Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 1425817
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 4 of 8
Found at i:399558 original size:18 final size:18
Alignment explanation
Indices: 399537--399575 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
399527 GTTTTATCAT
*
399537 AAATTTATTATTAAATTA
1 AAATATATTATTAAATTA
*
399555 AAATATATTTTTAAATTA
1 AAATATATTATTAAATTA
399573 AAA
1 AAA
399576 ACATAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATATTATTAAATTA
Found at i:399633 original size:18 final size:18
Alignment explanation
Indices: 399589--399639 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
399579 TAACAATTTA
*
399589 ATTATTAAA-TTTATTAT
1 ATTAATAAATTTTATTAT
399606 ATCATAATAAATTTTATTAT
1 AT--TAATAAATTTTATTAT
399626 ATTAATAAATTTTA
1 ATTAATAAATTTTA
399640 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.07
18 12 0.40
19 6 0.20
20 10 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAATAAATTTTATTAT
Found at i:400246 original size:7 final size:7
Alignment explanation
Indices: 400231--400267 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
400221 ATAACATACA
400231 TTAAAAT
1 TTAAAAT
*
400238 TTAATAT
1 TTAAAAT
400245 TTAAAAT
1 TTAAAAT
*
400252 TGAAAAT
1 TTAAAAT
400259 TTAAAAT
1 TTAAAAT
400266 TT
1 TT
400268 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (7 bp):
TTAAAAT
Found at i:400786 original size:15 final size:17
Alignment explanation
Indices: 400756--400788 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
400746 ATTTTTAAAA
400756 ATTTATATAATAATTTT
1 ATTTATATAATAATTTT
400773 ATTTATA-AAT-ATTTT
1 ATTTATATAATAATTTT
400788 A
1 A
400789 AAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTATATAATAATTTT
Found at i:400809 original size:26 final size:25
Alignment explanation
Indices: 400734--400810 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
400724 TAAATTTTAT
*
400734 TATT-TAAAAT-ATATTTTTAAAAA
1 TATTATAAAATAATTTTTTTAAAAA
* *
400757 T-TTATATAATAATTTTATTTATAAA
1 TATTATAAAATAATTTT-TTTAAAAA
* *
400782 TATTTTAAAATTTATTTTTTTAAAAA
1 TATTATAAAA-TAATTTTTTTAAAAA
400808 TAT
1 TAT
400811 ATTGATTGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
22 2 0.05
23 6 0.14
24 4 0.10
25 8 0.19
26 16 0.38
27 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATAAAATAATTTTTTTAAAAA
Found at i:401069 original size:21 final size:21
Alignment explanation
Indices: 401035--401074 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
401025 AATTTTTATT
401035 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
401056 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
401075 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:410811 original size:2 final size:2
Alignment explanation
Indices: 410806--410838 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
410796 CACATACATC
410806 TA 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 TA T
410839 CAGTTTGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:411946 original size:20 final size:19
Alignment explanation
Indices: 411901--411947 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
411891 ATTTTATTAT
* *
411901 TTATTATATTAATAAAATA
1 TTATTTTATAAATAAAATA
*
411920 ATA-TTTATAAATATAAATA
1 TTATTTTATAAATA-AAATA
411939 TTATTTTAT
1 TTATTTTAT
411948 TATTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTTTATAAATAAAATA
Found at i:412250 original size:6 final size:6
Alignment explanation
Indices: 412239--412294 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
412229 TTTAAAAAAT
*
412239 TTTAAA TTTAAA TTTAAA ATTAAA -TTAAA -TTAAA -TT-AA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
412281 TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TT
412295 ATTATTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
4 6 0.13
5 14 0.30
6 26 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:412265 original size:5 final size:5
Alignment explanation
Indices: 412240--412295 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
412230 TTAAAAAATT
* *
412240 TTAAA TTTAAA TTTAAAA TTAAA TTAAA TTAAA TT-AA TTTAT TTAAA
1 TTAAA -TTAAA -TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
412287 TTTAAA TTA
1 -TTAAA TTA
412296 TTATTTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
4 4 0.09
5 22 0.50
6 15 0.34
7 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (5 bp):
TTAAA
Found at i:412285 original size:19 final size:21
Alignment explanation
Indices: 412239--412340 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
412229 TTTAAAAAAT
* *
412239 TTTAAATTTAAATTTAAAATTAA
1 TTTAAATTTAAA-TT-ATATTTA
*
412262 ATTAAA-TTAAATTA-ATTTA
1 TTTAAATTTAAATTATATTTA
412281 TTTAAATTTAAATTATTATTTA
1 TTTAAATTTAAATTA-TATTTA
** *
412303 TTT-TTTTTAAAATTATTTTTA
1 TTTAAATTT-AAATTATATTTA
*
412324 TATT-AATATAAATTATA
1 T-TTAAATTTAAATTATA
412341 ATTAAATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
19 9 0.14
20 9 0.14
21 18 0.28
22 23 0.36
23 5 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAAATTTAAATTATATTTA
Found at i:412600 original size:16 final size:16
Alignment explanation
Indices: 412555--412643 Score: 81
Period size: 16 Copynumber: 5.6 Consensus size: 16
412545 TATTTTCAAG
**
412555 TTCGGGTCATTTTAGA
1 TTCGGGTCATTTCGGA
*
412571 TTCGAGTCATTTCGGA
1 TTCGGGTCATTTCGGA
*
412587 TTCGGGTCATTTCGGG
1 TTCGGGTCATTTCGGA
* * * *
412603 TTCGGATTATTTTGGG
1 TTCGGGTCATTTCGGA
*
412619 TTCGGGTCATTT-TGA
1 TTCGGGTCATTTCGGA
412634 GTTCGGGTCA
1 -TTCGGGTCA
412644 ATCGAGTTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
15 1 0.02
16 59 0.98
ACGTcount: A:0.13, C:0.15, G:0.30, T:0.42
Consensus pattern (16 bp):
TTCGGGTCATTTCGGA
Found at i:413737 original size:16 final size:16
Alignment explanation
Indices: 413699--413774 Score: 89
Period size: 16 Copynumber: 4.7 Consensus size: 16
413689 TATACGAGTC
* *
413699 ATTTCGGATTCAGGATC
1 ATTTCGGATTC-GAATT
413716 ATTTCGGATTCGAATT
1 ATTTCGGATTCGAATT
**
413732 ATTTCGGGCTCGAATT
1 ATTTCGGATTCGAATT
*
413748 ATTTCAGATTCGAATT
1 ATTTCGGATTCGAATT
*
413764 ATTTCGAATTC
1 ATTTCGGATTC
413775 AGATCATTCT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 39 0.78
17 11 0.22
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (16 bp):
ATTTCGGATTCGAATT
Found at i:413813 original size:16 final size:16
Alignment explanation
Indices: 413693--413823 Score: 63
Period size: 16 Copynumber: 8.1 Consensus size: 16
413683 GTTAATTATA
413693 CGAGTCATTTCGGATT
1 CGAGTCATTTCGGATT
413709 C-AGGATCATTTCGGATT
1 CGA-G-TCATTTCGGATT
* * **
413726 CGAATTATTTCGGGCT
1 CGAGTCATTTCGGATT
* * *
413742 CGAATTATTTCAGATT
1 CGAGTCATTTCGGATT
* * *
413758 CGAATTATTTCGAATT
1 CGAGTCATTTCGGATT
**
413774 C-AGATCA-TTCTAAATT
1 CGAG-TCATTTC-GGATT
*
413790 TG-GATCATTTCGGATT
1 CGAG-TCATTTCGGATT
*
413806 CGAGTCATTTCAGATT
1 CGAGTCATTTCGGATT
413822 CG
1 CG
413824 GATTGATGAT
Statistics
Matches: 90, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
15 5 0.06
16 67 0.74
17 17 0.19
18 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (16 bp):
CGAGTCATTTCGGATT
Found at i:422902 original size:4 final size:4
Alignment explanation
Indices: 422893--422922 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
422883 TTCATGGGAA
422893 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
422923 GTCAACAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:423511 original size:3 final size:3
Alignment explanation
