final size:20
Alignment explanation
Indices: 472417--472477 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
472407 TAAAGTAAAC
472417 TATATATAATTTGTGTATATA
1 TATATATAATTT-TGTATATA
*
472438 TATATATTATATTT-T-TATA
1 TATATATAAT-TTTGTATATA
*
472457 TAT-TATAATTATGTATATA
1 TATATATAATTTTGTATATA
472476 TA
1 TA
472478 ATTACATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 2 0.06
18 6 0.18
19 13 0.38
20 1 0.03
21 10 0.29
22 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATATATAATTTTGTATATA
Found at i:472473 original size:15 final size:15
Alignment explanation
Indices: 472436--472481 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
472426 TTTGTGTATA
*
472436 TATATATATTATATT
1 TATATATATTATAAT
*
472451 TTTATATATTATAAT
1 TATATATATTATAAT
*
472466 TATGTATA-TATAAT
1 TATATATATTATAAT
472480 TA
1 TA
472482 CATAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATATATATTATAAT
Found at i:475252 original size:38 final size:38
Alignment explanation
Indices: 475201--475276 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 38
475191 TAACTAGATA
**
475201 AAGTCAATAAGAAATTTGTTTTATATATTTTATTTTTTT
1 AAGTCAATAAGAAACGTG-TTTATATATTTTATTTTTTT
* * *
475240 AAGT-AATGAGAAACGTGTTTATTTTTTTTATTTTTTT
1 AAGTCAATAAGAAACGTGTTTATATATTTTATTTTTTT
475277 CATTTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 18 0.56
38 10 0.31
39 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.57
Consensus pattern (38 bp):
AAGTCAATAAGAAACGTGTTTATATATTTTATTTTTTT
Found at i:476285 original size:20 final size:21
Alignment explanation
Indices: 476255--476306 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
476245 CCACTATAAA
* * *
476255 ATTTTGAAAAAATTAATAATT
1 ATTTTTAAAAAATAAAAAATT
476276 ATTTTTAAAAAATAAAAAATT
1 ATTTTTAAAAAATAAAAAATT
476297 ATTTTTAAAA
1 ATTTTTAAAA
476307 GTTATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTTTTAAAAAATAAAAAATT
Found at i:476381 original size:33 final size:34
Alignment explanation
Indices: 476344--476407 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
476334 ATTTTAAAAA
*
476344 TAATAATTATTTTTAATATTATT-AAATTAATAG
1 TAATAATTATTTTTAATATAATTAAAATTAATAG
*
476377 TAATATTTATTTTTAATATAATTAAAATTAA
1 TAATAATTATTTTTAATATAATTAAAATTAA
476408 GATGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
TAATAATTATTTTTAATATAATTAAAATTAATAG
Found at i:477715 original size:15 final size:16
Alignment explanation
Indices: 477685--477731 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
477675 AATGAAAAGA
477685 TAAATATATCATTTTT
1 TAAATATATCATTTTT
*
477701 TAAAT-TATTATTTTT
1 TAAATATATCATTTTT
** *
477716 TATTTTTATCATTTTT
1 TAAATATATCATTTTT
477732 ACTTTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TAAATATATCATTTTT
Found at i:479774 original size:2 final size:2
Alignment explanation
Indices: 479767--479797 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
479757 TAGACCAAAA
479767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
479798 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:479808 original size:16 final size:16
Alignment explanation
Indices: 479789--479830 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
479779 ATATATATAT
479789 ATATATATAATA-AAAA
1 ATATA-ATAATATAAAA
479805 ATATAATAATATAAAA
1 ATATAATAATATAAAA
479821 A-ATAA-AATAT
1 ATATAATAATAT
479831 CTTGATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.20
15 10 0.40
16 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAATAATATAAAA
Found at i:480519 original size:16 final size:19
Alignment explanation
Indices: 480500--480535 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
480490 AGTTAGTATG
480500 TTAA-AAAA-ATTAA-ATA
1 TTAATAAAATATTAATATA
480516 TTAATAAAATATTAATATA
1 TTAATAAAATATTAATATA
480535 T
1 T
480536 CATTGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 5 0.29
19 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAATAAAATATTAATATA
Found at i:482368 original size:20 final size:21
Alignment explanation
Indices: 482345--482385 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
482335 ATATATATTT
*
482345 TATTTAAAT-TTATTATAAAA
1 TATTTAAATATTAATATAAAA
482365 TATTTAAATATTAATATAAAA
1 TATTTAAATATTAATATAAAA
482386 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAATATTAATATAAAA
Found at i:482447 original size:15 final size:15
Alignment explanation
Indices: 482427--482456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
482417 AGATCGATAG
482427 ATTAAATCAAATCGA
1 ATTAAATCAAATCGA
*
482442 ATTAAATTAAATCGA
1 ATTAAATCAAATCGA
482457 TACTTAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
ATTAAATCAAATCGA
Found at i:482610 original size:15 final size:15
Alignment explanation
Indices: 482590--482635 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
482580 ACGTTAAAAA
482590 AAAATTATAAATATT
1 AAAATTATAAATATT
482605 AAAATT-TAAA-ATT
1 AAAATTATAAATATT
* *
482618 TAAATTATTTAATATT
1 AAAATTA-TAAATATT
482634 AA
1 AA
482636 TTAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 9 0.36
16 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:516446 original size:22 final size:22
