Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 189 of 190
Found at i:56520715 original size:31 final size:30
Alignment explanation
Indices: 56520680--56520768 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
56520670 ATAGTCATTG
*
56520680 AACTATTCAAAAGTTTTCATTTAAGTGACTA
1 AACTATTCAAAAGTTTT-ATTTAAGTCACTA
** *
56520711 AACTATTTGAATGTTTTATTTAAGTCACTA
1 AACTATTCAAAAGTTTTATTTAAGTCACTA
* * *
56520741 AACTAATTGAATATTTTTATTTAAGTCA
1 AACT-ATTCAAAAGTTTTATTTAAGTCA
56520769 ATGGACTGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 16 0.33
31 32 0.67
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (30 bp):
AACTATTCAAAAGTTTTATTTAAGTCACTA
Found at i:56520734 original size:30 final size:31
Alignment explanation
Indices: 56520691--56520768 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 31
56520681 ACTATTCAAA
* *
56520691 AGTTTTCATTTAAGTGACTAAACTATTTGAAT
1 AGTTTT-ATTTAAGTCACTAAACTAATTGAAT
56520723 -GTTTTATTTAAGTCACTAAACTAATTGAAT
1 AGTTTTATTTAAGTCACTAAACTAATTGAAT
*
56520753 ATTTTTATTTAAGTCA
1 AGTTTTATTTAAGTCA
56520769 ATGGACTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 23 0.55
31 19 0.45
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (31 bp):
AGTTTTATTTAAGTCACTAAACTAATTGAAT
Found at i:56521772 original size:30 final size:30
Alignment explanation
Indices: 56521732--56521800 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
56521722 TTTCACTATC
*
56521732 TTTATAATTTTTAAAGGATT-AAATCAAAAT
1 TTTATTATTTTTAAAGGATTAAAAT-AAAAT
* * *
56521762 TTTATTATTTTTGAAGGGTTAAAATACAAT
1 TTTATTATTTTTAAAGGATTAAAATAAAAT
56521792 TTTATTATT
1 TTTATTATT
56521801 ACTAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (30 bp):
TTTATTATTTTTAAAGGATTAAAATAAAAT
Found at i:56523935 original size:5 final size:5
Alignment explanation
Indices: 56523927--56523954 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
56523917 TATTTTTCAA
56523927 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATT
56523955 TTTCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:56537790 original size:24 final size:24
Alignment explanation
Indices: 56537758--56537807 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
56537748 TTTGCACACT
56537758 CCTCAAAGGTATCCCTAAGGAGCC
1 CCTCAAAGGTATCCCTAAGGAGCC
56537782 CCTCAAAGGTATCCCTAAGGAGCC
1 CCTCAAAGGTATCCCTAAGGAGCC
56537806 CC
1 CC
56537808 CTTGCCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.36, G:0.20, T:0.16
Consensus pattern (24 bp):
CCTCAAAGGTATCCCTAAGGAGCC
Found at i:56540265 original size:24 final size:24
Alignment explanation
Indices: 56540227--56540274 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56540217 ACCGTCGTGG
*
56540227 ACACCGGCGATAACTCCTAGTGTA
1 ACACCGGCGACAACTCCTAGTGTA
* *
56540251 ACACCGGCTACAACTCTTAGTGTA
1 ACACCGGCGACAACTCCTAGTGTA
56540275 TGAAGCTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (24 bp):
ACACCGGCGACAACTCCTAGTGTA
Found at i:56543158 original size:46 final size:46
Alignment explanation
Indices: 56543059--56543310 Score: 406
Period size: 45 Copynumber: 5.6 Consensus size: 46
56543049 TTTGAGTACT
*
56543059 TCTGATCAAATGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
56543104 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
56543150 TCTGATCAAGTGAAAAATTGATAAGTGGTAG-TCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
56543195 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
56543241 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
56543286 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
56543311 ATCATACGTA
Statistics
Matches: 194, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 91 0.47
46 86 0.44
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:56543214 original size:91 final size:90
Alignment explanation
Indices: 56543059--56543310 Score: 418
Period size: 91 Copynumber: 2.8 Consensus size: 90
56543049 TTTGAGTACT
*
56543059 TCTGATCAAATGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TAGCTACACTTATCTGATCAAGTGACAAAGTG
56543124 ATAAGTGGTAGCTTTAGCTACACTTA
65 ATAAGTGGTAGCTTTAGCTACACTTA
* *
56543150 TCTGATCAAGTGAAAAATTGATAAGTGGTAGTCTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGACAAAGTG
*
56543215 ATAAGTGGTAGCTTTAGCTACATTTA
65 ATAAGTGGTAGCTTTAGCTACACTTA
*
56543241 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGAC-AAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGACAAAGTG
56543304 ATAAGTG
65 ATAAGTG
56543311 ATCATACGTA
Statistics
Matches: 152, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
89 12 0.08
90 5 0.03
91 134 0.88
92 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (90 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGACAAAGTGA
TAAGTGGTAGCTTTAGCTACACTTA
Found at i:56544666 original size:3 final size:3
Alignment explanation
Indices: 56544658--56544702 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
56544648 GTTAATTTGC
56544658 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56544703 TTACGATACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56545962 original size:24 final size:25
Alignment explanation
Indices: 56545916--56545965 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
56545906 ATTTATATAG
***
56545916 TGCTTCCTCTTCTCTTTTGTTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
56545941 TGCTTCC-CTTCTCTTCCATTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
56545965 T
1 T
56545966 TTTTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.02, C:0.36, G:0.06, T:0.56
Consensus pattern (25 bp):
TGCTTCCTCTTCTCTTCCATTCCTT
Found at i:56554974 original size:13 final size:13
Alignment explanation
Indices: 56554928--56554961 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
56554918 TTCATACCTT
*
56554928 TTTTAAATATGTA
1 TTTTATATATGTA
56554941 TTTTATATATGTA
1 TTTTATATATGTA
56554954 TTTTATAT
1 TTTTATAT
56554962 TTTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTTATATATGTA
Found at i:56557278 original size:16 final size:16
Alignment explanation
Indices: 56557244--56557277 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56557234 ATATTCAAAT
*
56557244 AAATGAATTATTAGAA
1 AAATGAATTAATAGAA
56557260 AAATG-ATTAATAGAA
1 AAATGAATTAATAGAA
56557275 AAA
1 AAA
56557278 ACTAATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
AAATGAATTAATAGAA
Found at i:56570247 original size:19 final size:17
Alignment explanation
Indices: 56570223--56570259 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
56570213 AATTTAAATT
56570223 TAATTAAATATATATAATA
1 TAATTAAA-A-ATATAATA
56570242 TAATTAAAAATATAATA
1 TAATTAAAAATATAATA
56570259 T
1 T
56570260 TTAATACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTAAAAATATAATA
Found at i:56570264 original size:19 final size:20
Alignment explanation
Indices: 56570183--56570264 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 20
56570173 ACTCAACCGA
56570183 ATTTAAGTTAAATAATATAAAT
1 ATTTAA-TTAAATAATAT-AAT
*