Indices: 423503--423530 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
423493 AAAAGGATAG
423503 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
423531 GCGTTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:425918 original size:24 final size:23
Alignment explanation
Indices: 425873--425919 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
425863 AATAAAATTA
**
425873 ATTAAAAATATTAAAATTTTTAT
1 ATTAAAAATATTAAAACCTTTAT
*
425896 ATTAAAATATATTTAAACCTTTAT
1 ATTAAAA-ATATTAAAACCTTTAT
425920 TTTATATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAAAAATATTAAAACCTTTAT
Found at i:427244 original size:16 final size:16
Alignment explanation
Indices: 427215--427266 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
427205 AAATAAAAAT
*
427215 TATT-TATTAATAATA
1 TATTATATTATTAATA
427230 TATTATATTATTAATA
1 TATTATATTATTAATA
*
427246 TATTAAATATAATTAATA
1 TATT--ATATTATTAATA
427264 TAT
1 TAT
427267 ATGTACATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
18 14 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATATTATTAATA
Found at i:427248 original size:18 final size:18
Alignment explanation
Indices: 427213--427268 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
427203 TAAAATAAAA
427213 ATTAT-TTATTAATAATAT
1 ATTATATTATTAAT-ATAT
427231 ATTATATTATTAATATAT
1 ATTATATTATTAATATAT
* *
427249 -TAAATATAATTAATATAT
1 AT-TATATTATTAATATAT
427267 AT
1 AT
427269 GTACATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 1 0.03
18 23 0.70
19 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTATATTATTAATATAT
Found at i:427742 original size:25 final size:25
Alignment explanation
Indices: 427714--427762 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
427704 ATAATTAAAA
427714 TATAATTTT-ATTATTATTATTATTT
1 TATAATTTTAATT-TTATTATTATTT
*
427739 TATAATTTTAATTTTTTTATTATT
1 TATAATTTTAATTTTATTATTATT
427763 AATATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TATAATTTTAATTTTATTATTATTT
Found at i:427769 original size:17 final size:17
Alignment explanation
Indices: 427719--427769 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
427709 TAAAATATAA
*
427719 TTTTATTATTATTATTA
1 TTTTATTATTATTATTT
*
427736 TTTTATAATT-TTAATTT
1 TTTTATTATTATT-ATTT
*
427753 TTTTATTATTAATATTT
1 TTTTATTATTATTATTT
427770 ATTATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 25 0.89
18 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTATTATTT
Found at i:430816 original size:28 final size:27
Alignment explanation
Indices: 430784--430847 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 27
430774 GTTTAAAAGC
430784 ATATTTTATTATTCATAATAATATTAAA
1 ATATTTTATTATTCATAATAATA-TAAA
* * *
430812 ATA--TTATT-TTGATATTAATATAGA
1 ATATTTTATTATTCATAATAATATAAA
430836 ATATTTT-TTATT
1 ATATTTTATTATT
430848 ATTAAAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
24 6 0.20
25 12 0.40
26 9 0.30
28 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (27 bp):
ATATTTTATTATTCATAATAATATAAA
Found at i:433965 original size:52 final size:53
Alignment explanation
Indices: 433870--433970 Score: 120
Period size: 52 Copynumber: 1.9 Consensus size: 53
433860 AAAATTATAT
433870 TAATATTTATTTTTATAATTAAATTTAAATAAAATATTAAAAT-ATTATTTTA
1 TAATATTTATTTTTATAATTAAATTTAAATAAAATATTAAAATAATTATTTTA
* * *
433922 TAATATTTATATATTTTTAA-T-AATTTAAATTTAAAT-TTTAAATAATTAT
1 TAATATTTAT-T-TTTATAATTAAATTTAAA-TAAAATATTAAAATAATTAT
433971 ATCCAAAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
52 24 0.57
53 12 0.29
54 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (53 bp):
TAATATTTATTTTTATAATTAAATTTAAATAAAATATTAAAATAATTATTTTA
Found at i:436036 original size:38 final size:37
Alignment explanation
Indices: 435984--436074 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
435974 ATTTACATAT
435984 TTTACTATT-ATATTATAATAATATTTAAAATAATTTATA
1 TTTA-TATTAATATTATAATAATATTTAAAA-AATTT-TA
* *
436023 TTTAT-TTAATATTAT-ATTATATTTTAAAAATTTTA
1 TTTATATTAATATTATAATAATATTTAAAAAATTTTA
*
436058 TTTATATTTATATTATA
1 TTTATATTAATATTATA
436075 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
35 7 0.15
36 14 0.30
37 13 0.28
38 8 0.17
39 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (37 bp):
TTTATATTAATATTATAATAATATTTAAAAAATTTTA
Found at i:436073 original size:11 final size:11
Alignment explanation
Indices: 435971--436078 Score: 57
Period size: 11 Copynumber: 9.7 Consensus size: 11
435961 TTACTCGTGC
*
435971 TATATTTACA-
1 TATATTTATAT
435981 TAT-TTTACTAT
1 TATATTTA-TAT
435992 TATA-TTATAAT
1 TATATTTAT-AT
* * *
436003 AATATTTAAAA
1 TATATTTATAT
436014 TA-ATTTATAT
1 TATATTTATAT
436024 T-TATTTAATAT
1 TATATTT-ATAT
*
436035 TATATTATATTT
1 TATATT-TATAT
*
436047 TAAAAATTT-TATT
1 T--ATATTTATA-T
436060 TATATTTATAT
1 TATATTTATAT
436071 TATATTTA
1 TATATTTA
436079 AAATTTTCAA
Statistics
Matches: 74, Mismatches: 11, Indels: 25
0.67 0.10 0.23
Matches are distributed among these distances:
9 4 0.05
10 16 0.22
11 32 0.43
12 14 0.19
13 4 0.05
14 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTTATAT
Found at i:436092 original size:31 final size:31
Alignment explanation
Indices: 436023--436085 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
436013 ATAATTTATA
436023 TTTATTTAATATTATATTATATTTTAAAAAT
1 TTTATTTAATATTATATTATATTTTAAAAAT
436054 TTTATTT-ATATTTATATTATA-TTT-AAAAT
1 TTTATTTAATA-TTATATTATATTTTAAAAAT
436083 TTT
1 TTT
436086 CAATTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 8 0.26
30 6 0.19
31 17 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTATTTAATATTATATTATATTTTAAAAAT
Found at i:436395 original size:3 final size:3
Alignment explanation
Indices: 436387--436423 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
436377 GCACTCTCGT
*
436387 TTA TTA TTA TT- GTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
436424 TTTCATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:437046 original size:16 final size:16
Alignment explanation
Indices: 437025--437057 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
437015 AAATAATATC
*
437025 ATCTAAAATTAGGATA
1 ATCTAAAATTAAGATA
437041 ATCTAAAATTAAGATA
1 ATCTAAAATTAAGATA
437057 A
1 A
437058 GATTGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (16 bp):
ATCTAAAATTAAGATA
Found at i:437458 original size:50 final size:50
Alignment explanation
Indices: 437398--437558 Score: 250
Period size: 50 Copynumber: 3.2 Consensus size: 50
437388 AGTTTCTTAA
* *
437398 AGTCAACAATTACGGCCACCTTTCTCTATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* *
437448 CGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
437498 AGCCAACAATTATGGCCACCTCTCTCGATTGTCAAACGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
437548 AAGTCAACAAT
1 -AGTCAACAAT
437559 GACAACACCT
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 91 0.91
51 9 0.09
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:441991 original size:50 final size:50
Alignment explanation
Indices: 441932--442180 Score: 277
Period size: 50 Copynumber: 5.0 Consensus size: 50
441922 GTTGCTTAGA
* * **
441932 GTTAACAATTATGGCCACATCTCTTTATTGTCAAAGATTGATGAAGAATC
1 GTTAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAATC
** * *
441982 GTTAACAATTACGATCACCTCTCTCTATTGTCAAAGGTTGATGAAGAATC
1 GTTAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAATC
* * *
442032 GTTAACAATTACGGTCACCTCTCTCAATTGTCAAAGATTGGTGAAGAATC