Alignment explanation
Indices: 516405--516449 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
516395 TAATATAATT
516405 ATATTTGTTATGTATTAATTTA
1 ATATTTGTTATGTATTAATTTA
516427 ATATTT-TTAT-TATATAAATTTA
1 ATATTTGTTATGTAT-T-AATTTA
516449 A
1 A
516450 AAAATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.14
21 5 0.24
22 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATATTTGTTATGTATTAATTTA
Found at i:516844 original size:21 final size:21
Alignment explanation
Indices: 516818--516862 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
516808 AAATTCAGCT
516818 AAAAATGATAAAAAAAATTTA
1 AAAAATGATAAAAAAAATTTA
* * *
516839 AAAAATTATTATAAAAATTTA
1 AAAAATGATAAAAAAAATTTA
516860 AAA
1 AAA
516863 TTAAGGATGT
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:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAATGATAAAAAAAATTTA
Found at i:517606 original size:18 final size:18
Alignment explanation
Indices: 517583--517622 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
517573 AAATTTAATT
517583 ATAAAATATAAAATATTA
1 ATAAAATATAAAATATTA
* *
517601 ATAAAATATAATATTTTA
1 ATAAAATATAAAATATTA
517619 ATAA
1 ATAA
517623 TATAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAATATAAAATATTA
Found at i:517616 original size:44 final size:44
Alignment explanation
Indices: 517527--517616 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
517517 ATTAAATCGA
* * ** **
517527 TTAAATTTAATTTAAATTATTATTTAATAATAAAATAATTTTAT
1 TTAAATTTAATTTAAAATATAAAATAATAATAAAATAATAATAT
*
517571 TTAAATTTAATTATAAAATATAAAATATTAATAAAAT-ATAATAT
1 TTAAATTTAATT-TAAAATATAAAATAATAATAAAATAATAATAT
517615 TT
1 TT
517617 TAATAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 19 0.50
45 19 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (44 bp):
TTAAATTTAATTTAAAATATAAAATAATAATAAAATAATAATAT
Found at i:517637 original size:15 final size:16
Alignment explanation
Indices: 517580--517642 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 16
517570 TTTAAATTTA
517580 ATTATAA-AATATAAAAT
1 ATTATAATAATAT--AAT
517597 ATTAATAA-AATATAAT
1 ATT-ATAATAATATAAT
*
517613 ATTTTAATAATATAAT
1 ATTATAATAATATAAT
*
517629 -TTATAATAAAATAA
1 ATTATAATAATATAA
517643 ATTTTTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 15 0.37
16 14 0.34
17 3 0.07
18 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATAATAATATAAT
Found at i:517637 original size:26 final size:26
Alignment explanation
Indices: 517608--517706 Score: 64
Period size: 26 Copynumber: 3.8 Consensus size: 26
517598 TTAATAAAAT
517608 ATAATATTTTAATAATATAATTTATA
1 ATAATATTTTAATAATATAATTTATA
*
517634 ATAAAATAAATTTT--TAAT-TCAATATATA
1 AT--AAT--ATTTTAATAATAT-AATTTATA
* * * *
517662 AAAAAATTTTAATAA-ATAAATTAAA
1 ATAATATTTTAATAATATAATTTATA
517687 TATAATATTTTAAT-ATATAA
1 -ATAATATTTTAATAATATAA
517707 AAATAATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
24 5 0.09
25 6 0.11
26 23 0.42
27 1 0.02
28 15 0.27
30 5 0.09
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAATATTTTAATAATATAATTTATA
Found at i:517645 original size:16 final size:16
Alignment explanation
Indices: 517548--517651 Score: 56
Period size: 15 Copynumber: 6.6 Consensus size: 16
517538 TTAAATTATT
517548 ATTTAATAATAAAATAA
1 ATTT-ATAATAAAATAA
* * * *
517565 TTTTAT-TTAAATTTA
1 ATTTATAATAAAATAA
*
517580 A-TTATAA-AATATAA
1 ATTTATAATAAAATAA
*
517594 A-ATATTAATAAAATATA
1 ATTTA-TAATAAAATA-A
* *
517611 ATATTTTAATAATAT-A
1 AT-TTATAATAAAATAA
517627 ATTTATAATAAAATAA
1 ATTTATAATAAAATAA
*
517643 ATTTTTAAT
1 ATTTATAAT
517652 TCAATATATA
Statistics
Matches: 63, Mismatches: 17, Indels: 15
0.66 0.18 0.16
Matches are distributed among these distances:
14 11 0.17
15 19 0.30
16 19 0.30
17 5 0.08
18 8 0.13
19 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTATAATAAAATAA
Found at i:517651 original size:23 final size:23
Alignment explanation
Indices: 517631--517706 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 23
517621 AATATAATTT
*
517631 ATAATAAAATAAATTTTTAATTCA
1 ATAATAAAATAAATTTTTAA-TAA
517655 ATATATAAAA-AAA-TTTTAATAA
1 ATA-ATAAAATAAATTTTTAATAA
* *
517677 ATAAATTAAATATAATATTTTAATAT
1 AT-AATAAAATA-AAT-TTTTAATAA
517703 ATAA
1 ATAA
517707 AAATAATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
22 9 0.21
23 8 0.19
24 8 0.19
25 8 0.19
26 10 0.23
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATAAAATAAATTTTTAATAA
Found at i:518292 original size:22 final size:22
Alignment explanation
Indices: 518246--518303 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
518236 ATTAAAATAT
**
518246 TATTTTTATATTAATATTTTTA
1 TATTTTTATATTAATATTTAAA
518268 TATTTTTATATTTAA-ATTTAAA
1 TATTTTTATA-TTAATATTTAAA
*
518290 TATTATTATTATTA
1 TATTTTTA-TATTA
518304 TTAAATACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTAAA
Found at i:518588 original size:15 final size:14
Alignment explanation
Indices: 518546--518638 Score: 57
Period size: 15 Copynumber: 6.4 Consensus size: 14
518536 TTAAAGTGAT
*
518546 ATTTAATTGATTTAA
1 ATTTAATT-AATTAA
518561 ATTTGAGATTAATATAA
1 ATTT-A-ATTAAT-TAA