56570205 ATTT-GTTAAAT--T-TAA-
1 ATTTAATTAAATAATATAAT
56570220 ATTTAATTAAATATATATAAT
1 ATTTAATTAAATA-ATATAAT
56570241 A--TAATTAAA-AATATAAT
1 ATTTAATTAAATAATATAAT
56570258 ATTTAAT
1 ATTTAAT
56570265 ACTTTAAGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 19
0.70 0.03 0.27
Matches are distributed among these distances:
15 4 0.08
16 8 0.16
17 9 0.18
18 2 0.04
19 13 0.26
20 9 0.18
21 1 0.02
22 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTTAATTAAATAATATAAT
Found at i:56572476 original size:2 final size:2
Alignment explanation
Indices: 56572432--56572463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56572422 TATGATTATT
56572432 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
56572464 CATGCATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56575293 original size:31 final size:32
Alignment explanation
Indices: 56575258--56575323 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
56575248 CTACAATTCG
56575258 AAAAGTA-TATAG-ACTAAAATTGATCAAATAA
1 AAAAGTATTA-AGTACTAAAATTGATCAAATAA
** *
56575289 AAAAGTATTAAGTGTTAAAATTGATCAAATTA
1 AAAAGTATTAAGTACTAAAATTGATCAAATAA
56575321 AAA
1 AAA
56575324 TATAAGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.29
Consensus pattern (32 bp):
AAAAGTATTAAGTACTAAAATTGATCAAATAA
Found at i:56600032 original size:2 final size:2
Alignment explanation
Indices: 56600025--56600049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56600015 TATTTATACC
56600025 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
56600050 AATGTTTGGT
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:56607648 original size:15 final size:15
Alignment explanation
Indices: 56607614--56607642 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56607604 TCCTTCTACT
56607614 TAAAAATAATCAAAA
1 TAAAAATAATCAAAA
56607629 TAAAAATAATCAAA
1 TAAAAATAATCAAA
56607643 TCAAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAATAATCAAAA
Found at i:56618381 original size:15 final size:16
Alignment explanation
Indices: 56618345--56618396 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
56618335 TACATCTTAA
* *
56618345 TAAAATAAATAAAATAT
1 TAAAATATATATAAT-T
56618362 TAAAA-ATATATAATT
1 TAAAATATATATAATT
* *
56618377 TAAAATCTATTTAATT
1 TAAAATATATATAATT
56618393 TAAA
1 TAAA
56618397 CTAATATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 6 0.20
16 19 0.63
17 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATATATATAATT
Found at i:56621246 original size:21 final size:21
Alignment explanation
Indices: 56621218--56621264 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
56621208 TCAAGCCAAT
56621218 TCAT-TTTTAATGTTTTA-ATA
1 TCATATTTT-ATGTTTTATATA
*
56621238 TCATATTTTATTTTTTATATA
1 TCATATTTTATGTTTTATATA
*
56621259 TTATAT
1 TCATAT
56621265 AACTAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
TCATATTTTATGTTTTATATA
Found at i:56632862 original size:6 final size:6
Alignment explanation
Indices: 56632851--56632888 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
56632841 ACCATCTATA
56632851 TATATT TATATT TATATT TATATT TATATT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TA
56632889 AGTCATTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:56640585 original size:122 final size:122
Alignment explanation
Indices: 56640413--56640633 Score: 336
Period size: 122 Copynumber: 1.8 Consensus size: 122
56640403 CAGATTTGAG
*
56640413 CTCCAAGTTTCAATTATTTCATGTCTGGGCTGAATTACTTTTATGGTCACATAGGGTTAGATATG
1 CTCCAAGTTTCAATTATTTCATGTCTGGGCTGAATTACTTTTATGCTCACATAGGGTTAGATATG
* * *
56640478 ATTTTAGATTTGAGTTGATTAGGTCTAGTTTTCAGGTTCGGATTCAGATTCTGATCA
66 ATATTAGATTTGAGTTGATTAGGTCCAGCTTTCAGGTTCGGATTCAGATTCTGATCA
* * * *
56640535 CTCCGAGTTTCAATTATTTCATGTTTGGGTTGAATT-GTTGTTATGCTCACATAGGGTTAGATAT
1 CTCCAAGTTTCAATTATTTCATGTCTGGGCTGAATTACTT-TTATGCTCACATAGGGTTAGATAT
* *
56640599 TATATTGGATTTGAGTTGATTAGGTCCAGCTTTCA
65 GATATTAGATTTGAGTTGATTAGGTCCAGCTTTCA
56640634 AGTTTGATTC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 2 0.02
122 86 0.98
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.43
Consensus pattern (122 bp):
CTCCAAGTTTCAATTATTTCATGTCTGGGCTGAATTACTTTTATGCTCACATAGGGTTAGATATG
ATATTAGATTTGAGTTGATTAGGTCCAGCTTTCAGGTTCGGATTCAGATTCTGATCA
Found at i:56642410 original size:11 final size:11
Alignment explanation
Indices: 56642394--56642418 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56642384 TATACCTTTT
56642394 ATTTTTTCGAA
1 ATTTTTTCGAA
56642405 ATTTTTTCGAA
1 ATTTTTTCGAA
56642416 ATT
1 ATT
56642419 ATCATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTTTTTCGAA
Found at i:56647565 original size:21 final size:23
Alignment explanation
Indices: 56647513--56647568 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
56647503 GGATGATCCT
*
56647513 AATTATATTTTTGAATTTTTTTAC
1 AATTA-ATTTTTGAATTTTTATAC
* *
56647537 TATCAATTTTT-AATTTTTATA-
1 AATTAATTTTTGAATTTTTATAC
56647558 AATTAATTTTT
1 AATTAATTTTT
56647569 TCTAACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 6 0.22
24 3 0.11
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
AATTAATTTTTGAATTTTTATAC
Found at i:56650617 original size:42 final size:42
Alignment explanation
Indices: 56650565--56650650 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
56650555 AAAAGCCAAA
56650565 TTCTATTCATAATAATAAAGGAAGTTAGGTAATTTAAAAAAG
1 TTCTATTCATAATAATAAAGGAAGTTAGGTAATTTAAAAAAG
* *
56650607 TTCTATTCATAATAATAGAGGAAGTTAGGTAATTTAAGAAAG
1 TTCTATTCATAATAATAAAGGAAGTTAGGTAATTTAAAAAAG
56650649 TT
1 TT
56650651 ACATTGAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (42 bp):
TTCTATTCATAATAATAAAGGAAGTTAGGTAATTTAAAAAAG
Found at i:56652425 original size:19 final size:20
Alignment explanation
Indices: 56652401--56652440 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
56652391 CGCTTTAGCA
56652401 GCCACCAACTC-CTGCCACC
1 GCCACCAACTCTCTGCCACC
**
56652420 GCCACCTGCTCTCTGCCACC
1 GCCACCAACTCTCTGCCACC
56652440 G
1 G
56652441 TCGTCGTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (20 bp):
GCCACCAACTCTCTGCCACC
Found at i:56653242 original size:33 final size:33
Alignment explanation
Indices: 56653195--56653265 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
56653185 TTATAAAATT
56653195 TGCC-CTAAAATTTTTTAATATTTTCAATTTAG
1 TGCCGCTAAAATTTTTTAATATTTTCAATTTAG
*
56653227 TGCCGCTAAATTTTTTTAATATTTTCAATTTAG
1 TGCCGCTAAAATTTTTTAATATTTTCAATTTAG
*
56653260 TCCCGC
1 TGCCGC
56653266 GTCCTCTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (33 bp):
TGCCGCTAAAATTTTTTAATATTTTCAATTTAG
Found at i:56655326 original size:30 final size:30
Alignment explanation
Indices: 56655284--56655352 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
56655274 TAAGTTATGG
*
56655284 GGGCTCAATT-AAATTTATAAAAAATTT-GA
1 GGGCTTAATTAAAATTTAT-AAAAATTTAGA
* *
56655313 GGGTCTTAATTAAAATTTCTAAAATTTTAGA
1 GGG-CTTAATTAAAATTTATAAAAATTTAGA
56655344 GGGCTTAAT
1 GGGCTTAAT