1 GTTAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAATC
** * * * * *
442082 GGCAACAATTACGACCACCTCTCTCGATTGTCAAAGATTGGTAAAAAATA
1 GTTAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAATC
* * *
442132 GTCAATAATTA-GGACCACATCTCTCGATTGTCAAAGATT-ATTGAAGAAT
1 GTTAACAATTACGG-CCACCTCTCTCGATTGTCAAAGATTGA-TGAAGAAT
442181 AATCAATAAT
Statistics
Matches: 172, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
49 1 0.01
50 171 0.99
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (50 bp):
GTTAACAATTACGGCCACCTCTCTCGATTGTCAAAGATTGATGAAGAATC
Found at i:444131 original size:1 final size:1
Alignment explanation
Indices: 444125--444154 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
444115 TTGGCATCTT
*
444125 GGGGGGGGGGGGGGGGGGGGGGGAGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
444155 TTTCTGGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:444411 original size:18 final size:19
Alignment explanation
Indices: 444388--444423 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
444378 TAAATATATC
*
444388 AATATATATT-TAATTATG
1 AATATAAATTATAATTATG
444406 AATATAAATTATAATTAT
1 AATATAAATTATAATTAT
444424 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AATATAAATTATAATTATG
Found at i:445188 original size:23 final size:22
Alignment explanation
Indices: 445158--445211 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
445148 TATTTTTATT
445158 AAATATAAA-TTTAATTTAATATA
1 AAATATAAATTTTAATTT-ATA-A
*
445181 AAATATAAATTTTAATTTTTAA
1 AAATATAAATTTTAATTTATAA
445203 AAATATAAA
1 AAATATAAA
445212 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.34
23 11 0.38
24 8 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATAAATTTTAATTTATAA
Found at i:445234 original size:26 final size:27
Alignment explanation
Indices: 445157--445234 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 27
445147 ATATTTTTAT
445157 TAAATATAAATTT-AA--TTTAATATA
1 TAAATATAAATTTAAATTTTTAATATA
* *
445181 -AAATATAAATTTTAATTTTTAAAAATA
1 TAAATATAAATTTAAATTTTT-AATATA
445208 TAAA-A-AAATTTAAAATTTTTAATATA
1 TAAATATAAATTT-AAATTTTTAATATA
445234 T
1 T
445235 TCATAATCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
23 12 0.27
24 2 0.04
26 15 0.33
27 13 0.29
28 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAAATATAAATTTAAATTTTTAATATA
Found at i:446165 original size:28 final size:29
Alignment explanation
Indices: 446134--446192 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
446124 TTATTTTTTA
446134 TTAAAAAATTATAA-ATAAATATTTAAAT
1 TTAAAAAATTATAATATAAATATTTAAAT
** * *
446162 TT-AAATCTTTTAATATAATTATTTAAAT
1 TTAAAAAATTATAATATAAATATTTAAAT
446190 TTA
1 TTA
446193 TATGATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAAAAATTATAATATAAATATTTAAAT
Found at i:446166 original size:14 final size:14
Alignment explanation
Indices: 446149--446192 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
446139 AAATTATAAA
446149 TAAATATTTAAATT
1 TAAATATTTAAATT
* * *
446163 TAAATCTTTTAATA
1 TAAATATTTAAATT
*
446177 TAATTATTTAAATT
1 TAAATATTTAAATT
446191 TA
1 TA
446193 TATGATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATATTTAAATT
Found at i:446203 original size:28 final size:28
Alignment explanation
Indices: 446143--446203 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
446133 ATTAAAAAAT
*
446143 TATAA-ATAAATATTTAAATTTAAATCT
1 TATAATATAAATATTTAAATTTAAATCA
* * * *
446170 TTTAATATAATTATTTAAATTTATATGA
1 TATAATATAAATATTTAAATTTAAATCA
446198 TATAAT
1 TATAAT
446204 TTATTAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TATAATATAAATATTTAAATTTAAATCA
Found at i:446226 original size:25 final size:26
Alignment explanation
Indices: 446172--446238 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
446162 TTAAATCTTT
*
446172 TAATATAA-TTATT--TAAATTTATA
1 TAATATAATTTATTAATAAATTGATA
*
446195 TGATATAATTTATTAATAAA-TGATA
1 TAATATAATTTATTAATAAATTGATA
*
446220 TAATATAATTTACTAATAA
1 TAATATAATTTATTAATAA
446239 TGACATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.19
24 5 0.14
25 21 0.57
26 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (26 bp):
TAATATAATTTATTAATAAATTGATA
Found at i:448000 original size:16 final size:16
Alignment explanation
Indices: 447979--448009 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
447969 ACCGGCCTAG
447979 GAAAGTGATGGCTTAA
1 GAAAGTGATGGCTTAA
447995 GAAAGTGATGGCTTA
1 GAAAGTGATGGCTTA
448010 TAAGAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (16 bp):
GAAAGTGATGGCTTAA
Found at i:453346 original size:30 final size:30
Alignment explanation
Indices: 453312--453373 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
453302 ATAATTTTTA
453312 ATATAA-TATA-AAAATAAATATATTAAATTT
1 ATATAATTATATAAAATAAAT-TATT-AATTT
*
453342 ATATAATTATATAATATAAATTATTAATTT
1 ATATAATTATATAAAATAAATTATTAATTT
453372 AT
1 AT
453374 TAAAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 13 0.45
31 8 0.28
32 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATAATTATATAAAATAAATTATTAATTT
Found at i:453394 original size:41 final size:38
Alignment explanation
Indices: 453312--453399 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 38
453302 ATAATTTTTA
453312 ATATAATATAAAAATAAATATATTAAATTTATATAATT
1 ATATAATATAAAAATAAATATATTAAATTTATATAATT
* * * *
453350 ATATAATATAAATTATTAATTTATTAAAATATTATATATTT
1 ATATAATATAAA-AATAAATATATT-AAAT-TTATATAATT
453391 ATATAATAT
1 ATATAATAT
453400 TTTAAATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 12 0.28
39 9 0.21
40 4 0.09
41 18 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
ATATAATATAAAAATAAATATATTAAATTTATATAATT
Found at i:453420 original size:41 final size:41
Alignment explanation
Indices: 453336--453438 Score: 103
Period size: 41 Copynumber: 2.6 Consensus size: 41
453326 TAAATATATT
*
453336 AAAT-TTATATAATTATATAATATAAATTATTAATTTATTA
1 AAATATTATATAATTATATAATATAAATTATTAATTTATAA
*
453376 AAATATTATATATTTATATAATATTTTAAA-TA-TAA-TTATAA
1 AAATATTATATAATTATATAATA---TAAATTATTAATTTATAA
*
453417 AAATA-AATATAA-TATA-AATATA
1 AAATATTATATAATTATATAATATA
453439 CAAATAATCA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
35 2 0.04
38 4 0.07
39 4 0.07
40 9 0.16
41 27 0.49
42 3 0.05
43 2 0.04
44 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (41 bp):
AAATATTATATAATTATATAATATAAATTATTAATTTATAA
Found at i:456682 original size:2 final size:2
Alignment explanation
Indices: 456675--456699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
456665 CTTCAGTCGA
456675 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 A
456700 AGAGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:463425 original size:22 final size:22
Alignment explanation
Indices: 463397--463442 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
463387 AATGTGTCAA
463397 TTTATTGTTGGTTTCCCAAGTT
1 TTTATTGTTGGTTTCCCAAGTT
463419 TTTATTGTTGGTTTCCCAAGTT
1 TTTATTGTTGGTTTCCCAAGTT
463441 TT
1 TT
463443 CTCTTAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (22 bp):
TTTATTGTTGGTTTCCCAAGTT
Found at i:470739 original size:24 final size:24
Alignment explanation
Indices: 470707--470754 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
470697 CAACAATCCC
470707 TCATAAAAATGATAAAAACTTCGG
1 TCATAAAAATGATAAAAACTTCGG
*
470731 TCATAAAAATGATAAAATCTTCGG
1 TCATAAAAATGATAAAAACTTCGG
470755 GGGGGGGGGG
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:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (24 bp):