**
518578 ATTTAATTAATTTT
1 ATTTAATTAATTAA
*
518592 ATTTAA--AATTAT
1 ATTTAATTAATTAA
* *
518604 TTTTAA-TAAATAA
1 ATTTAATTAATTAA
518617 TATTTAATTAATTTAA
1 -ATTTAATTAA-TTAA
518633 ATTTAA
1 ATTTAA
518639 AATTATTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
12 10 0.16
13 4 0.06
14 12 0.19
15 19 0.31
16 7 0.11
17 10 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
ATTTAATTAATTAA
Found at i:518630 original size:40 final size:41
Alignment explanation
Indices: 518574--518650 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
518564 TGAGATTAAT
*
518574 ATAAATTTAATTAATTT-TATTTAAAATTATT-TTTAATAA
1 ATAAATTTAATTAATTTAAATTTAAAATTATTATTTAATAA
518613 ATAATATTTAATTAATTTAAATTTAAAATTATTATTTA
1 ATAA-ATTTAATTAATTTAAATTTAAAATTATTATTTA
518651 TAATTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
39 4 0.12
40 13 0.38
41 13 0.38
42 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
ATAAATTTAATTAATTTAAATTTAAAATTATTATTTAATAA
Found at i:518675 original size:16 final size:14
Alignment explanation
Indices: 518644--518674 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
518634 TTTAAAATTA
518644 TTATTTATAATTTT
1 TTATTTATAATTTT
518658 TTATATTATAATTTT
1 TTAT-TTATAATTTT
518673 TT
1 TT
518675 TGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTATAATTTT
Found at i:521832 original size:52 final size:52
Alignment explanation
Indices: 521771--521869 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
521761 GATCCATAAC
*
521771 AATTTAAAATTTAA-TTT-A-ATTAATTAATATTTTTTATTTATAATATTTAATA
1 AATTTAAAATTAAATTTTAATATTAA-TAAT-TTTTTTATTTAT-ATATTTAATA
*
521823 AATTTAAAATTAAATTTTAATATTGATAATTTTTTTATTTATATATT
1 AATTTAAAATTAAATTTTAATATTAATAATTTTTTTATTTATATATT
521870 AAGACTTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
52 18 0.43
53 15 0.36
54 5 0.12
55 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (52 bp):
AATTTAAAATTAAATTTTAATATTAATAATTTTTTTATTTATATATTTAATA
Found at i:523480 original size:18 final size:20
Alignment explanation
Indices: 523444--523483 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
523434 TTAAATTAAT
523444 TATTATAAATATTTATTTGA
1 TATTATAAATATTTATTTGA
*
523464 TATTTTAAAT-TTT-TTTGA
1 TATTATAAATATTTATTTGA
523482 TA
1 TA
523484 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TATTATAAATATTTATTTGA
Found at i:523741 original size:13 final size:13
Alignment explanation
Indices: 523700--523741 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
523690 ATCATGTATT
523700 TTTAAAAAA-ATA
1 TTTAAAAAATATA
523712 TTATAAAAAAT-TA
1 TT-TAAAAAATATA
523725 -TTAAAAAATATA
1 TTTAAAAAATATA
523737 TTTAA
1 TTTAA
523742 TTATTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 8 0.31
12 5 0.19
13 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAAAATATA
Found at i:523760 original size:19 final size:20
Alignment explanation
Indices: 523720--523758 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
523710 TATTATAAAA
*
523720 AATTATTAAAAAATATATTT
1 AATTATTAAAAAATAGATTT
*
523740 AATTATTAAAAATTAGATT
1 AATTATTAAAAAATAGATT
523759 AAAATATTTT
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:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTATTAAAAAATAGATTT
Found at i:523766 original size:20 final size:20
Alignment explanation
Indices: 523718--523766 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
523708 AATATTATAA
*
523718 AAAATTATTAAAAAATATATT
1 AAAA-TATTAAAAAATAGATT
* * *
523739 TAATTATTAAAAATTAGATT
1 AAAATATTAAAAAATAGATT
523759 AAAATATT
1 AAAATATT
523767 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAATATTAAAAAATAGATT
Found at i:524176 original size:19 final size:18
Alignment explanation
Indices: 524131--524177 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
524121 CAAATTTATT
*
524131 TAAAAAT-TTTAAAAAAT
1 TAAAAATATTTAAAAAAA
* *
524148 TTAAATTATTGTAAAAAAA
1 TAAAAATATT-TAAAAAAA
524167 TAAAAATATTT
1 TAAAAATATTT
524178 TTATATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAAAATATTTAAAAAAA
Found at i:524654 original size:20 final size:20
Alignment explanation
Indices: 524626--524676 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
524616 ATTTGAATCG
*
524626 ATTTGAATTATTATTTA-ATA
1 ATTTAAATTATT-TTTATATA
*
524646 ATTTAAATTATTTTTATTTA
1 ATTTAAATTATTTTTATATA
*
524666 ATTTTAATTAT
1 ATTTAAATTAT
524677 AAAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTAAATTATTTTTATATA
Found at i:525191 original size:52 final size:53
Alignment explanation
Indices: 525120--525225 Score: 178
Period size: 52 Copynumber: 2.0 Consensus size: 53
525110 TTATACGATT
*
525120 TTTTCTTCATCAAAAATACGAATGCAAACAAAAAAATATACTTTTCATATATA
1 TTTTCTTCATCAAAAATACGAATGCAAACAAAAAAATATACTTTCCATATATA
* *
525173 TTTT-TTCATCAAAGATACGAATGCAAACAAAAAAATATGCTTTCCATATATA
1 TTTTCTTCATCAAAAATACGAATGCAAACAAAAAAATATACTTTCCATATATA
525225 T
1 T
525226 ACCATTTTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
52 46 0.92
53 4 0.08
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (53 bp):
TTTTCTTCATCAAAAATACGAATGCAAACAAAAAAATATACTTTCCATATATA
Found at i:531225 original size:13 final size:13