56655353 GGGAATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.09
30 19 0.56
31 12 0.35
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (30 bp):
GGGCTTAATTAAAATTTATAAAAATTTAGA
Found at i:56658146 original size:54 final size:54
Alignment explanation
Indices: 56658064--56658175 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
56658054 TACCAAGGAG
56658064 TTTAAGTTTGAATATGAACAAGTTTAAATTTCAGTAGAAAAATTGATAAACGAC
1 TTTAAGTTTGAATATGAACAAGTTTAAATTTCAGTAGAAAAATTGATAAACGAC
56658118 TTTAAGTTTGAATATGAACAAGTTTAAATTTCAGTAGAAAAATTGATAAACGAC
1 TTTAAGTTTGAATATGAACAAGTTTAAATTTCAGTAGAAAAATTGATAAACGAC
56658172 TTTA
1 TTTA
56658176 TTTGAGTCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (54 bp):
TTTAAGTTTGAATATGAACAAGTTTAAATTTCAGTAGAAAAATTGATAAACGAC
Found at i:56669820 original size:4 final size:4
Alignment explanation
Indices: 56669811--56669847 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
56669801 ATTTAAGGGA
56669811 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
56669848 CGATGTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:56674071 original size:18 final size:19
Alignment explanation
Indices: 56674030--56674076 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
56674020 CATTACAACC
56674030 CAAAAAGAAAAAGGAGATA
1 CAAAAAGAAAAAGGAGATA
* * *
56674049 GAAAAAGAAAAGGGGGAT-
1 CAAAAAGAAAAAGGAGATA
56674067 CAAAAAGAAA
1 CAAAAAGAAA
56674077 GAACATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAAGGAGATA
Found at i:56695159 original size:13 final size:13
Alignment explanation
Indices: 56695143--56695184 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
56695133 AATAAATATA
56695143 TATTTTTTATTTT
1 TATTTTTTATTTT
56695156 TATTTTTTAATTTT
1 TATTTTTT-ATTTT
* *
56695170 TAATTTTTAATTT
1 TATTTTTTATTTT
56695183 TA
1 TA
56695185 AAATACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:56695185 original size:6 final size:7
Alignment explanation
Indices: 56695144--56695183 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
56695134 ATAAATATAT
*
56695144 ATTTTTT
1 ATTTTTA
56695151 ATTTTTA
1 ATTTTTA
*
56695158 TTTTTTA
1 ATTTTTA
56695165 ATTTTTA
1 ATTTTTA
56695172 ATTTTTA
1 ATTTTTA
56695179 ATTTT
1 ATTTT
56695184 AAAATACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
ATTTTTA
Found at i:56695226 original size:26 final size:26
Alignment explanation
Indices: 56695191--56695243 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
56695181 TTTAAAATAC
* * *
56695191 TTTTAAAATATTTTTTTATTTTTTAT
1 TTTTAAAATAATTTTTTAATGTTTAT
56695217 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAATAATTTTTTAATGTTTAT
56695243 T
1 T
56695244 AAAAAATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTAAAATAATTTTTTAATGTTTAT
Found at i:56701830 original size:17 final size:16
Alignment explanation
Indices: 56701808--56701839 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
56701798 TCTTCTTATA
56701808 GTTTTGTAAATGAAATG
1 GTTTTGTAAAT-AAATG
56701825 GTTTTGTAAATAAAT
1 GTTTTGTAAATAAAT
56701840 AAATTTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
GTTTTGTAAATAAATG
Found at i:56705583 original size:58 final size:58
Alignment explanation
Indices: 56705445--56705583 Score: 147
Period size: 58 Copynumber: 2.4 Consensus size: 58
56705435 TTAAAACTCC
* * * *
56705445 AAAAGTTTAGACCTCAACATGGGAACAATTGCCAAGTTCAAGGACTAATTTAGAAAAA
1 AAAAGTTTAGGCCTCAACGTGGGAACAATTACCAAGTTCAAGGACTAACTTAGAAAAA
* * * * * * *
56705503 AAAAGTTCAAGCCCCAATGTGGGAA-AATTACCAAGTTCAGGGCCTAACTTGGACCAAAA
1 AAAAGTTTAGGCCTCAACGTGGGAACAATTACCAAGTTCAAGGACTAACTTAGA--AAAA
56705562 AAAAGTTTAGGCCTCAA-GTGGG
1 AAAAGTTTAGGCCTCAACGTGGG
56705584 GATAGTTGCC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
57 23 0.35
58 24 0.37
59 18 0.28
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (58 bp):
AAAAGTTTAGGCCTCAACGTGGGAACAATTACCAAGTTCAAGGACTAACTTAGAAAAA
Found at i:56705820 original size:12 final size:12
Alignment explanation
Indices: 56705803--56705839 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
56705793 AATAATGTTT
56705803 TGTTTTGATTTA
1 TGTTTTGATTTA
*
56705815 TGTTTTGATTCA
1 TGTTTTGATTTA
*
56705827 TGTTTTGGTTTA
1 TGTTTTGATTTA
56705839 T
1 T
56705840 TTATGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.03, G:0.19, T:0.65
Consensus pattern (12 bp):
TGTTTTGATTTA
Found at i:56707709 original size:12 final size:12
Alignment explanation
Indices: 56707692--56707724 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
56707682 AACTGAATTG
56707692 TTTTTTTCCTTT
1 TTTTTTTCCTTT
*
56707704 TTTTTTTCTTTT
1 TTTTTTTCCTTT
56707716 TTTTTTTCC
1 TTTTTTTCC
56707725 AATAGGCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTCCTTT
Found at i:56707721 original size:11 final size:11
Alignment explanation
Indices: 56707692--56707721 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
56707682 AACTGAATTG
*
56707692 TTTTTTTCCTT
1 TTTTTTTTCTT
56707703 TTTTTTTTCTT
1 TTTTTTTTCTT
56707714 TTTTTTTT
1 TTTTTTTT
56707722 TCCAATAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:56708359 original size:2 final size:2
Alignment explanation
Indices: 56708352--56708391 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
56708342 CTCTTCTTCT
56708352 TA TA TA 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 TA TA TA
56708392 ATTTTTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56709822 original size:43 final size:43
Alignment explanation
Indices: 56709774--56709860 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
56709764 CATTGTATTG
**
56709774 ACTTATATCATTATGGTTATCAAAATGACTAAATTGTAATTCT
1 ACTTATATCATTATGGTTATCAAAATGACTAAATTAAAATTCT
56709817 ACTTATATCATTATGGTTATCAAAATGACTAAATTAAAATTCT
1 ACTTATATCATTATGGTTATCAAAATGACTAAATTAAAATTCT
56709860 A
1 A
56709861 ACATTTTGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (43 bp):
ACTTATATCATTATGGTTATCAAAATGACTAAATTAAAATTCT
Found at i:56725917 original size:29 final size:28
Alignment explanation
Indices: 56725847--56725919 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 28
56725837 CATTTAATTA
* *
56725847 ATTTTTAAAAATTTAAAAATATTTTTAT
1 ATTTTTTAAATTTTAAAAATATTTTTAT
56725875 A-TTTTTAATTATTTTAAAAATAGTTTTTAT
1 ATTTTTTAA--ATTTTAAAAATA-TTTTTAT
56725905 ATTTTTTAAATTTTA
1 ATTTTTTAAATTTTA
56725920 TATTTAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.15
28 1 0.03
29 17 0.44
30 8 0.21
31 7 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTTTTAAATTTTAAAAATATTTTTAT
Found at i:56733937 original size:22 final size:21
Alignment explanation
Indices: 56733911--56733963 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
56733901 TTTAATTTTC
56733911 TAAATTTTATATAAAATTATTT
1 TAAATTTTATAT-AAATTATTT
*
56733933 TAAATTTTATATAAATTTTTT
1 TAAATTTTATATAAATTATTT
56733954 TAAAATTTTA
1 T-AAATTTTA
56733964 GGTAATGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATTTTATATAAATTATTT
Found at i:56742421 original size:18 final size:17
Alignment explanation