TCATAAAAATGATAAAAACTTCGG
Found at i:472047 original size:31 final size:27
Alignment explanation
Indices: 471990--472046 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
471980 AAGAAAAATT
471990 AGTTTAAATTAATTAATTTTTTAAGTA
1 AGTTTAAATTAATTAATTTTTTAAGTA
472017 AGTTTAAATTAATTAATTTTTTAAGTA
1 AGTTTAAATTAATTAATTTTTTAAGTA
472044 AGT
1 AGT
472047 ACAAGTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (27 bp):
AGTTTAAATTAATTAATTTTTTAAGTA
Found at i:473442 original size:16 final size:17
Alignment explanation
Indices: 473402--473443 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
473392 TAAAAAATTT
*
473402 ATAATATTTAATTTAAA
1 ATAATATTTAATGTAAA
* *
473419 CTATTATTT-ATGTAAA
1 ATAATATTTAATGTAAA
473435 ATAATATTT
1 ATAATATTT
473444 TATCTAAATG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
ATAATATTTAATGTAAA
Found at i:480267 original size:19 final size:19
Alignment explanation
Indices: 480243--480285 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
480233 CAATGAAGTG
* *
480243 ATTTAATTATAAAATTATT
1 ATTTAATAATAAAAATATT
480262 ATTTAATAATAAAAATATT
1 ATTTAATAATAAAAATATT
*
480281 TTTTA
1 ATTTA
480286 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTAATAATAAAAATATT
Found at i:487501 original size:17 final size:19
Alignment explanation
Indices: 487468--487517 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
487458 ATATAAATAA
487468 TTAATAT-ATTA-AA-ATT
1 TTAATATAATTATAATATT
487484 TT-ATA-AATTATAATATT
1 TTAATATAATTATAATATT
487501 TTAAATATAATTATAAT
1 TT-AATATAATTATAAT
487518 GTTATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.25
16 4 0.14
17 5 0.18
19 3 0.11
20 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATAATTATAATATT
Found at i:488201 original size:11 final size:10
Alignment explanation
Indices: 488166--488217 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 10
488156 AATCAATTTG
488166 ATTAATTAAA
1 ATTAATTAAA
488176 ATTAATATATTAA
1 ATTAAT-TA--AA
488189 ATTAATATAAA
1 ATTAAT-TAAA
*
488200 ATAAACTTAAA
1 ATTAA-TTAAA
488211 ATTAATT
1 ATTAATT
488218 TTATTAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 16 0.44
12 1 0.03
13 11 0.31
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAATTAAA
Found at i:489973 original size:23 final size:20
Alignment explanation
Indices: 489947--489998 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
489937 TTTGATTCAT
*
489947 AATTTTTTATATATTTTTTAAA
1 AATTTTTTATA-ATATTTT-AA
* *
489969 AAATTATTATAATATTTTAA
1 AATTTTTTATAATATTTTAA
489989 AATTTTTTAT
1 AATTTTTTAT
489999 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTTATAATATTTTAA
Found at i:491978 original size:17 final size:16
Alignment explanation
Indices: 491954--491996 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
491944 TTTAAAAATT
491954 TAAATTATTTTTAAAA
1 TAAATTATTTTTAAAA
*
491970 TAAATTTATTTTTAACA
1 TAAA-TTATTTTTAAAA
491987 -AAATTATTTT
1 TAAATTATTTT
491997 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 7 0.28
16 7 0.28
17 11 0.44
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTATTTTTAAAA
Found at i:492232 original size:7 final size:7
Alignment explanation
Indices: 492204--492241 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
492194 TTAAAAGAAG
492204 AAGA-AA
1 AAGACAA
492210 AAGACAA
1 AAGACAA
*
492217 CATGACAA
1 -AAGACAA
492225 AAGACAA
1 AAGACAA
492232 AAGACAA
1 AAGACAA
492239 AAG
1 AAG
492242 GTGGAAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 4 0.14
7 18 0.64
8 6 0.21
ACGTcount: A:0.68, C:0.13, G:0.16, T:0.03
Consensus pattern (7 bp):
AAGACAA
Found at i:493728 original size:21 final size:21
Alignment explanation
Indices: 493702--493750 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
493692 TAAAAAGAAT
493702 GAGGGAAGGGTGAAGGGGGAAG
1 GAGGGAAGGG-GAAGGGGGAAG
*
493724 G-GGGAAAGGGGAAGGTGGAAG
1 GAGGG-AAGGGGAAGGGGGAAG
493745 GAGGGA
1 GAGGGA
493751 TGAGGGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.63, T:0.04
Consensus pattern (21 bp):
GAGGGAAGGGGAAGGGGGAAG
Found at i:493732 original size:8 final size:7
Alignment explanation
Indices: 493704--493750 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
493694 AAAAGAATGA
493704 GGGAAGG
1 GGGAAGG
*
493711 GTGAAGG
1 GGGAAGG
493718 GGGAAGG
1 GGGAAGG
*
493725 GGGAAAG
1 GGGAAGG
493732 GGGAAGG
1 GGGAAGG
*
493739 TGGAAGG
1 GGGAAGG
493746 AGGGA
1 -GGGA
493751 TGAGGGATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
7 30 0.91
8 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.64, T:0.04
Consensus pattern (7 bp):
GGGAAGG
Found at i:494881 original size:146 final size:148
Alignment explanation
Indices: 494613--494905 Score: 416
Period size: 146 Copynumber: 2.0 Consensus size: 148
494603 TTCTCGCAGT
*
494613 TTTGTGGTAGTTATCCATGCATTATAGAGGCTTTTCTGTTATAGGAACATGATGACAAAAAGATT
1 TTTGTGGTAGCTATCCATGCATTATAGAGGCTTTTCTGTTATAGGAACATGATGACAAAAAG--T
* * *
494678 CTTTGTAAGATTTTAACTAACTCAAATGAAGATAATCGGAAACATAAACTGTAAGTAACCTGAGA
64 CTTTGCAAGATTTTAACTAACTCAAATGAAGATAATAGAAAACATAAACTGTAAGTAACCTGAGA
494743 AACAAGAGGACAGTTAATGA
129 AACAAGAGGACAGTTAATGA
* *
494763 TTTGTGGTAGCTGTCCATGCATATTATAGAGGCTTTTTTGTTATAGGAACATGATGA-AAAAAG-
1 TTTGTGGTAGCTATCCATGC--ATTATAGAGGCTTTTCTGTTATAGGAACATGATGACAAAAAGT
* * *
494826 GTTT-CATG-TTTTAACTAAC-CATCATGAAGATAATAGAAAACATAAACTGTAAGTAACCTGAG
64 CTTTGCAAGATTTTAACTAACTCA-AATGAAGATAATAGAAAACATAAACTGTAAGTAACCTGAG
*
494888 AAACAAGTGGACAGTTAA
128 AAACAAGAGGACAGTTAA
494906 AAATGAAGCA
Statistics
Matches: 130, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
145 2 0.02
146 65 0.50
147 2 0.02
148 3 0.02
150 18 0.14
151 6 0.05
152 34 0.26
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (148 bp):
TTTGTGGTAGCTATCCATGCATTATAGAGGCTTTTCTGTTATAGGAACATGATGACAAAAAGTCT
TTGCAAGATTTTAACTAACTCAAATGAAGATAATAGAAAACATAAACTGTAAGTAACCTGAGAAA
CAAGAGGACAGTTAATGA
Found at i:498772 original size:2 final size:2
Alignment explanation
Indices: 498759--498819 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
498749 TGTCTTTTAC
* * *
498759 AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
498801 AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
498820 CACATATAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:498778 original size:14 final size:14
Alignment explanation
Indices: 498759--498827 Score: 88
Period size: 14 Copynumber: 5.1 Consensus size: 14
498749 TGTCTTTTAC
498759 ATATATACATATAT
1 ATATATACATATAT
*
498773 ATATAT--ATGTAT
1 ATATATACATATAT
* *
498785 ATATATATATGTAT
1 ATATATACATATAT
498799 ATATATACATATAT
1 ATATATACATATAT
*
498813 ATATATACACATAT
1 ATATATACATATAT
498827 A
1 A
498828 GTTGCTTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.22
14 38 0.78
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:498826 original size:8 final size:8
Alignment explanation
Indices: 498756--498827 Score: 72
Period size: 8 Copynumber: 9.0 Consensus size: 8
498746 ACCTGTCTTT
498756 TACATATA
1 TACATATA
498764 TACATATA
1 TACATATA
*
498772 TATATATA
1 TACATATA
**
498780 TGTATATA
1 TACATATA
* *
498788 TATATATG
1 TACATATA
*
498796 TATATATA
1 TACATATA
498804 TACATATA
1 TACATATA
*
498812 TATATATA
1 TACATATA
*
498820 CACATATA
1 TACATATA
498828 GTTGCTTGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 55 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (8 bp):
TACATATA
Found at i:498937 original size:3 final size:3