Alignment explanation
Indices: 531209--531233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
531199 CATCCATGGG
531209 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
531222 GAAAAAAAAAAA
1 GAAAAAAAAAAA
531234 GGCAAACCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:533128 original size:12 final size:11
Alignment explanation
Indices: 533095--533131 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
533085 AATTATATAG
*
533095 ATACAAAGTAA
1 ATACAAAATAA
533106 ATACAAAATAA
1 ATACAAAATAA
533117 ATACATAAATAA
1 ATACA-AAATAA
533129 ATA
1 ATA
533132 AAAGTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (11 bp):
ATACAAAATAA
Found at i:533557 original size:35 final size:33
Alignment explanation
Indices: 533499--533572 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 33
533489 AAAAATTTAA
* *
533499 TAAAAAATAAAATATATGATAAATTTCAATTTATT
1 TAAAAAATAAAATATATCATAAATTT-AAATT-TT
*
533534 TAAAAAATTAAAA-ATATCTTAAATTTAAATTTT
1 TAAAAAA-TAAAATATATCATAAATTTAAATTTT
533567 TAAAAA
1 TAAAAA
533573 TTATTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 8 0.23
34 4 0.11
35 18 0.51
36 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (33 bp):
TAAAAAATAAAATATATCATAAATTTAAATTTT
Found at i:533899 original size:33 final size:33
Alignment explanation
Indices: 533858--533944 Score: 126
Period size: 31 Copynumber: 2.7 Consensus size: 33
533848 TCTATGAATT
*
533858 TATA-TAATATTATATATTTATATAAATTTTAA
1 TATATTAATATTATTTATTTATATAAATTTTAA
533890 TATATTAATA--ATTTATTTATATAAATTTTAA
1 TATATTAATATTATTTATTTATATAAATTTTAA
* *
533921 TATATTCATATTATTTTTTTATAT
1 TATATTAATATTATTTATTTATAT
533945 TTTCAACGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
31 29 0.59
32 4 0.08
33 16 0.33
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TATATTAATATTATTTATTTATATAAATTTTAA
Found at i:533924 original size:14 final size:14
Alignment explanation
Indices: 533876--533925 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
533866 ATTATATATT
533876 TATATAAATTTTAA
1 TATATAAATTTTAA
* *
533890 TATATTAATAATTTATT
1 TATA-TAA-ATTTTA-A
533907 TATATAAATTTTAA
1 TATATAAATTTTAA
533921 TATAT
1 TATAT
533926 TCATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 8 0.28
17 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:535811 original size:18 final size:18
Alignment explanation
Indices: 535790--535829 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
535780 TAAAATATAT
*
535790 AATTTTATTTAAATT-TTA
1 AATTTT-TTAAAATTATTA
535808 AATTTTTTAAAATTATTA
1 AATTTTTTAAAATTATTA
535826 AATT
1 AATT
535830 ACATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTTTAAAATTATTA
Found at i:536207 original size:13 final size:12
Alignment explanation
Indices: 536180--536212 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
536170 TCCCTACTGC
536180 TATTTGTT-TTT
1 TATTTGTTCTTT
536191 TATTTGTTCTATT
1 TATTTGTTCT-TT
536204 TATTTGTTC
1 TATTTGTTC
536213 CCATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (12 bp):
TATTTGTTCTTT
Found at i:537623 original size:13 final size:13
Alignment explanation
Indices: 537600--537643 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
537590 ATTATTAAAT
537600 TTTTAAAAATATAA
1 TTTT-AAAATATAA
537614 TTTTAAAATATAA
1 TTTTAAAATATAA
*
537627 TTGTT-AAGTATAA
1 TT-TTAAAATATAA
537640 TTTT
1 TTTT
537644 TTTATCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 2 0.07
13 20 0.71
14 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (13 bp):
TTTTAAAATATAA
Found at i:544071 original size:18 final size:18
Alignment explanation
Indices: 544050--544106 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
544040 ATTAAATACA
* *
544050 TATTTTTTATTAATTATT
1 TATTTATTAATAATTATT
*
544068 TATTTATTAATATTTATT
1 TATTTATTAATAATTATT
*
544086 TA-ATATTAA-AATTATT
1 TATTTATTAATAATTATT
544102 T-TTTA
1 TATTTA
544107 AAATATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 9 0.28
17 6 0.19
18 17 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTATTAATAATTATT
Found at i:544081 original size:14 final size:14
Alignment explanation
Indices: 544049--544087 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
544039 TATTAAATAC
544049 ATATTT-TTTATTA
1 ATATTTATTTATTA
544062 ATTATTTATTTATTA
1 A-TATTTATTTATTA
544077 ATATTTATTTA
1 ATATTTATTTA
544088 ATATTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 15 0.62
15 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTATTTATTA
Found at i:544111 original size:21 final size:21
Alignment explanation
Indices: 544080--544129 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
544070 TTTATTAATA
544080 TTTATTT--AATA-TTAAAAT
1 TTTATTTAAAATATTTAAAAT
*
544098 TATTTTTTAAAATATTTAAAAT
1 T-TTATTTAAAATATTTAAAAT
544120 TTTATTTAAA
1 TTTATTTAAA
544130 TAAATGGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 5 0.19
21 12 0.46
22 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATTTAAAATATTTAAAAT
Found at i:545729 original size:33 final size:34
Alignment explanation
Indices: 545674--545742 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