Indices: 56742387--56742435 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
56742377 TAACATTTTA
* *
56742387 AATATAAATTTTTATTTT
1 AATATAAA-TTTAAATTT
*
56742405 TATATAAATTTAAATTT
1 AATATAAATTTAAATTT
56742422 AATTATAAATTTAA
1 AA-TATAAATTTAA
56742436 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATAAATTTAAATTT
Found at i:56757415 original size:2 final size:2
Alignment explanation
Indices: 56757410--56757437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56757400 GTGATGTTAA
56757410 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
56757438 TTTATGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56760523 original size:57 final size:58
Alignment explanation
Indices: 56760452--56760574 Score: 151
Period size: 57 Copynumber: 2.2 Consensus size: 58
56760442 TCGGTCCACT
* * **
56760452 CGGCTTAA-AGAAGTAGCCAAATCAGAAATCTTATCACCAGTTGTTCATTGGTCCCCC
1 CGGCTTAAGAGAAGTAGCAAAACCAGAAATCTTATCACCAGTTGTTCATCAGTCCCCC
** * * *
56760509 CGGCTTAAGA-AAGTAGCAAAACCAGATCTTTTATCACCAGTTGTTCGTCAGTCCCCT
1 CGGCTTAAGAGAAGTAGCAAAACCAGAAATCTTATCACCAGTTGTTCATCAGTCCCCC
56760566 CGGCTTAAG
1 CGGCTTAAG
56760575 GTATTATATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 55 0.98
58 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (58 bp):
CGGCTTAAGAGAAGTAGCAAAACCAGAAATCTTATCACCAGTTGTTCATCAGTCCCCC
Found at i:56762554 original size:17 final size:18
Alignment explanation
Indices: 56762530--56762583 Score: 85
Period size: 17 Copynumber: 3.1 Consensus size: 18
56762520 ATGTAATCTT
56762530 AGAGTTCTAATTGTGTAC
1 AGAGTTCTAATTGTGTAC
56762548 A-AGTTCTAATTGTGTA-
1 AGAGTTCTAATTGTGTAC
*
56762564 AGAGTTCTAATTGTATAC
1 AGAGTTCTAATTGTGTAC
56762582 AG
1 AG
56762584 CTTTTAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.88
18 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (18 bp):
AGAGTTCTAATTGTGTAC
Found at i:56767659 original size:17 final size:17
Alignment explanation
Indices: 56767637--56767698 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
56767627 AATCTTAGAG
56767637 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* *
56767654 TTCTAATTGTGTA-AGAG
1 TTCTAATTGTATACA-AC
*
56767671 ATCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
56767688 TTTTAATTGTA
1 TTCTAATTGTA
56767699 GCCATTGATG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 1 0.03
17 34 0.94
18 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:56767681 original size:34 final size:34
Alignment explanation
Indices: 56767633--56767697 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
56767623 ATGTAATCTT
*
56767633 AGAGTTCTAATTGTATACAACTTCTAATTGTGTA
1 AGAGATCTAATTGTATACAACTTCTAATTGTGTA
*
56767667 AGAGATCTAATTGTATACAACTTTTAATTGT
1 AGAGATCTAATTGTATACAACTTCTAATTGT
56767698 AGCCATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.42
Consensus pattern (34 bp):
AGAGATCTAATTGTATACAACTTCTAATTGTGTA
Found at i:56778271 original size:25 final size:25
Alignment explanation
Indices: 56778243--56778293 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
56778233 TAAATAATTT
56778243 AAAAT-TCATAAAA-TATAAAAATATA
1 AAAATATCATAAAAGT-T-AAAATATA
*
56778268 AAAATATTATAAAAGTTAAAATATA
1 AAAATATCATAAAAGTTAAAATATA
56778293 A
1 A
56778294 CATTATGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.61
26 8 0.35
27 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATATCATAAAAGTTAAAATATA
Found at i:56785306 original size:61 final size:61
Alignment explanation
Indices: 56785211--56785333 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
56785201 TCAAATTTGC
56785211 CTCTGTCCATTAGGTTTGTTGAATTGACAAAGAATATAAAATAATCAAACATTGTATGTCG
1 CTCTGTCCATTAGGTTTGTTGAATTGACAAAGAATATAAAATAATCAAACATTGTATGTCG
56785272 CTCTGTCCATTAGGTTTGTTGAATTGACAAAGAATATAAAATAATCAAACATTGTATGTCG
1 CTCTGTCCATTAGGTTTGTTGAATTGACAAAGAATATAAAATAATCAAACATTGTATGTCG
56785333 C
1 C
56785334 AAAATTAATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (61 bp):
CTCTGTCCATTAGGTTTGTTGAATTGACAAAGAATATAAAATAATCAAACATTGTATGTCG
Found at i:56785654 original size:17 final size:17
Alignment explanation
Indices: 56785609--56785655 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
56785599 TGGATGTTAC
56785609 ATAATAAAATTATTAAA
1 ATAATAAAATTATTAAA
** *
56785626 ATTTTAATATTATT-AA
1 ATAATAAAATTATTAAA
56785642 ATAAATAAAATTAT
1 AT-AATAAAATTAT
56785656 ATAGTTAAAG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAAAATTATTAAA
Found at i:56787330 original size:10 final size:10
Alignment explanation
Indices: 56787317--56787341 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56787307 ATTTAAATAA
56787317 TTTTATATTT
1 TTTTATATTT
56787327 TTTTATATTT
1 TTTTATATTT
56787337 TTTTA
1 TTTTA
56787342 CAATTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTATATTT
Found at i:56789707 original size:26 final size:27
Alignment explanation
Indices: 56789655--56789717 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
56789645 ATAAAAAATA
56789655 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
56789682 ACCAAAATATTATAA-TTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
56789708 ACCAAAATAT
1 ACCAAAATAT
56789718 ACCAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 21 0.58
27 15 0.42
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:56790079 original size:18 final size:18
Alignment explanation
Indices: 56790043--56790080 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56790033 ATTTTATTAG
*
56790043 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
56790061 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
56790079 AG
1 AG
56790081 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:56790737 original size:26 final size:28
Alignment explanation
Indices: 56790685--56790745 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
56790675 TTTTTTTGGT
56790685 ATATTTTAGTAAATAAAAAAAATTTATA
1 ATATTTTAGTAAATAAAAAAAATTTATA
56790713 ATATTTTAGTAAAT-AAAAAAA-TTATA
1 ATATTTTAGTAAATAAAAAAAATTTATA
56790739 ATATTTT
1 ATATTTT
56790746 GGTTAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 12 0.36
27 7 0.21
28 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
ATATTTTAGTAAATAAAAAAAATTTATA
Found at i:56792297 original size:12 final size:12
Alignment explanation
Indices: 56792280--56792305 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56792270 TCTTATATCC
56792280 TAAATAAAAAAT
1 TAAATAAAAAAT
56792292 TAAATAAAAAAT
1 TAAATAAAAAAT
56792304 TA
1 TA
56792306 GAGTAGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:56799800 original size:21 final size:21
Alignment explanation
Indices: 56799763--56799814 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
56799753 GGGTTCGATG
*
56799763 TTTAGTGTTTGAGGTTT-AGGA
1 TTTAGTGTTAGAGGTTTGA-GA
56799784 TTTAGTGTTCAGA-GTTTGAGA
1 TTTAGTGTT-AGAGGTTTGAGA
*
56799805 TTTAGGGTTA
1 TTTAGTGTTA
56799815 AGGATTCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (21 bp):