Alignment explanation
Indices: 498929--498963 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
498919 AATAAATAAC
*
498929 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
498964 TTTGAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:499227 original size:29 final size:29
Alignment explanation
Indices: 499171--499227 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
499161 TATGTTTTTA
* *
499171 TTATATTAAATAATTTTTTAATTTTAAAT
1 TTATATTAAATAAATTTTTAATTATAAAT
499200 TTATACTTAAATAAATTTTTAA-TATAAA
1 TTATA-TTAAATAAATTTTTAATTATAAA
499228 CCTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATATTAAATAAATTTTTAATTATAAAT
Found at i:499327 original size:20 final size:20
Alignment explanation
Indices: 499298--499363 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
499288 TGAGTACAAC
*
499298 AAAATTTTAAGAATTTACTT
1 AAAATATTAAGAATTTACTT
* *
499318 AAAATATT-A-AA-TAATTT
1 AAAATATTAAGAATTTACTT
*
499335 AAAATTTTAAGAATTTACTT
1 AAAATATTAAGAATTTACTT
*
499355 AAAAAATTA
1 AAAATATTA
499364 TATTGGTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
17 11 0.31
18 3 0.09
19 3 0.09
20 18 0.51
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAATATTAAGAATTTACTT
Found at i:501220 original size:10 final size:10
Alignment explanation
Indices: 501205--501240 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
501195 TTAAATATAA
501205 ATATATTTTT
1 ATATATTTTT
501215 ATATA-TTTT
1 ATATATTTTT
501224 A-ATATTTTT
1 ATATATTTTT
501233 ATATATTT
1 ATATATTT
501241 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 10 0.42
10 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATATTTTT
Found at i:501248 original size:18 final size:18
Alignment explanation
Indices: 501209--501249 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
501199 ATATAAATAT
* *
501209 ATTTTTATATATTTTAAT
1 ATTTTTATATATTTAAAA
501227 ATTTTTATATATTTAAAA
1 ATTTTTATATATTTAAAA
501245 ATTTT
1 ATTTT
501250 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTATATATTTAAAA
Found at i:503038 original size:2 final size:2
Alignment explanation
Indices: 503031--503068 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
503021 GTCTCATACC
503031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
503069 ATTACACTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505936 original size:23 final size:21
Alignment explanation
Indices: 505905--505976 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 21
505895 AAATAAATAC
*
505905 TAAACTTTTAATTTACATCCAAA
1 TAAATTTTTAATTTACAT--AAA
505928 TAAATTTTTAATTTTAACATAAA
1 TAAATTTTTAA-TTT-ACATAAA
*
505951 TCAATTTTTAATTTACACTTAAA
1 TAAATTTTTAATTTACA--TAAA
505974 TAA
1 TAA
505977 CACTTTAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.07
22 3 0.07
23 29 0.69
24 3 0.07
25 4 0.10
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTTTAATTTACATAAA
Found at i:509879 original size:10 final size:10
Alignment explanation
Indices: 509864--509893 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
509854 TTAAGATTTA
509864 AATTTTCAAT
1 AATTTTCAAT
509874 AATTTTCAAT
1 AATTTTCAAT
509884 AATTTTCAAT
1 AATTTTCAAT
509894 GAAGGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTTCAAT
Found at i:510150 original size:2 final size:2
Alignment explanation
Indices: 510135--510167 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
510125 AATCTTAAAT
510135 TA TA -A TA T- 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 TA TA T
510168 GTAAATCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:513681 original size:19 final size:18
Alignment explanation
Indices: 513650--513693 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
513640 AAAAATAAAA
513650 ATATTT-ATATTAAATAT
1 ATATTTAATATTAAATAT
*
513667 ATATTTAATATTTAAATTT
1 ATATTTAATA-TTAAATAT
*
513686 AAATTTAA
1 ATATTTAA
513694 ATTCGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 3 0.13
19 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTTAATATTAAATAT
Found at i:514072 original size:7 final size:7
Alignment explanation
Indices: 514060--514084 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
514050 ATAGTGTGAC
514060 GAAACTT
1 GAAACTT
514067 GAAACTT
1 GAAACTT
514074 GAAACTT
1 GAAACTT
514081 GAAA
1 GAAA
514085 GGAGCTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (7 bp):
GAAACTT
Found at i:514645 original size:18 final size:18
Alignment explanation
Indices: 514622--514656 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
514612 ATAATGGTGC
514622 TGGCCATCATTTGCCATA
1 TGGCCATCATTTGCCATA
514640 TGGCCATCATTTGCCAT
1 TGGCCATCATTTGCCAT
514657 TTGATTCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (18 bp):
TGGCCATCATTTGCCATA
Found at i:518348 original size:47 final size:46
Alignment explanation
Indices: 518279--518371 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 46
518269 AGGATTTTGT
*
518279 CATAGTAAAGCTAAAGGAAACAAGGAAAAAAACAAGAAGAAACTGGC
1 CATAGTAAAGCTAAAGGAAACAAGG-AAAAAACAACAAGAAACTGGC
*
518326 CATAGTAAAGCTAAAGGAAACAAGGAAAAAACAACCAGAAACTGGC
1 CATAGTAAAGCTAAAGGAAACAAGGAAAAAACAACAAGAAACTGGC
518372 GAAAATGCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 19 0.43
47 25 0.57
ACGTcount: A:0.56, C:0.15, G:0.20, T:0.09
Consensus pattern (46 bp):
CATAGTAAAGCTAAAGGAAACAAGGAAAAAACAACAAGAAACTGGC
Found at i:525418 original size:19 final size:19
Alignment explanation
Indices: 525378--525419 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
525368 TTATTAAAAT
*
525378 AAATTATCTACTCTCTCAA
1 AAATTATCTACTCTATCAA
*
525397 AAATTTTCTACTC-ATCATA
1 AAATTATCTACTCTATCA-A
525416 AAAT
1 AAAT
525420 CTATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTATCTACTCTATCAA
Found at i:527386 original size:20 final size:21
Alignment explanation
Indices: 527363--527409 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
527353 GAAAGGGATC
527363 AAATTTTAATAT-ATATTTTA
1 AAATTTTAATATAATATTTTA
* *
527383 AAATTTTTATATAATTTTTTA
1 AAATTTTAATATAATATTTTA
527404 AAATTT
1 AAATTT
527410 GATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTTTAATATAATATTTTA
Found at i:527414 original size:20 final size:21
Alignment explanation
Indices: 527363--527416 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
527353 GAAAGGGATC
* *
527363 AAATTTTAATAT-ATATTTTA
1 AAATTTTGATATAATTTTTTA
*
527383 AAATTTTTATATAATTTTTTA
1 AAATTTTGATATAATTTTTTA
527404 AAA-TTTGATATAA
1 AAATTTTGATATAA
527417 AAATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATTTTGATATAATTTTTTA
Found at i:527461 original size:42 final size:42
Alignment explanation
Indices: 527415--527495 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
527405 AATTTGATAT
527415 AAAAATA-TATATGAAAAAATTTTAAAAAATAAATATTTTTTTA
1 AAAAATATTATAT--AAAAATTTTAAAAAATAAATATTTTTTTA
*
527458 AAAAATATTATATAAAAATTTTAAAATATAAATATTTT
1 AAAAATATTATATAAAAATTTTAAAAAATAAATATTTT
527496 ATATTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
42 24 0.67
43 7 0.19
44 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (42 bp):
AAAAATATTATATAAAAATTTTAAAAAATAAATATTTTTTTA
Found at i:528307 original size:15 final size:15
Alignment explanation
Indices: 528272--528315 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
528262 TTCACTTATA
*
528272 TATATTTATATAACT
1 TATATTTATATAATT
528287 T-T-TTTATATAATT
1 TATATTTATATAATT
*
528300 TATATTTATTTAATT
1 TATATTTATATAATT
528315 T
1 T