545664 AAAAAACTAA
*
545674 AAAATTATAATTTAATAATTTAATTAAAAATATT
1 AAAATTATAATTTAATAATTTAAATAAAAATATT
*
545708 AAAA-TATAATTTTAAT-TTTTAAATAAAAATATT
1 AAAATTATAA-TTTAATAATTTAAATAAAAATATT
545741 AA
1 AA
545743 TTAATTGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 22 0.69
34 10 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
AAAATTATAATTTAATAATTTAAATAAAAATATT
Found at i:546357 original size:23 final size:22
Alignment explanation
Indices: 546318--546360 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
546308 AATTTTTATA
*
546318 TTTTTATTATAATTAAATAAGT
1 TTTTTATTATAAATAAATAAGT
*
546340 TTTTATATTGTAAATAAATAA
1 TTTT-TATTATAAATAAATAA
546361 ATTCTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTTATTATAAATAAATAAGT
Found at i:546368 original size:23 final size:23
Alignment explanation
Indices: 546322--546368 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
546312 TTTATATTTT
* * *
546322 TATTATAATTAAATAAGTTTTTA
1 TATTATAAATAAATAAATTCTTA
*
546345 TATTGTAAATAAATAAATTCTTA
1 TATTATAAATAAATAAATTCTTA
546368 T
1 T
546369 TTCAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TATTATAAATAAATAAATTCTTA
Found at i:546377 original size:17 final size:18
Alignment explanation
Indices: 546355--546388 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
546345 TATTGTAAAT
546355 AAAT-AAATTCTTATTTC
1 AAATAAAATTCTTATTTC
*
546372 AAATAAAATTTTTATTT
1 AAATAAAATTCTTATTT
546389 ATATTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAAATTCTTATTTC
Found at i:547644 original size:20 final size:21
Alignment explanation
Indices: 547606--547645 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
547596 AACATATTAT
547606 AATAAATTATATAAAATATTG
1 AATAAATTATATAAAATATTG
*
547627 AATAAATT-TATCAAATATT
1 AATAAATTATATAAAATATT
547646 CATTTGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
AATAAATTATATAAAATATTG
Found at i:547857 original size:35 final size:34
Alignment explanation
Indices: 547793--547868 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 34
547783 TTTTTATTCG
* **
547793 TATTTATTATATTATTTTTGATATGATTATTTATT
1 TATTTATTATATTATTTTTAATACAATTA-TTATT
547828 TATTTATT-TATTATTTTTCAATACAATTATTATT
1 TATTTATTATATTATTTTT-AATACAATTATTATT
547862 TCATTTA
1 T-ATTTA
547869 CTACACAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 16 0.44
35 20 0.56
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (34 bp):
TATTTATTATATTATTTTTAATACAATTATTATT
Found at i:548171 original size:20 final size:21
Alignment explanation
Indices: 548137--548178 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
548127 TTAATAACGA
548137 TAAATAATTACTTTTAAAAAT
1 TAAATAATTACTTTTAAAAAT
* *
548158 TAAA-AATTATTTTTTAAAAT
1 TAAATAATTACTTTTAAAAAT
548178 T
1 T
548179 TTAAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAATAATTACTTTTAAAAAT
Found at i:548996 original size:26 final size:27
Alignment explanation
Indices: 548959--549038 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 27
548949 ACATAAAATA
* *
548959 ATATGAATATAAAATATTTTAAAATTT
1 ATATAAATATAAATTATTTTAAAATTT
548986 ATATAAA-ATAAATTATTATCATATTAAATTT
1 ATATAAATATAAATTATT-T--TA--AAATTT
549017 ATATAAATATAAATTATTTTAA
1 ATATAAATATAAATTATTTTAA
549039 GCATGATTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
26 9 0.20
27 8 0.18
29 4 0.09
31 14 0.31
32 10 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATAAATATAAATTATTTTAAAATTT
Found at i:549029 original size:16 final size:16
Alignment explanation
Indices: 548980--549031 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
548970 AAATATTTTA
548980 AAATTTATATAAA-AT
1 AAATTTATATAAATAT
*
548995 AAA-TTAT-TATCATATT
1 AAATTTATATA-AATA-T
549011 AAATTTATATAAATAT
1 AAATTTATATAAATAT
549027 AAATT
1 AAATT
549032 ATTTTAAGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 2 0.07
14 5 0.17
15 4 0.13
16 10 0.33
17 7 0.23
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTATATAAATAT
Found at i:550121 original size:13 final size:13
Alignment explanation
Indices: 550095--550133 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
550085 TAATATTTTA
550095 AAAAATTAAA--T
1 AAAAATTAAATTT
550106 AAAAATTAAATTT
1 AAAAATTAAATTT
*
550119 AAAAAATAAATTT
1 AAAAATTAAATTT
550132 AA
1 AA
550134 GTTAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTAAATTT
Found at i:550245 original size:37 final size:37
Alignment explanation
Indices: 550172--550250 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
550162 AAAATAAAAG
* *
550172 CTTAAATAAAATATTTTAAGCCCAAACTCAATCCAAC
1 CTTAAATAAAACATTTTAAGCCCAAACTCAACCCAAC
* **
550209 CTTAAATAAAACATTTTAAGCCTAAACTCGGCCCAAC
1 CTTAAATAAAACATTTTAAGCCCAAACTCAACCCAAC
550246 CTTAA
1 CTTAA
550251 GACTTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (37 bp):
CTTAAATAAAACATTTTAAGCCCAAACTCAACCCAAC
Found at i:550454 original size:12 final size:12
Alignment explanation
Indices: 550434--550463 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
550424 ATTATTAAGG
550434 AATAAATTTAAA
1 AATAAATTTAAA
*
550446 AATATATTTAAA
1 AATAAATTTAAA
550458 AATAAA
1 AATAAA
