Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 20 of 120
Found at i:5313526 original size:17 final size:16
Alignment explanation
Indices: 5313459--5313524 Score: 91
Period size: 17 Copynumber: 4.1 Consensus size: 16
5313449 TTAGTATTTT
5313459 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TA
*
5313476 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
5313490 AATTTAAATTTAAGATA
1 AATTTAAATTTAA-ATA
5313507 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
5313523 AA
1 AA
5313525 ATCAATTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.23
15 3 0.07
16 8 0.18
17 23 0.52
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:5318169 original size:3 final size:3
Alignment explanation
Indices: 5318161--5318191 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5318151 CTCAACGCTA
5318161 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
5318192 GACTATCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5319500 original size:14 final size:15
Alignment explanation
Indices: 5319481--5319509 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5319471 CTACCAATTT
5319481 TTTTAATT-TTTTCG
1 TTTTAATTGTTTTCG
5319495 TTTTAATTGTTTTCG
1 TTTTAATTGTTTTCG
5319510 ATATTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTAATTGTTTTCG
Found at i:5319668 original size:29 final size:30
Alignment explanation
Indices: 5319626--5319699 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
5319616 CAATGCTTAA
**
5319626 TTATTAATGGTAATAC-G-AAAATTTAAATT
1 TTATTAATTTTAATACTGTAAAATTT-AATT
* * *
5319655 TTATTTATTTTAATACTGTTAAATTTATTT
1 TTATTAATTTTAATACTGTAAAATTTAATT
5319685 TTATTAATTTTAATA
1 TTATTAATTTTAATA
5319700 TAAATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 13 0.35
30 18 0.49
31 6 0.16
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (30 bp):
TTATTAATTTTAATACTGTAAAATTTAATT
Found at i:5323041 original size:242 final size:242
Alignment explanation
Indices: 5322616--5323094 Score: 958
Period size: 242 Copynumber: 2.0 Consensus size: 242
5322606 TATCTTTGCA
5322616 GCACGCTTTTCCTCTGCCTTGTGGCACGCTTCTACCTTATGGTACTTTTTTGTCTACCTTCGTGG
1 GCACGCTTTTCCTCTGCCTTGTGGCACGCTTCTACCTTATGGTACTTTTTTGTCTACCTTCGTGG
5322681 TAGATTAGCGTTCGTGGATAGTTTTCTCACAACGCTCGGCTTTGATTTGCAGTTATTGGTGGTCT
66 TAGATTAGCGTTCGTGGATAGTTTTCTCACAACGCTCGGCTTTGATTTGCAGTTATTGGTGGTCT
5322746 TTCAATAGTTTGATCCCCTTTTGTAGTTCGTTTTTCGATGCAGTCAGATCTGTTTTGCGAAGCAA
131 TTCAATAGTTTGATCCCCTTTTGTAGTTCGTTTTTCGATGCAGTCAGATCTGTTTTGCGAAGCAA
5322811 CCTGCAAGATTATTGGTTTCACTCACCACTCCTACTTTGATCTTGTG
196 CCTGCAAGATTATTGGTTTCACTCACCACTCCTACTTTGATCTTGTG
5322858 GCACGCTTTTCCTCTGCCTTGTGGCACGCTTCTACCTTATGGTACTTTTTTGTCTACCTTCGTGG
1 GCACGCTTTTCCTCTGCCTTGTGGCACGCTTCTACCTTATGGTACTTTTTTGTCTACCTTCGTGG
5322923 TAGATTAGCGTTCGTGGATAGTTTTCTCACAACGCTCGGCTTTGATTTGCAGTTATTGGTGGTCT
66 TAGATTAGCGTTCGTGGATAGTTTTCTCACAACGCTCGGCTTTGATTTGCAGTTATTGGTGGTCT
5322988 TTCAATAGTTTGATCCCCTTTTGTAGTTCGTTTTTCGATGCAGTCAGATCTGTTTTGCGAAGCAA
131 TTCAATAGTTTGATCCCCTTTTGTAGTTCGTTTTTCGATGCAGTCAGATCTGTTTTGCGAAGCAA
5323053 CCTGCAAGATTATTGGTTTCACTCACCACTCCTACTTTGATC
196 CCTGCAAGATTATTGGTTTCACTCACCACTCCTACTTTGATC
5323095 CTTAAGCGTG
Statistics
Matches: 237, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 237 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.40
Consensus pattern (242 bp):
GCACGCTTTTCCTCTGCCTTGTGGCACGCTTCTACCTTATGGTACTTTTTTGTCTACCTTCGTGG
TAGATTAGCGTTCGTGGATAGTTTTCTCACAACGCTCGGCTTTGATTTGCAGTTATTGGTGGTCT