528316 TAAGTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 11 0.44
14 2 0.08
15 12 0.48
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:528389 original size:18 final size:19
Alignment explanation
Indices: 528353--528390 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
528343 ATTTTATATG
528353 AAATATATGATACATAAAA
1 AAATATATGATACATAAAA
528372 AAATATTATGA-A-ATAAAA
1 AAATA-TATGATACATAAAA
528390 A
1 A
528391 GTAATAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATATATGATACATAAAA
Found at i:529837 original size:21 final size:20
Alignment explanation
Indices: 529802--529907 Score: 60
Period size: 21 Copynumber: 5.1 Consensus size: 20
529792 ATTTTATGAA
*
529802 ATTTATGTA-TTAATATTAT
1 ATTTATATATTTAATATTAT
529821 ATTTATATAATTTAATATTTTAT
1 ATTTATAT-ATTTAATA--TTAT
* * *
529844 AATTATAT-TTAAAATTTATAT
1 ATTTATATATT-TAATAT-TAT
529865 ATTTATATAAATTTTAATA-TATT
1 ATTTATAT--A-TTTAATATTA-T
529888 ATTT-TATATTT-ATATTAT
1 ATTTATATATTTAATATTAT
529906 AT
1 AT
529908 AAATTTGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
18 6 0.09
19 12 0.18
20 3 0.04
21 18 0.26
22 8 0.12
23 16 0.24
24 3 0.04
25 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (20 bp):
ATTTATATATTTAATATTAT
Found at i:529855 original size:20 final size:20
Alignment explanation
Indices: 529830--529902 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
529820 TATTTATATA
529830 ATTTAATATTTTATA-ATTAT
1 ATTTAA-ATTTTATATATTAT
*
529850 ATTTAAAATTTATATATT-T
1 ATTTAAATTTTATATATTAT
*
529869 ATATAAATTTTAATATATTAT
1 ATTTAAATTTT-ATATATTAT
*
529890 -TTTATA-TTTATAT
1 ATTTAAATTTTATAT
529903 TATATAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 4 0.09
19 20 0.44
20 20 0.44
21 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTAAATTTTATATATTAT
Found at i:529870 original size:8 final size:8
Alignment explanation
Indices: 529818--529902 Score: 53
Period size: 7 Copynumber: 11.4 Consensus size: 8
529808 GTATTAATAT
529818 TATATTTA
1 TATATTTA
529826 TATAATTTA
1 TAT-ATTTA
529835 -ATATTT-
1 TATATTTA
*
529841 TATA-AT-
1 TATATTTA
529847 TATATTTA
1 TATATTTA
*
529855 -AAATTTA
1 TATATTTA
529862 TATATTTA
1 TATATTTA
529870 TATAAATTT-
1 TAT--ATTTA
*
529879 TA-ATATA
1 TATATTTA
529886 T-TATTT-
1 TATATTTA
529892 TATATTTA
1 TATATTTA
529900 TAT
1 TAT
529903 TATATAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
6 9 0.15
7 23 0.38
8 17 0.28
9 7 0.12
10 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATATTTA
Found at i:530097 original size:2 final size:2
Alignment explanation
Indices: 530046--530080 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
530036 GGAAAAAATT
530046 TA TA 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 TA TA T
530081 GTACAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:530536 original size:20 final size:19
Alignment explanation
Indices: 530505--530545 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 19
530495 TGTATCTATA
530505 ATTTTTTAATTTAATAAAAAT
1 ATTTTTTAATTT--TAAAAAT
530526 ATTTTTT-ATTTTAAAAAT
1 ATTTTTTAATTTTAAAAAT
530544 AT
1 AT
530546 CATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTAATTTTAAAAAT
Found at i:531444 original size:17 final size:17
Alignment explanation
Indices: 531376--531445 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
531366 AAAAATATAT
531376 TAAATTT-ATATAAA-A
1 TAAATTTAATATAAATA
*
531391 TAAATTATTAA-ATAATATTT
1 TAAA-T-TTAATATAA-A-TA
531411 TAAATTTAAT-TATAATA
1 TAAATTTAATATA-AATA
531428 TAAATTTAATATAAATA
1 TAAATTTAATATAAATA
531445 T
1 T
531446 TTAAAATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
15 4 0.09
16 1 0.02
17 22 0.50
18 11 0.25
19 2 0.05
20 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAATATAAATA
Found at i:533770 original size:23 final size:24
Alignment explanation
Indices: 533737--533786 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
533727 AACTTGTTTT
* *
533737 ACTTTATTTGAGTTTGATTTAAAC
1 ACTTTATTTGAATGTGATTTAAAC
*
533761 ACTTT-TTTGAATGTGATTTAACC
1 ACTTTATTTGAATGTGATTTAAAC
533784 ACT
1 ACT
533787 GCCAAGCCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (24 bp):
ACTTTATTTGAATGTGATTTAAAC
Found at i:533903 original size:26 final size:24
Alignment explanation
Indices: 533874--533930 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
533864 AACTCAATTT
533874 AAATTTAAACTTAAACACAAATAATC
1 AAATTTAAA-TTAAACACAAA-AATC
* * *
533900 AAATATGAAATTGAACACGAAAATC
1 AAAT-TTAAATTAAACACAAAAATC
533925 AAATTT
1 AAATTT
533931 GTTTTTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 1 0.04
25 8 0.31
26 13 0.50
27 4 0.15
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.26
Consensus pattern (24 bp):
AAATTTAAATTAAACACAAAAATC
Found at i:539615 original size:24 final size:22
Alignment explanation
Indices: 539577--539649 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
539567 AATAAATTTT
* *
539577 ATTTAAAATAAAAAATAAAATTA
1 ATTTAATATATAAAATAAAA-TA
* *
539600 ATTTAAGTATATAAAATTACAATG
1 ATTTAA-TATATAAAA-TAAAATA
*
539624 ATTTATATAAATAAAATAAAATA
1 ATTTA-ATATATAAAATAAAATA
539647 ATT
1 ATT
539650 CTTAAACTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
23 14 0.35
24 21 0.52
25 5 0.12
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (22 bp):
ATTTAATATATAAAATAAAATA
Found at i:541056 original size:21 final size:20
Alignment explanation
Indices: 541018--541056 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
541008 ATCAAATAAC
*
541018 ATAAAAATTTAAATTAAATT
1 ATAAAAATTTAAAATAAATT
*
541038 ATAAAACTTATAAAATAAA
1 ATAAAAATT-TAAAATAAA
541057 AGTTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAAATTTAAAATAAATT
Found at i:541423 original size:14 final size:15
Alignment explanation
Indices: 541396--541438 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
541386 TAATGTGTAT
*
541396 ATATATATTGTTTTTC
1 ATATATATT-TTTTAC
541412 ATATATATTTTTTAC
1 ATATATATTTTTTAC
*
541427 AT-TAGATTTTTT
1 ATATATATTTTTT
541439 TTCCACTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (15 bp):
ATATATATTTTTTAC
Found at i:542729 original size:25 final size:25
Alignment explanation
Indices: 542695--542747 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
542685 ATCAAGTTTA
* *
542695 GAAAGAAAGAAGCATTCGAATTTCT
1 GAAAGAAAGAAACAATCGAATTTCT
542720 GAAAGAAAGAAACAATCGAATTTCT
1 GAAAGAAAGAAACAATCGAATTTCT
542745 GAA
1 GAA
542748 TCGTTAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (25 bp):
GAAAGAAAGAAACAATCGAATTTCT
Found at i:544281 original size:25 final size:25
Alignment explanation
Indices: 544246--544299 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
544236 GTGTGCATAC
*
544246 TAAATAGTATTG-AAATTATTTAAAA
1 TAAATAGTATTGTAAA-TATTAAAAA
* *
544271 TAAATATTATTGTGAATATTAAAAA
1 TAAATAGTATTGTAAATATTAAAAA
544296 TAAA
1 TAAA
544300 AAATAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (25 bp):
TAAATAGTATTGTAAATATTAAAAA
Found at i:544369 original size:24 final size:25
Alignment explanation
Indices: 544324--544370 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
544314 AAATAGTAAA
* **
544324 TATAATATTAAATTGATTTTAATAT
1 TATAATATTAAATTCAAGTTAATAT
544349 TATAAT-TTAAATTCAAGTTAAT
1 TATAATATTAAATTCAAGTTAAT
544371 TATATTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (25 bp):
TATAATATTAAATTCAAGTTAATAT
Found at i:545615 original size:23 final size:24
Alignment explanation
Indices: 545572--545621 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