550464 AAATATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAAATTTAAA
Found at i:551295 original size:32 final size:31
Alignment explanation
Indices: 551243--551304 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
551233 TATAATTAAA
* **
551243 TAAATTTTTATTTAAATTTAATTATAAATAT
1 TAAATATTTATTTAAATTTAAAAATAAATAT
551274 TAAATATTT-TTTAATATTTTAAAAATAAATA
1 TAAATATTTATTTAA-A-TTTAAAAATAAATA
551305 AATTTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 5 0.19
31 9 0.35
32 12 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TAAATATTTATTTAAATTTAAAAATAAATAT
Found at i:553318 original size:27 final size:26
Alignment explanation
Indices: 553275--553326 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
553265 TTTATTCGTA
553275 TATTCATATCATATTTATATTATTTTTT
1 TATTCATATCATATTTA-ATT-TTTTTT
*
553303 TATT-ATATCATTTTTAATTTTTTT
1 TATTCATATCATATTTAATTTTTTT
553327 ATCGCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 3 0.13
27 11 0.48
28 4 0.17
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTCATATCATATTTAATTTTTTTT
Found at i:553743 original size:24 final size:24
Alignment explanation
Indices: 553697--553754 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
553687 TGATTTTTTA
* * *
553697 ATTATA-TAATATGTTTTTTACAT
1 ATTATATTATTATGTGTTTCACAT
553720 ATTATATTATTATGTGTTTCACAT
1 ATTATATTATTATGTGTTTCACAT
553744 ATTATATTATT
1 ATTATATTATT
553755 TATATCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 6 0.19
24 25 0.81
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (24 bp):
ATTATATTATTATGTGTTTCACAT
Found at i:554644 original size:14 final size:14
Alignment explanation
Indices: 554625--554651 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
554615 TTGAAAAAAA
554625 ATAAAAATATTAAG
1 ATAAAAATATTAAG
554639 ATAAAAATATTAA
1 ATAAAAATATTAA
554652 AAATTAATTT
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:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
ATAAAAATATTAAG
Found at i:554701 original size:26 final size:25
Alignment explanation
Indices: 554641--554710 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
554631 ATATTAAGAT
*
554641 AAAAATATTAAAAATTAATTTTAAA
1 AAAAATATAAAAAATTAATTTTAAA
* **
554666 AATTAAATA-AATAAATTTTTTTTAAA
1 AA--AAATATAAAAAATTAATTTTAAA
554692 AAAAATATAAAAATATTAA
1 AAAAATATAAAAA-ATTAA
554711 AATAACGTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
24 5 0.15
25 6 0.18
26 18 0.53
27 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAAATATAAAAAATTAATTTTAAA
Found at i:560268 original size:32 final size:33
Alignment explanation
Indices: 560224--560298 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 33
560214 TTATGTATTA
*
560224 TATATTTATAT-AATTTTGACATATTAATAATAT
1 TATATTTATATAAATTTTAACATATT-ATAATAT
* *
560257 TATA-TTATATAAATTTTAATATATTATTATAT
1 TATATTTATATAAATTTTAACATATTATAATAT
560289 TA-ATTTATAT
1 TATATTTATAT
560299 TATATATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 20 0.54
33 16 0.43
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (33 bp):
TATATTTATATAAATTTTAACATATTATAATAT
Found at i:560276 original size:22 final size:21
Alignment explanation
Indices: 560251--560303 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
560241 GACATATTAA
560251 TAATATTATATTATATAAATTT
1 TAATATTATATTATATAAA-TT
*
560273 TAATA-TATTATTATATTAATT
1 TAATATTA-TATTATATAAATT
560294 T-ATATTATAT
1 TAATATTATAT
560304 ATGTATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.21
21 7 0.25
22 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATATTATATTATATAAATT
Found at i:560299 original size:18 final size:18
Alignment explanation
Indices: 560276--560325 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 18
560266 TAAATTTTAA
560276 TATATTATTATATTAATT
1 TATATTATTATATTAATT
560294 TATATTA-TATATGT-A-T
1 TATATTATTATAT-TAATT
560310 TAT-TTATTATATTAAT
1 TATATTATTATATTAAT
560326 AATTATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
17 6 0.21
18 8 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TATATTATTATATTAATT
Found at i:560319 original size:23 final size:25
Alignment explanation
Indices: 560259--560331 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 25
560249 AATAATATTA
*
560259 TATTATATAAATTT-TA--ATATAT
1 TATTATATTAATTTATATTATATAT
560281 TATTATATTAATTTATATTATATAT
1 TATTATATTAATTTATATTATATAT
560306 GTATTAT-TT-A-TTATATTA-ATAAT
1 -TATTATATTAATTTATATTATAT-AT
560329 TAT
1 TAT
560332 ATCATATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
22 18 0.40
23 12 0.27
24 1 0.02
25 8 0.18
26 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (25 bp):
TATTATATTAATTTATATTATATAT
Found at i:560925 original size:14 final size:14
Alignment explanation
Indices: 560901--560954 Score: 62
Period size: 13 Copynumber: 4.1 Consensus size: 14
560891 TCAAATTGCG
560901 TATTT-AATATATA
1 TATTTAAATATATA
*
560914 TATTTAAATATAAA
1 TATTTAAATATATA
*
560928 TA-TAAAATATA-A
1 TATTTAAATATATA
560940 TATTTAAA-ATATA
1 TATTTAAATATATA
560953 TA
1 TA
560955 AAAAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
12 6 0.17
13 20 0.57