TTTAGTGTTAGAGGTTTGAGA
Found at i:56809636 original size:12 final size:13
Alignment explanation
Indices: 56809617--56809653 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
56809607 ATTTTTTAAA
56809617 TATTATTTAATTT
1 TATTATTTAATTT
56809630 T-TTATTTAATTT
1 TATTATTTAATTT
*
56809642 TATAATTTAATT
1 TATTATTTAATT
56809654 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTAATTT
Found at i:56810031 original size:86 final size:86
Alignment explanation
Indices: 56809865--56810031 Score: 253
Period size: 86 Copynumber: 1.9 Consensus size: 86
56809855 AACCCAAAAA
56809865 CCCTAAGTAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
1 CCCTAAGTAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
**
56809930 TGCCTGACATGAGGAAGAATG
66 TGCCTGACACAAGGAAGAATG
* * * ** *
56809951 CCCTAATTAGCAAATAACCCACTGGGGATTACACGGCCAAAAGTGCTTCCACGTCAGAGCGCTTT
1 CCCTAAGTAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
*
56810016 TGCCTGGCACAAGGAA
66 TGCCTGACACAAGGAA
56810032 AAAAGTGTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (86 bp):
CCCTAAGTAGCAAATAACCCACTCGAGATTACACGGCCAAAAACGCTTCCACGTCAGAGCGATTT
TGCCTGACACAAGGAAGAATG
Found at i:56816968 original size:6 final size:6
Alignment explanation
Indices: 56816957--56816987 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56816947 CCACCATGAT
*
56816957 CATCAC CATCAC CATCAC CATCAC CACCAC C
1 CATCAC CATCAC CATCAC CATCAC CATCAC C
56816988 GTCATCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.13
Consensus pattern (6 bp):
CATCAC
Found at i:56816971 original size:18 final size:18
Alignment explanation
Indices: 56816945--56816987 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
56816935 TCATCCTGAT
* *
56816945 CACCACCATGATCATCAC
1 CACCACCATCACCATCAC
*
56816963 CATCACCATCACCATCAC
1 CACCACCATCACCATCAC
56816981 CACCACC
1 CACCACC
56816988 GTCATCTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.51, G:0.02, T:0.14
Consensus pattern (18 bp):
CACCACCATCACCATCAC
Found at i:56817238 original size:3 final size:3
Alignment explanation
Indices: 56817230--56817261 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56817220 CTTTTTAGTT
56817230 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
56817262 GAAACACAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56817539 original size:21 final size:22
Alignment explanation
Indices: 56817515--56817556 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56817505 ATTTTCGTCC
* *
56817515 TTCTA-TTTTTATTTTAAAATT
1 TTCTACTTTTCATTTAAAAATT
56817536 TTCTACTTTTCATTTAAAAAT
1 TTCTACTTTTCATTTAAAAAT
56817557 GCATGTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (22 bp):
TTCTACTTTTCATTTAAAAATT
Found at i:56834447 original size:2 final size:2
Alignment explanation
Indices: 56834442--56834469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56834432 ACACACACAC
56834442 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
56834470 CAAGTTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56846829 original size:2 final size:2
Alignment explanation
Indices: 56846822--56846855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56846812 AAAATCCAAT
56846822 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
56846856 AATTTCCTTG
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:56855520 original size:20 final size:21
Alignment explanation
Indices: 56855497--56855535 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
56855487 TTTTGTAATA
* *
56855497 ATTTT-TATTTTTTAAATTGT
1 ATTTTATAATTTTAAAATTGT
56855517 ATTTTATAATTTTAAAATT
1 ATTTTATAATTTTAAAATT
56855536 TTAAATGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTATAATTTTAAAATTGT
Found at i:56856010 original size:2 final size:2
Alignment explanation
Indices: 56856003--56856032 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
56855993 CTTATGTTAA
56856003 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
56856033 TAGTTNNNNN
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:56864607 original size:2 final size:2
Alignment explanation
Indices: 56864600--56864636 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
56864590 CTGATCCTTT
*
56864600 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
56864637 ATTAGCATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:56876597 original size:6 final size:6
Alignment explanation
Indices: 56876588--56876612 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56876578 ATGGAGTTTG
56876588 AGCTTC AGCTTC AGCTTC AGCTTC A
1 AGCTTC AGCTTC AGCTTC AGCTTC A
56876613 CGGTACCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (6 bp):
AGCTTC
Found at i:56877573 original size:19 final size:19
Alignment explanation
Indices: 56877540--56877587 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
56877530 TAAACAATTC
56877540 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
56877557 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
56877576 AATAATATAAAT
1 AATAATATAAAT
56877588 AGTAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:56878102 original size:9 final size:9
Alignment explanation
Indices: 56878088--56878124 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56878078 TATAGTTTGA
56878088 TATTCGAAT
1 TATTCGAAT
56878097 TATTCGAAT
1 TATTCGAAT
*
56878106 TATTCGAGT
1 TATTCGAAT
56878115 TATTCGAAT
1 TATTCGAAT
56878124 T
1 T
56878125 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56879891 original size:44 final size:44
Alignment explanation
Indices: 56879837--56879931 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
56879827 TACAAAGTAG
** * *
56879837 TATCTAAATATTAAATT-GTTAAAAATAAAGTTTAATAATTACAA
1 TATCTAAATATT-AATTAGACAAAAATAAACTTAAATAATTACAA
*
56879881 TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTATAA
1 TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTACAA
*
56879925 AATCTAA
1 TATCTAA
56879932 GACAAATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (44 bp):
TATCTAAATATTAATTAGACAAAAATAAACTTAAATAATTACAA
Found at i:56882425 original size:31 final size:30
Alignment explanation
Indices: 56882390--56882449 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
56882380 GGAGGTGGGA
56882390 TGGGAAGAGAATAAAAATTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
56882421 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
56882450 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:56885046 original size:3 final size:3
Alignment explanation
Indices: 56885040--56885071 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56885030 TTATATAATA
56885040 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56885072 GTTAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56885969 original size:40 final size:41
Alignment explanation
Indices: 56885899--56885986 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
56885889 AATTATGGAA
* * *
56885899 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGG
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
* * * *
56885940 TACTGAATATTG-TTATGTGTATTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
56885980 TACTGAA
1 TACTGAA
56885987 GTAATGAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 28 0.70
41 12 0.30
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAG
Found at i:56886285 original size:45 final size:45
Alignment explanation
Indices: 56886186--56886286 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 45
56886176 ATATGTCGAC
*
56886186 TACTGTTACTGTTACCGATTCGACACTTTATGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTATGTGTCGAATACTGT
** * * *
56886231 TACCATTACTGTTATAGATTC-AGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGA-CACTTTATGTGTCGAATACTGT
56886276 TACTGTTACTG
1 TACTGTTACTG
56886287 CTGCCGTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTATGTGTCGAATACTGT
Found at i:56886924 original size:37 final size:37
Alignment explanation
Indices: 56886874--56886959 Score: 172
Period size: 37 Copynumber: 2.3 Consensus size: 37
56886864 TGCTACATTT
56886874 ATAGAGTTATTAAATGAGAATAGTTTATTAAATTAAA
1 ATAGAGTTATTAAATGAGAATAGTTTATTAAATTAAA
56886911 ATAGAGTTATTAAATGAGAATAGTTTATTAAATTAAA
1 ATAGAGTTATTAAATGAGAATAGTTTATTAAATTAAA
56886948 ATAGAGTTATTA
1 ATAGAGTTATTA
56886960 CTTAATTAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
ATAGAGTTATTAAATGAGAATAGTTTATTAAATTAAA
Found at i:56886964 original size:18 final size:19
Alignment explanation
Indices: 56886874--56886959 Score: 104
Period size: 18 Copynumber: 4.6 Consensus size: 19
56886864 TGCTACATTT
* *
56886874 ATAGAGTTATTAAATGAGA
1 ATAGAGTTATTAAATTAAA
*
56886893 ATAG-TTTATTAAATTAAA
1 ATAGAGTTATTAAATTAAA
* *
56886911 ATAGAGTTATTAAATGAGA
1 ATAGAGTTATTAAATTAAA
*
56886930 ATAG-TTTATTAAATTAAA
1 ATAGAGTTATTAAATTAAA
56886948 ATAGAGTTATTA
1 ATAGAGTTATTA
56886960 CTTAATTAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
18 30 0.55
19 25 0.45
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
ATAGAGTTATTAAATTAAA
Found at i:56887546 original size:27 final size:27
Alignment explanation
Indices: 56887514--56887565 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
56887504 CATTTTAGTC
*
56887514 CTTTGGCACCATTGGTGCTGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
**
56887541 CTTTGGCACTTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
56887566 GTGATTGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.13, C:0.29, G:0.23, T:0.35
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:56887573 original size:27 final size:27
Alignment explanation
Indices: 56887516--56887574 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
56887506 TTTTAGTCCT
* *
56887516 TTGGCACCATTGGTGCTGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
** * *
56887543 TTGGCACTTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
56887570 TTGGC
1 TTGGC
56887575 TTGATCAGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:56887697 original size:26 final size:27
Alignment explanation
Indices: 56887625--56887719 Score: 156
Period size: 26 Copynumber: 3.5 Consensus size: 27
56887615 TTTTTTGGGT
* *
56887625 ATATTTTAGTAAATAAAAAAAATTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
56887653 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
56887680 ATATTTTGGTAAAT-AAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
56887706 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
56887720 TTTTATTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
26 26 0.40
27 26 0.40
28 13 0.20
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:56899030 original size:12 final size:12
Alignment explanation
Indices: 56899013--56899037 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56899003 CCTGTTTGTT
56899013 GTAGATATTGAA
1 GTAGATATTGAA
56899025 GTAGATATTGAA
1 GTAGATATTGAA
56899037 G
1 G
56899038 AGGTACCACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GTAGATATTGAA
Found at i:56900444 original size:20 final size:18
Alignment explanation
Indices: 56900400--56900444 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
56900390 TATTATTTTG
56900400 GTTTTTTTTAATTTTTAA
1 GTTTTTTTTAATTTTTAA
* *
56900418 ATATTTTTTAGAATTTTTAA
1 GT-TTTTTT-TAATTTTTAA
56900438 GTTTTTT
1 GTTTTTT
56900445 AAATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (18 bp):
GTTTTTTTTAATTTTTAA
Found at i:56900516 original size:20 final size:19
Alignment explanation
Indices: 56900484--56900545 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
56900474 ATTTTAGATT
*
56900484 TTTTATAAA-TATTTTAAAA
1 TTTTAAAAATTATTTT-AAA
* **
56900503 TTTTGAAAATTATTTCGAA
1 TTTTAAAAATTATTTTAAA
56900522 TTTCTAAAAATTATTTTAAA
1 TTT-TAAAAATTATTTTAAA
56900542 TTTT
1 TTTT
56900546 TTTGTTGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:56907950 original size:13 final size:13
Alignment explanation
Indices: 56907934--56907960 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56907924 TAAATTAATA
56907934 AATGTAATTATAT
1 AATGTAATTATAT
56907947 AATGTAATTATAT
1 AATGTAATTATAT
56907960 A
1 A
56907961 TTTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AATGTAATTATAT
Found at i:56910887 original size:82 final size:82
Alignment explanation
Indices: 56910745--56910913 Score: 302
Period size: 82 Copynumber: 2.1 Consensus size: 82
56910735 TTGTGAGATG
*
56910745 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAATTTGATAATATATCTTAAG
1 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCTTAAG
*
56910810 ATTGTCAAATTCCAACT
66 ATTGCCAAATTCCAACT
* *
56910827 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATGTATCTTAGG
1 TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCTTAAG
56910892 ATTGCCAAATTCCAACT
66 ATTGCCAAATTCCAACT
56910909 TCTTT
1 TCTTT
56910914 TGAGTAACTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 83 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (82 bp):
TCTTTATTTAAGGTGTGATCGGATGCTGAAGTTTCATTTGCCCCAACTTGATAATATATCTTAAG
ATTGCCAAATTCCAACT
Found at i:56925546 original size:17 final size:18
Alignment explanation
Indices: 56925513--56925547 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
56925503 TCCCCAAAGG
56925513 ATTCTCGATCATATTCTT
1 ATTCTCGATCATATTCTT
*
56925531 ATTCTC-ATCATCTTCTT
1 ATTCTCGATCATATTCTT
56925548 TCTTCCTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.26, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTCTCGATCATATTCTT
Found at i:56928257 original size:24 final size:24
Alignment explanation
Indices: 56928230--56928277 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56928220 TATGGACGAA
* *
56928230 GATGAAGATGATGAGGAAGAGGAG
1 GATGAAGAGGAGGAGGAAGAGGAG
*
56928254 GATGAAGAGGGGGAGGAAGAGGAG
1 GATGAAGAGGAGGAGGAAGAGGAG
56928278 AAAGAGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.52, T:0.08
Consensus pattern (24 bp):
GATGAAGAGGAGGAGGAAGAGGAG
Found at i:56928260 original size:12 final size:12
Alignment explanation