545562 ATTTTAATTT
545572 ATTTCATTATTTTTATAAAAAA-G
1 ATTTCATTATTTTTATAAAAAATG
* * *
545595 ATTTTATTATTTTTTTTAAAAATG
1 ATTTCATTATTTTTATAAAAAATG
545619 ATT
1 ATT
545622 CTACTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTCATTATTTTTATAAAAAATG
Found at i:545629 original size:25 final size:24
Alignment explanation
Indices: 545577--545629 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
545567 AATTTATTTC
*
545577 ATTA-TTTTTATAAAAAAGATTTT
1 ATTATTTTTTATAAAAAAGATTCT
* *
545600 ATTATTTTTTTTAAAAATGATTCT
1 ATTATTTTTTATAAAAAAGATTCT
545624 ACTTAT
1 A-TTAT
545630 CTACATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 17 0.68
25 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTATTTTTTATAAAAAAGATTCT
Found at i:546029 original size:22 final size:22
Alignment explanation
Indices: 546004--546045 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
545994 AAATAAAAAT
546004 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
546026 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
546046 AATAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:546046 original size:29 final size:28
Alignment explanation
Indices: 546013--546084 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
546003 TTATTTTTAT
546013 ATTAATATTTATATATTTTTATAATTAA
1 ATTAATATTTATATATTTTTATAATTAA
* * *
546041 ATTTAA-ATAATAAATATTTTTATTATTAA
1 A-TTAATAT-TTATATATTTTTATAATTAA
546070 A-TAATAATTTATATA
1 ATTAAT-ATTTATATA
546085 AAATTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.09
28 8 0.23
29 24 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTAATATTTATATATTTTTATAATTAA
Found at i:546090 original size:51 final size:51
Alignment explanation
Indices: 545990--546114 Score: 134
Period size: 50 Copynumber: 2.5 Consensus size: 51
545980 TTAAATTATT
* *
545990 ATTTAAATAA-AAATTATTTTTA-TATTAATATTTATATATTTTTATAATTAA
1 ATTTAAATAATAAA-TATTTTTATTATTAATATTAATATATTTTTAAAATT-A
546041 ATTTAAATAATAAATATTTTTATTATTAA-A-TAATA-ATTTATATAAAATTA
1 ATTTAAATAATAAATATTTTTATTATTAATATTAATATATTT-T-TAAAATTA
* * *
546091 ATTTAAATTATAAAAATTTATATT
1 ATTTAAATAATAAATATTTTTATT
546115 CAAAATCTAA
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
49 4 0.06
50 27 0.42
51 25 0.38
52 9 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (51 bp):
ATTTAAATAATAAATATTTTTATTATTAATATTAATATATTTTTAAAATTA
Found at i:552975 original size:14 final size:15
Alignment explanation
Indices: 552951--553000 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
552941 AAAGTTTAGT
*
552951 TTAAGTTAAAAAA-A
1 TTAAATTAAAAAATA
* *
552965 TTAGATTAAAAAATT
1 TTAAATTAAAAAATA
552980 TTAAATTAAAAAATA
1 TTAAATTAAAAAATA
552995 TGTAAA
1 T-TAAA
553001 AATTATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 11 0.38
15 14 0.48
16 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
TTAAATTAAAAAATA
Found at i:556691 original size:28 final size:33
Alignment explanation
Indices: 556625--556694 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 33
556615 TATATCAAGC
*
556625 ATTTTATATTAATCATATTTATTATATCATTAA
1 ATTTTATATTAATCATATTAATTATATCATTAA
*
556658 ATTTTAT-TTAAT-GTATTAATTATAT-A-T-A
1 ATTTTATATTAATCATATTAATTATATCATTAA
556686 ATTTTATAT
1 ATTTTATAT
556695 ATTATTAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.24
29 2 0.06
30 1 0.03
31 11 0.32
32 5 0.15
33 7 0.21
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (33 bp):
ATTTTATATTAATCATATTAATTATATCATTAA
Found at i:556737 original size:25 final size:25
Alignment explanation
Indices: 556709--556763 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
556699 TTAGTAAATT
* *
556709 AAATTATTTCAT-TTTATTTTTATAA
1 AAATTATTT-ATATTTATTTTCAAAA
*
556734 AAATAATTTATATTTATTTTCAAAA
1 AAATTATTTATATTTATTTTCAAAA
556759 AAATT
1 AAATT
556764 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATTATTTATATTTATTTTCAAAA
Found at i:561409 original size:25 final size:24
Alignment explanation
Indices: 561354--561411 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
561344 AATTAAATTT
*
561354 ATATT-ATTAATTTATTAAATAAA
1 ATATTAATTAATTTACTAAATAAA
* *
561377 ATATTTAATTAATTTAACTAATTTAA
1 ATA-TTAATTAATTT-ACTAAATAAA
561403 ATATTAATT
1 ATATTAATT
561412 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 2 0.07
25 14 0.48
26 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTAATTAATTTACTAAATAAA
Found at i:561476 original size:13 final size:13
Alignment explanation
Indices: 561458--561507 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
561448 ATTCATAATT
*
561458 AATTAAATTTTAA
1 AATTAAATTATAA
*
561471 AATTAAATAATAA
1 AATTAAATTATAA
*
561484 AATTAAATTAATTA
1 AATTAAATT-ATAA
*
561498 AATTTAATTA
1 AATTAAATTA
561508 ATGCAACTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTAAATTATAA
Found at i:561499 original size:28 final size:27
Alignment explanation
Indices: 561458--561533 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
561448 ATTCATAATT
561458 AATTAAATT-TTAAAATTAAATAATAA
1 AATTAAATTATTAAAATTAAATAATAA
* * **
561484 AATTAAATTAATTAAATTTAATTAATGC
1 AATTAAATT-ATTAAAATTAAATAATAA
*
561512 AACTAAATTATTAATAATTAAA
1 AATTAAATTATTAA-AATTAAA
561534 AAAATCGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 9 0.22
27 5 0.12
28 26 0.65
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTAAATTATTAAAATTAAATAATAA
Found at i:564411 original size:34 final size:35
Alignment explanation
Indices: 564352--564417 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
564342 CAATATGTAA
564352 ATTTTTATTTAAAATTTGATAAATTTA-ATAATTT
1 ATTTTTATTTAAAATTTGATAAATTTACATAATTT
*
564386 ATTTTATATTTAAAATTTGA-CAATTTACATAA
1 ATTTT-TATTTAAAATTTGATAAATTTACATAA
564418 AAAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (35 bp):
ATTTTTATTTAAAATTTGATAAATTTACATAATTT
Found at i:568143 original size:17 final size:18
Alignment explanation
Indices: 568121--568155 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
568111 TCATAGCAAA
568121 TAATTATATT-TTTATTT
1 TAATTATATTATTTATTT
568138 TAATTATATTATTTATTT
1 TAATTATATTATTTATTT
568156 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTATATTATTTATTT
Found at i:568156 original size:17 final size:17
Alignment explanation
Indices: 568121--568172 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
568111 TCATAGCAAA
568121 TAATTATATT-TTTATTT
1 TAATTATATTATTTA-TT
568138 TAATTATATTATTTATT
1 TAATTATATTATTTATT
*
568155 T-ATT-TATTA-ATATT
1 TAATTATATTATTTATT
568169 TAAT
1 TAAT
568173 ATGAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 7 0.22
16 3 0.09
17 13 0.41
18 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTATATTATTTATT
Found at i:569495 original size:18 final size:20
Alignment explanation
Indices: 569464--569516 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
569454 TTTAAAAAAA
569464 TTAAAATATATAAAAATATT
1 TTAAAATATATAAAAATATT
*
569484 TTAAAA-AT-TAAATATATT
1 TTAAAATATATAAAAATATT
569502 TATATCAAATATATA
1 T-TA--AAATATATA
569517 TATATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 10 0.37
19 4 0.15
20 6 0.22
21 3 0.11
22 2 0.07
23 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATATATAAAAATATT
Found at i:569515 original size:2 final size:2
Alignment explanation
Indices: 569495--569564 Score: 113
Period size: 2 Copynumber: 34.5 Consensus size: 2
569485 TAAAAATTAA
* *
569495 AT AT AT TT AT AT CAA 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