14 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTTAAATATATA
Found at i:560955 original size:16 final size:15
Alignment explanation
Indices: 560901--560955 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
560891 TCAAATTGCG
560901 TATTT-AATATAT-A
1 TATTTAAATATATAA
560914 TATTTAAATATA-AA
1 TATTTAAATATATAA
560928 TA--TAAA-ATATAA
1 TATTTAAATATATAA
560940 TATTTAAAATATATAA
1 TATTT-AAATATATAA
560956 AAAAATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.09
12 8 0.23
13 5 0.14
14 10 0.29
15 3 0.09
16 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTTAAATATATAA
Found at i:560959 original size:25 final size:27
Alignment explanation
Indices: 560906--560959 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
560896 TTGCGTATTT
*
560906 AATATATATATTTAAATATAAATATAA
1 AATATATATATTTAAATATAAATAAAA
*
560933 AATATA-ATATTTAAA-ATATATAAAA
1 AATATATATATTTAAATATAAATAAAA
560958 AA
1 AA
560960 ATTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 9 0.36
27 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATATATATATTTAAATATAAATAAAA
Found at i:573070 original size:51 final size:50
Alignment explanation
Indices: 572994--573093 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 50
572984 TAGAAAGAAA
*
572994 TATATATATATATATATATAAATGTTCAATGTATATTCAAATGTAATAAGC
1 TATATATATATATATATATAAATGTTCAATGCATA-TCAAATGTAATAAGC
573045 TATATATATATATATATATAAATGTTCAATGCATATCAAATGTAATAAG
1 TATATATATATATATATATAAATGTTCAATGCATATCAAATGTAATAAG
573094 TGAACTGCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 14 0.29
51 34 0.71
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (50 bp):
TATATATATATATATATATAAATGTTCAATGCATATCAAATGTAATAAGC
Found at i:573280 original size:3 final size:3
Alignment explanation
Indices: 573272--573308 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
573262 TTCAATGCAT
573272 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
573309 CCCTTCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:573972 original size:13 final size:13
Alignment explanation
Indices: 573956--573991 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
573946 CTTTAAATAT
573956 AATTTAATATAAA
1 AATTTAATATAAA
573969 AATTTTTAATATAAA
1 AA--TTTAATATAAA
573984 AATTTAAT
1 AATTTAAT
573992 CCAACTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAATATAAA
Found at i:573978 original size:15 final size:15
Alignment explanation
Indices: 573958--573988 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
573948 TTAAATATAA
573958 TTTAATATAAAAATT
1 TTTAATATAAAAATT
573973 TTTAATATAAAAATT
1 TTTAATATAAAAATT
573988 T
1 T
573989 AATCCAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTAATATAAAAATT
Found at i:575535 original size:30 final size:30
Alignment explanation
Indices: 575499--575595 Score: 103
Period size: 29 Copynumber: 3.3 Consensus size: 30
575489 TATGTTATGA
*
575499 ATTTATTTAAATATAAATTAAAATTTAAAG
1 ATTTATTTAAATAAAAATTAAAATTTAAAG
*
575529 ATTTATTT-AATAAAAATTAAAAGTT-AAG
1 ATTTATTTAAATAAAAATTAAAATTTAAAG
* *
575557 AGTTTATTTAAGTACAAATT-AAATATTAAA-
1 A-TTTATTTAAATAAAAATTAAAAT-TTAAAG
*
575587 ACTTATTTA
1 ATTTATTTA
575596 GATACACTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 4 0.07
29 32 0.56
30 19 0.33
31 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTTATTTAAATAAAAATTAAAATTTAAAG
Found at i:575867 original size:3 final size:3
Alignment explanation
Indices: 575818--575848 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
575808 AGGCAAGTAT
575818 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
575849 AGGAATTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:578247 original size:20 final size:20
Alignment explanation
Indices: 578222--578294 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
578212 ATATTATTTT
578222 TATTAAATTAAAAAATAATA
1 TATTAAATTAAAAAATAATA
*
578242 TATTAAA--AATTTAAATAATA
1 TATTAAATTAA--AAAATAATA
* * *
578262 TTTTAAATTTTAAAAATAAAA
1 TATTAAA-TTAAAAAATAATA
*
578283 TTTTAAATTAAA
1 TATTAAATTAAA
578295 TTTAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 2 0.05
20 25 0.60
21 14 0.33
23 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTAAATTAAAAAATAATA
Found at i:578400 original size:5 final size:5
Alignment explanation
Indices: 578385--578501 Score: 50
Period size: 5 Copynumber: 23.6 Consensus size: 5
578375 AAATAATTAA
* *
578385 TATATT TATAT TATAT TATACT ATTTAT TATAT TATAAT TATAT T-TAA
1 TATA-T TATAT TATAT TATA-T -TATAT TATAT TAT-AT TATAT TATAT
* * * * * *
578433 AATAT TATA- TAT-T TATA- TAAAT T-TAA TATA- TAAAT AAT-T TATTT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
578477 TATATT TATTT TATATT TATAT TAT
1 TATA-T TATAT TATA-T TATAT TAT
578502 TTTAATTTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
4 19 0.23
5 41 0.49
6 20 0.24
7 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:578401 original size:11 final size:11
Alignment explanation
Indices: 578385--578505 Score: 65
Period size: 11 Copynumber: 10.7 Consensus size: 11
578375 AAATAATTAA
578385 TATATTTATAT
1 TATATTTATAT
578396 TATATTATACTAT
1 TATATT-TA-TAT
578409 T-TA-TTATAT
1 TATATTTATAT