Indices: 56928242--56928277 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
56928232 TGAAGATGAT
56928242 GAGGAAGAGGAG
1 GAGGAAGAGGAG
* *
56928254 GATGAAGAGGGG
1 GAGGAAGAGGAG
56928266 GAGGAAGAGGAG
1 GAGGAAGAGGAG
56928278 AAAGAGAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.03
Consensus pattern (12 bp):
GAGGAAGAGGAG
Found at i:56943272 original size:33 final size:33
Alignment explanation
Indices: 56943235--56943302 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
56943225 ATACTTTAAA
56943235 ATAAAATATATGAAAAAGCTTGAAGAAGCTAAT
1 ATAAAATATATGAAAAAGCTTGAAGAAGCTAAT
56943268 ATAAAATATATGAAAAAGCTTGAAGAAGCTAAT
1 ATAAAATATATGAAAAAGCTTGAAGAAGCTAAT
56943301 AT
1 AT
56943303 GGATTGACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.15, T:0.25
Consensus pattern (33 bp):
ATAAAATATATGAAAAAGCTTGAAGAAGCTAAT
Found at i:56959905 original size:16 final size:16
Alignment explanation
Indices: 56959884--56959914 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56959874 GGTTCAATGT
56959884 AATGGAATAGAGCTGA
1 AATGGAATAGAGCTGA
56959900 AATGGAATAGAGCTG
1 AATGGAATAGAGCTG
56959915 TAATCAATAA
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:0.42, C:0.06, G:0.32, T:0.19
Consensus pattern (16 bp):
AATGGAATAGAGCTGA
Found at i:56960151 original size:62 final size:57
Alignment explanation
Indices: 56960085--56960213 Score: 141
Period size: 62 Copynumber: 2.2 Consensus size: 57
56960075 TTGTTATTAA
* * * * *
56960085 ATTTTAATAAAATTATTGTTAAATATATTTTTATTAAAAATAATAATAAATAATTTAATCAT
1 ATTTTAATAAAATTATTATTAAATATA-ATTTAAT-AAAATAAT-AT--ACAATTTAATAAT
* *
56960147 ATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATACAATTTAATAAT
1 ATTTTAATAAAATTATTATTAAATATAATTTAATAAAATAATATACAATTTAATAAT
56960204 ATTCTTAATA
1 ATT-TTAATA
56960214 GAATAAGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 14 0.24
58 5 0.09
59 2 0.03
60 8 0.14
61 5 0.09
62 24 0.41
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (57 bp):
ATTTTAATAAAATTATTATTAAATATAATTTAATAAAATAATATACAATTTAATAAT
Found at i:56965094 original size:46 final size:46
Alignment explanation
Indices: 56965030--56965211 Score: 346
Period size: 46 Copynumber: 4.0 Consensus size: 46
56965020 GGAAAAATGT
*
56965030 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
56965076 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
56965122 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
*
56965168 GAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAGTT
1 GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTT
56965212 ATAGCAATGT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 134 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (46 bp):
GAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGC
Found at i:56965676 original size:29 final size:29
Alignment explanation
Indices: 56965643--56965702 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
56965633 GGGAATTGAA
56965643 ATAAAAAGTATTAGTATGAATGACTAAGT
1 ATAAAAAGTATTAGTATGAATGACTAAGT
56965672 ATAAAAAGTATTAGTATGAATGACTAAGT
1 ATAAAAAGTATTAGTATGAATGACTAAGT
56965701 AT
1 AT
56965703 GCAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.32
Consensus pattern (29 bp):
ATAAAAAGTATTAGTATGAATGACTAAGT
Found at i:56967839 original size:24 final size:24
Alignment explanation
Indices: 56967805--56967854 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
56967795 TTTCTAAAAG
* *
56967805 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
56967829 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
56967853 AT
1 AT
56967855 GTGACTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:56983756 original size:31 final size:29
Alignment explanation
Indices: 56983717--56983792 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
56983707 TTAAAATTAG
*
56983717 ACAT-AATTTTGATTTAATATATAATTATAT
1 ACATGAATTTTAATTT--TATATAATTATAT
* *
56983747 ACATGAATTTTAATTTTGTATAATTTTAT
1 ACATGAATTTTAATTTTATATAATTATAT
56983776 ACATGAAATTTTAATTT
1 ACATG-AATTTTAATTT
56983793 GGTCAAATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 16 0.39
30 15 0.37
31 10 0.24
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.51
Consensus pattern (29 bp):
ACATGAATTTTAATTTTATATAATTATAT
Found at i:56983770 original size:29 final size:30
Alignment explanation
Indices: 56983736--56983792 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
56983726 TGATTTAATA
56983736 TATAATTATATACATG-AATTTTAATTTTG
1 TATAATTATATACATGAAATTTTAATTTTG
*
56983765 TATAATTTTATACATGAAATTTTAATTT
1 TATAATTATATACATGAAATTTTAATTT
56983793 GGTCAAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (30 bp):
TATAATTATATACATGAAATTTTAATTTTG
Found at i:56983807 original size:29 final size:29
Alignment explanation
Indices: 56983736--56983807 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
56983726 TGATTTAATA
* *
56983736 TATAATTATATACATGAATTTTAATTTTG
1 TATAATTCTATACATGAATTTTAATTTGG
*
56983765 TATAATTTTATACATGAAATTTTAATTTGG
1 TATAATTCTATACATG-AATTTTAATTTGG
56983795 TCA-AATTCT-TACA
1 T-ATAATTCTATACA
56983808 AATTATTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 19 0.50
30 18 0.47
31 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (29 bp):
TATAATTCTATACATGAATTTTAATTTGG
Found at i:56988490 original size:30 final size:31
Alignment explanation
Indices: 56988447--56988506 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
56988437 TATAAAATAG
56988447 TCACTGAAATATTCG-AAATTTTCATTTAAA
1 TCACTGAAATATTCGTAAATTTTCATTTAAA
*
56988477 TCACT-AAACTATTCGTAAATTTTTATTTAA
1 TCACTGAAA-TATTCGTAAATTTTCATTTAA
56988507 GACATTGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (31 bp):
TCACTGAAATATTCGTAAATTTTCATTTAAA
Found at i:56989321 original size:12 final size:11
Alignment explanation
Indices: 56989300--56989334 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
56989290 ACTACCCAAG
56989300 CTTTTTTCTTT
1 CTTTTTTCTTT
56989311 CTTTCTTTCTTT
1 CTTT-TTTCTTT
56989323 CTTTTTT-TTT
1 CTTTTTTCTTT
56989333 CT
1 CT
56989335 GTATTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 7 0.30
12 11 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:56995525 original size:3 final size:3
Alignment explanation
Indices: 56995519--56995568 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
56995509 ATAATGACAA
* *
56995519 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56995567 AA
1 AA
56995569 AGGAATGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:57000985 original size:2 final size:2
Alignment explanation
Indices: 57000978--57001002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57000968 ATCGACTTTT
57000978 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
57001003 AGAAAAAAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57001033 original size:16 final size:16
Alignment explanation
Indices: 57001014--57001045 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57001004 GAAAAAAAAA