569538 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 A
569565 GATTTGAGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 62 0.98
3 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:584078 original size:27 final size:27
Alignment explanation
Indices: 584023--584078 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
584013 AAACTCAATT
* ** *
584023 ATTATTCTACATTGCAAATTTTTCGAC
1 ATTATTCTACAGTGCAAATTTCCCAAC
584050 ATTATTCTACAGTGCAAATTTCCCAAC
1 ATTATTCTACAGTGCAAATTTCCCAAC
584077 AT
1 AT
584079 CCCTTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (27 bp):
ATTATTCTACAGTGCAAATTTCCCAAC
Found at i:584961 original size:16 final size:16
Alignment explanation
Indices: 584931--584990 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 16
584921 ATAAATTTTA
584931 TATATAAAATT-AAAAT
1 TATA-AAAATTAAAAAT
584947 TATAAAAATTAAAAAT
1 TATAAAAATTAAAAAT
584963 TA-AATAAA-TAAAAAT
1 TATAA-AAATTAAAAAT
584978 T-T--AAATTAAAAAT
1 TATAAAAATTAAAAAT
584991 AATATATTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.08
13 7 0.17
15 16 0.40
16 14 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAAATTAAAAAT
Found at i:584994 original size:22 final size:23
Alignment explanation
Indices: 584936--584994 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
584926 TTTTATATAT
*
584936 AAAATT-AAAATTATAAAAATTA
1 AAAATTAAAAATAATAAAAATTA
*
584958 AAAATTAAATA-AATAAAAATT-
1 AAAATTAAAAATAATAAAAATTA
*
584979 TAAATTAAAAATAATA
1 AAAATTAAAAATAATA
584995 TATTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.29
22 19 0.61
23 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTAAAAATAATAAAAATTA
Found at i:585263 original size:30 final size:31
Alignment explanation
Indices: 585224--585285 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
585214 ATTGTATTTG
*
585224 TATTATTTTATATATTTTATTA-TATAATAAT
1 TATTATTTTAAATATTTT-TTATTATAATAAT
*
585255 TATT-TTTTAAATATTTTTTATTATATTAAT
1 TATTATTTTAAATATTTTTTATTATAATAAT
585285 T
1 T
585286 TAATAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 21 0.75
31 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTATTTTAAATATTTTTTATTATAATAAT
Found at i:585312 original size:21 final size:21
Alignment explanation
Indices: 585288--585378 Score: 53
Period size: 23 Copynumber: 4.0 Consensus size: 21
585278 TATTAATTTA
585288 ATAATTAATAATTTATATTAT
1 ATAATTAATAATTTATATTAT
*
585309 ATAAAATTTAA-ATTTTATATTATT
1 AT--AA-TTAATAATTTATATTA-T
*
585333 ATTATATTATTATATATTATATTTAT
1 A-TA-ATTAATA-AT-TTATA-TTAT
585359 ATAATT-AT-ATTTAATATTAT
1 ATAATTAATAATTT-ATATTAT
585379 TAAATTTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 23
0.67 0.05 0.28
Matches are distributed among these distances:
20 6 0.11
21 7 0.13
23 17 0.31
24 11 0.20
25 4 0.07
26 7 0.13
27 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATAATTAATAATTTATATTAT
Found at i:585375 original size:15 final size:15
Alignment explanation
Indices: 585333--585386 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
585323 TTATATTATT
*
585333 ATTATA-TTATTATA
1 ATTATATTTAATATA
585347 TATTATATTT-ATATA
1 -ATTATATTTAATATA
*
585362 ATTATATTTAATATT
1 ATTATATTTAATATA
*
585377 ATTAAATTTA
1 ATTATATTTA
585387 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.26
15 23 0.68
16 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATTTAATATA
Found at i:585375 original size:26 final size:25
Alignment explanation
Indices: 585296--585378 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 25
585286 TAATAATTAA
585296 TAAT-TTATATTATATAA--A-ATT
1 TAATATTATATTATATAATTATATT
*
585317 TAAATTTTATATTAT-T-ATTATATTAT
1 T-AATATTATATTATATAATTATA-T-T
585343 TATATATTATATTTATATAATTATATT
1 TA-ATATTATA-TTATATAATTATATT
585370 TAATATTAT
1 TAATATTAT
585379 TAAATTTATT
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
21 2 0.04
22 4 0.08
23 10 0.20
24 1 0.02
25 2 0.04
26 16 0.32
27 7 0.14
28 2 0.04
29 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATATTATATTATATAATTATATT
Found at i:587718 original size:34 final size:34
Alignment explanation
Indices: 587654--587868 Score: 263
Period size: 34 Copynumber: 6.4 Consensus size: 34
587644 TATTGTAATT
* *
587654 ATTGTTGATTAAAT-GATGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
587687 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
587721 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
587755 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
587789 ATTATTGATTAAATTGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
587823 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
587857 ATTGTTGATTAA
1 ATTGTTGATTAA
587869 GTGATGGTTT
Statistics
Matches: 157, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
33 16 0.10
34 141 0.90
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:587829 original size:102 final size:101
Alignment explanation
Indices: 587654--587874 Score: 354
Period size: 102 Copynumber: 2.2 Consensus size: 101
587644 TATTGTAATT
* *
587654 ATTGTTGATTAAATGATGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTA
1 ATTGTTGATTAAATGATGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
587719 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
587755 ATTGTTGATTAAATGA-GAAATTTGGTAGCTTACCATTATTGATTAAATTGGTGATTTGGTGGCT
1 ATTGTTGATTAAATGATG--ATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCT
* * *
587819 TACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
64 TACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
587857 ATTGTTGATTAAGTGATG
1 ATTGTTGATTAAATGATG
587875 GTTTTTACCA
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 16 0.15
102 92 0.84
103 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGATGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:592338 original size:34 final size:34
Alignment explanation
Indices: 592281--592499 Score: 289
Period size: 34 Copynumber: 6.5 Consensus size: 34
592271 AAGTGGGAGA
*
592281 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
592314 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
592348 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
592382 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
592416 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
592450 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
592484 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
592500 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:592424 original size:102 final size:101
Alignment explanation
Indices: 592281--592499 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
592271 AAGTGGGAGA
** * * * *
592281 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
592346 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
592382 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
592447 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
592484 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
592500 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:597438 original size:27 final size:27
Alignment explanation
Indices: 597383--597438 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
597373 AAACTCAATT
* ** *
597383 ATTATTCTACATTGCAAATTTTTCGAC
1 ATTATTCTACAGTGCAAATTTCCCAAC
597410 ATTATTCTACAGTGCAAATTTCCCAAC
1 ATTATTCTACAGTGCAAATTTCCCAAC
597437 AT
1 AT
597439 CCCTTCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (27 bp):
ATTATTCTACAGTGCAAATTTCCCAAC
Done.