*
578418 TATAATTATAT
1 TATATTTATAT
**
578429 T-TA-AAATAT
1 TATATTTATAT
578438 TATATATT-TAT
1 TATAT-TTATAT
*
578449 ATAAATTTAATAT
1 -TATATTT-ATAT
*
578462 ATAAATAATTTATTT
1 -T--AT-ATTTATAT
*
578477 TATATTTATTT
1 TATATTTATAT
578488 TATATTTATAT
1 TATATTTATAT
578499 TAT-TTTA
1 TATATTTA
578506 ATTTTTATAG
Statistics
Matches: 89, Mismatches: 8, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
9 9 0.10
10 12 0.13
11 40 0.45
12 10 0.11
13 9 0.10
14 1 0.01
15 4 0.04
16 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:578416 original size:28 final size:27
Alignment explanation
Indices: 578375--578506 Score: 86
Period size: 26 Copynumber: 5.0 Consensus size: 27
578365 TAATTAGATC
578375 AAATAATTAATATATTTATATTATA-TTA
1 AAAT-ATT-ATATATTTATATTATATTTA
* *
578403 TACTATT-TATTATATTATAATTATATTTA
1 AAATATTATA-TAT-TTAT-ATTATATTTA
*
578432 AAATATTATATATTTATA-TAAATTTA
1 AAATATTATATATTTATATTATATTTA
* * *
578458 ATATA-TAAATAATTTATTTTATATTT-
1 AAATATTATAT-ATTTATATTATATTTA
578484 --AT-TT-TATATTTATATTAT-TTTA
1 AAATATTATATATTTATATTATATTTA
578506 A
1 A
578507 TTTTTATAGT
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
21 3 0.04
22 10 0.12
23 2 0.02
24 3 0.04
25 6 0.07
26 20 0.24
27 14 0.17
28 12 0.14
29 11 0.13
30 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATTATATATTTATATTATATTTA
Found at i:578431 original size:20 final size:20
Alignment explanation
Indices: 578377--578441 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
578367 ATTAGATCAA
*
578377 ATAATTA-ATATATTTATATT
1 ATAATTATATTTA-TTATATT
*
578397 ATATTATACTATTTATTATATT
1 ATAAT-TA-TATTTATTATATT
**
578419 ATAATTATATTTAAAATATT
1 ATAATTATATTTATTATATT
578439 ATA
1 ATA
578442 TATTTATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 18 0.49
21 4 0.11
22 11 0.30
23 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATTATATTTATTATATT
Found at i:578438 original size:48 final size:47
Alignment explanation
Indices: 578381--578499 Score: 124
Period size: 46 Copynumber: 2.6 Consensus size: 47
578371 GATCAAATAA
* *
578381 TTAATATATTTATATTATATTATACTATTTATTATAT-TATAATTATAT
1 TTAATATATTTATATTATATTATA-TATTTAATATATAAATAATT-TAT
* *
578429 TTAAAATATTATATATT-TA-TATAAATTTAATATATAAATAATTTAT
1 TTAATATATT-TATATTATATTATATATTTAATATATAAATAATTTAT
*
578475 TT--TATATTTATTTTATATT-TATATT
1 TTAATATATTTATATTATATTATATATT
578500 ATTTTAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
43 5 0.08
44 12 0.20
45 1 0.02
46 15 0.25
47 10 0.17
48 11 0.18
49 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (47 bp):
TTAATATATTTATATTATATTATATATTTAATATATAAATAATTTAT
Found at i:578480 original size:16 final size:17
Alignment explanation
Indices: 578419--578497 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 17
578409 TTATTATATT
578419 ATAA-TTATATTTA-AA
1 ATAATTTATATTTATAA
*
578434 AT-ATTATATATTTATAT
1 ATAATT-TATATTTATAA
*
578451 A-AATTTA-ATATATAA
1 ATAATTTATATTTATAA
*
578466 ATAATTTAT-TTTATAT
1 ATAATTTATATTTATAA
* *
578482 TTATTTTATATTTATA
1 ATAATTTATATTTATA
578498 TTATTTTAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
14 1 0.02
15 10 0.20
16 28 0.56
17 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATTTATATTTATAA
Found at i:578496 original size:22 final size:22
Alignment explanation
Indices: 578469--578510 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
578459 TATATAAATA
*
578469 ATTTATTTTATATTT-ATTTTAT
1 ATTTATATTAT-TTTAATTTTAT
578491 ATTTATATTATTTTAATTTT
1 ATTTATATTATTTTAATTTT
578511 TATAGTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTATATTATTTTAATTTTAT
Found at i:578507 original size:48 final size:46
Alignment explanation
Indices: 578385--578503 Score: 118
Period size: 48 Copynumber: 2.6 Consensus size: 46
578375 AAATAATTAA
* * * *
578385 TATATTTATATTATA-TTATACTATTTATTATATTATAATTATATT
1 TATATTTATTTTATATTTATATTATTTAATATATAATAATTATATT
** * *
578430 TA-AAATATTATATATTTATATAAATTTAATATATAAATAATT-TATTT
1 TATATTTATTTTATATTTATAT-TATTTAATATAT-AATAATTATA-TT
578477 TATATTTATTTTATATTTATATTATTT
1 TATATTTATTTTATATTTATATTATTT
578504 TAATTTTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
44 8 0.14
45 7 0.12
46 12 0.21
47 14 0.25
48 16 0.28
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (46 bp):
TATATTTATTTTATATTTATATTATTTAATATATAATAATTATATT
Found at i:578512 original size:17 final size:17
Alignment explanation
Indices: 578470--578514 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
578460 ATATAAATAA
578470 TTTA-TTTTATATTTAT
1 TTTATTTTTATATTTAT
*
578486 TTTATATTTATA-TTAT
1 TTTATTTTTATATTTAT
578502 TTTAATTTTTATA
1 TTT-ATTTTTATA
578515 GTGTGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTTATATTTAT
Found at i:579413 original size:27 final size:28
Alignment explanation
Indices: 579382--579434 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
579372 TATAATTATT
579382 TTTAAAAATAATATT-AAATAAATTTAA
1 TTTAAAAATAATATTAAAATAAATTTAA
***
579409 TTTAATTTTAATATTAAAATAAATTT
1 TTTAAAAATAATATTAAAATAAATTT
579435 GATTCAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTAAAAATAATATTAAAATAAATTTAA
Done.