57001014 AGAGACAGACAGAGAC
1 AGAGACAGACAGAGAC
*
57001030 AGAGACAGAGAGAGAC
1 AGAGACAGACAGAGAC
57001046 GGCAAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.16, G:0.34, T:0.00
Consensus pattern (16 bp):
AGAGACAGACAGAGAC
Found at i:57009363 original size:20 final size:20
Alignment explanation
Indices: 57009335--57009375 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
57009325 CACTTGAGCT
* *
57009335 TAAACATTTCTGATTTCTCA
1 TAAAAATTTCTCATTTCTCA
*
57009355 TAAAAATTTCTCCTTTCTCA
1 TAAAAATTTCTCATTTCTCA
57009375 T
1 T
57009376 TTCTTTGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.46
Consensus pattern (20 bp):
TAAAAATTTCTCATTTCTCA
Found at i:57011476 original size:48 final size:46
Alignment explanation
Indices: 57011401--57011493 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 46
57011391 ATATTGGTGT
* * *
57011401 TTTCTTTGGTTTTTTGGAGTATTGTGTTTTACTGCTTTTTCAGAGAA
1 TTTCTTTGGTTTTTTGAAGTATTGTGTTTTAATGC-CTTTCAGAGAA
57011448 TTTCATTTGGTTTTCTT-AAGTATTGTGTTTTAATGCCTTTCAGAGA
1 TTTC-TTTGGTTTT-TTGAAGTATTGTGTTTTAATGCCTTTCAGAGA
57011494 TTTAAAAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
47 13 0.32
48 26 0.63
49 2 0.05
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (46 bp):
TTTCTTTGGTTTTTTGAAGTATTGTGTTTTAATGCCTTTCAGAGAA
Found at i:57019105 original size:18 final size:18
Alignment explanation
Indices: 57019076--57019110 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
57019066 ATATATTTAA
57019076 TATATATTTGATTAAAAAG
1 TATATATTTGA-TAAAAAG
57019095 TATAT-TTTGATAAAAA
1 TATATATTTGATAAAAA
57019111 ATAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
TATATATTTGATAAAAAG
Found at i:57019111 original size:18 final size:19
Alignment explanation
Indices: 57019076--57019111 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
57019066 ATATATTTAA
*
57019076 TATATATTTGATTAAAAAG
1 TATATATTTGATAAAAAAG
57019095 TATAT-TTTGATAAAAAA
1 TATATATTTGATAAAAAA
57019112 TAAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (19 bp):
TATATATTTGATAAAAAAG
Found at i:57023223 original size:15 final size:16
Alignment explanation
Indices: 57023192--57023226 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
57023182 GTGTTTCTTT
*
57023192 AACAACTTCTGAAGAA
1 AACAAATTCTGAAGAA
57023208 AACAAATTCT-AAGAA
1 AACAAATTCTGAAGAA
57023223 AACA
1 AACA
57023227 GAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (16 bp):
AACAAATTCTGAAGAA
Found at i:57032597 original size:12 final size:12
Alignment explanation
Indices: 57032580--57032604 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57032570 CAGCAGAAAG
57032580 GAGTGAAGAGAA
1 GAGTGAAGAGAA
57032592 GAGTGAAGAGAA
1 GAGTGAAGAGAA
57032604 G
1 G
57032605 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:57038844 original size:22 final size:22
Alignment explanation
Indices: 57038784--57038827 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
57038774 AATCTTTAGG
57038784 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
57038803 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
57038825 GAT
1 GAT
57038828 TTTGTAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:57052557 original size:6 final size:6
Alignment explanation
Indices: 57052522--57052554 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
57052512 ATGCCCCCAC
*
57052522 AGAAAA A-AAAA AGAAAA AGAAAA AGAAGA AGAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAA
57052555 GAACCAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:57052826 original size:3 final size:3
Alignment explanation
Indices: 57052818--57052853 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
57052808 GCTTGCTATG
*
57052818 CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
57052854 GGTGGTGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:57057149 original size:13 final size:13
Alignment explanation
Indices: 57057131--57057157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57057121 TAATTTTATG
57057131 TATAAGTAAATAA
1 TATAAGTAAATAA
57057144 TATAAGTAAATAA
1 TATAAGTAAATAA
57057157 T
1 T
57057158 TTAAACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (13 bp):
TATAAGTAAATAA
Found at i:57058785 original size:21 final size:21
Alignment explanation
Indices: 57058759--57058809 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
57058749 GTCCAAGTAC
57058759 CGATACATAAATACAATGTAT
1 CGATACATAAATACAATGTAT
57058780 CGATACATAAATACAATGTAT
1 CGATACATAAATACAATGTAT
57058801 CGATACATA
1 CGATACATA
57058810 TATAGATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (21 bp):
CGATACATAAATACAATGTAT
Found at i:57059418 original size:20 final size:19
Alignment explanation
Indices: 57059333--57059418 Score: 61
Period size: 18 Copynumber: 4.5 Consensus size: 19
57059323 AAATTAAGTG
*
57059333 ATTCTTAAAACATGAAAAT
1 ATTCTTAAAACATGAAAAA
* * *
57059352 ATTC-TAAAAAATTAAATA
1 ATTCTTAAAACATGAAAAA
*
57059370 ATT-TTAAAACATTAAAGATA
1 ATTCTTAAAACATGAAA-A-A
* *
57059390 AGT-TAAAAACATGAAAAA
1 ATTCTTAAAACATGAAAAA
57059408 ATTACTTAAAA
1 ATT-CTTAAAA
57059419 TATAAAAGGC
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
18 27 0.53
19 5 0.10
20 19 0.37
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (19 bp):
ATTCTTAAAACATGAAAAA
Found at i:57063344 original size:38 final size:38
Alignment explanation
Indices: 57063302--57063375 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
57063292 CAGAGATTAC
57063302 CTTGTATTCTTAACATGTCATTCTTGGTCTGTGATAGT
1 CTTGTATTCTTAACATGTCATTCTTGGTCTGTGATAGT
57063340 CTTGTATTCTTAACATGTCATTCTTGGTCTGTGATA
1 CTTGTATTCTTAACATGTCATTCTTGGTCTGTGATA
57063376 CTGGAAAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (38 bp):
CTTGTATTCTTAACATGTCATTCTTGGTCTGTGATAGT
Found at i:57068348 original size:13 final size:11
Alignment explanation
Indices: 57068320--57068362 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
57068310 AGTTAAAAAT
57068320 TATTTTATTAA
1 TATTTTATTAA
57068331 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
57068344 TA-TTTATTAT
1 TATTTTATTAA
57068354 TATTTTATT
1 TATTTTATT
57068363 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:57068349 original size:23 final size:23
Alignment explanation
Indices: 57068323--57068366 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
57068313 TAAAAATTAT
57068323 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
57068346 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
57068367 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:57070641 original size:24 final size:24
Alignment explanation
Indices: 57070609--57070658 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
57070599 GTATAATTTG
57070609 AACCAAAATCACATTTGAGGTGAT
1 AACCAAAATCACATTTGAGGTGAT
*
57070633 AACCCAAATCACATTTGAGGTGAT
1 AACCAAAATCACATTTGAGGTGAT
57070657 AA
1 AA
57070659 ATACTTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
AACCAAAATCACATTTGAGGTGAT
Done.