TTCAATAGTTTGATCCCCTTTTGTAGTTCGTTTTTCGATGCAGTCAGATCTGTTTTGCGAAGCAA
CCTGCAAGATTATTGGTTTCACTCACCACTCCTACTTTGATCTTGTG
Found at i:5323719 original size:9 final size:9
Alignment explanation
Indices: 5323706--5323782 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 9
5323696 ATTTAAAATT
5323706 TTATAAAAA
1 TTATAAAAA
*
5323715 GTATAAAAA
1 TTATAAAAA
*
5323724 TTCTTAAAAA
1 TT-ATAAAAA
5323734 TTATAAAAAAA
1 TTAT--AAAAA
*
5323745 TTAAAAAAA
1 TTATAAAAA
* *
5323754 ATATTAAAA
1 TTATAAAAA
*
5323763 TTGATATAAAT
1 TT-ATA-AAAA
5323774 TTATAAAAA
1 TTATAAAAA
5323783 GAATCATAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
9 25 0.49
10 13 0.25
11 13 0.25
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:5323721 original size:19 final size:18
Alignment explanation
Indices: 5323699--5323741 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5323689 TTAAAATATT
*
5323699 TAAAATTTTATAAAAAGTA
1 TAAAATTCT-TAAAAAGTA
*
5323718 TAAAAATTCTTAAAAATTA
1 T-AAAATTCTTAAAAAGTA
5323737 TAAAA
1 TAAAA
5323742 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 10 0.48
20 7 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAAATTCTTAAAAAGTA
Found at i:5323734 original size:30 final size:30
Alignment explanation
Indices: 5323691--5323762 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
5323681 AAATATATTT
* * * *
5323691 AAAATATTTAAAATTTTATAAAAAGTATAA
1 AAAATATTAAAAATTATAAAAAAAGTAAAA
* * *
5323721 AAATTCTTAAAAATTATAAAAAAATTAAAA
1 AAAATATTAAAAATTATAAAAAAAGTAAAA
5323751 AAAATATTAAAA
1 AAAATATTAAAA
5323763 TTGATATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (30 bp):
AAAATATTAAAAATTATAAAAAAAGTAAAA
Found at i:5324370 original size:22 final size:21
Alignment explanation
Indices: 5324334--5324388 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5324324 AATTTTTATA
** *
5324334 ATTTATAAGAATTTATTATATT
1 ATTTATAAGTTTTTATGA-ATT
5324356 ATTTATAAGTTTTTATGAATT
1 ATTTATAAGTTTTTATGAATT
*
5324377 -TTCATAAGTTTT
1 ATTTATAAGTTTT
5324389 CATAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.38
21 3 0.10
22 15 0.52
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTTATAAGTTTTTATGAATT
Found at i:5324378 original size:10 final size:9
Alignment explanation
Indices: 5324317--5324654 Score: 109
Period size: 10 Copynumber: 35.0 Consensus size: 9
5324307 TTAAATGATT
5324317 TTTTTATAA
1 TTTTTATAA
5324326 TTTTTATAA
1 TTTTTATAA
* *
5324335 TTTATAAGAA
1 TTT-TTATAA
5324345 TTTATTAT-A
1 TTT-TTATAA
5324354 TTATTTATAA
1 TT-TTTATAA
5324364 GTTTTTATGAA
1 -TTTTTAT-AA
*
5324375 TTTTCATAA
1 TTTTTATAA
*
5324384 GTTTTCATAAA
1 -TTTTTAT-AA
* *
5324395 ATTTTAAATA
1 TTTTTATA-A
5324405 TATTTTATAA
1 T-TTTTATAA
5324415 TTTTTATAAA
1 TTTTTAT-AA
**
5324425 TTTTTATGG
1 TTTTTATAA
5324434 TTTCTTAT-A
1 TTT-TTATAA
5324443 TTTTTATAA
1 TTTTTATAA
*
5324452 GTTTATATCAA
1 -TTTTTAT-AA
*
5324463 TTTTAAT-A
1 TTTTTATAA
*
5324471 -TTAT-TAA
1 TTTTTATAA
*
5324478 TATTTAATAAA
1 T-TTTTAT-AA
5324489 TCTTTT-TATA
1 T-TTTTATA-A
5324499 TTTTTATAA
1 TTTTTATAA
*
5324508 GTTTTTAAGAA
1 -TTTTT-ATAA
5324519 TTTTTAT-A
1 TTTTTATAA
*
5324527 TGTTTCCATAAA
1 T-TTT-TAT-AA
*
5324539 ATTTTA-AA
1 TTTTTATAA
5324547 TATGTTTAATTAA
1 T-T-TTT-A-TAA
5324560 -TTTTATAA
1 TTTTTATAA
****
5324568 AAAATATAA
1 TTTTTATAA
5324577 TTTATTATAA
1 TTT-TTATAA
5324587 CTTTTATATAA
1 -TTTT-TATAA
*
5324598 TATTTATAA
1 TTTTTATAA
**
5324607 GTTTTTATTG
1 -TTTTTATAA
5324617 TTTTTAATAA
1 TTTTT-ATAA
*
5324627 TTTTTATGA
1 TTTTTATAA
*
5324636 TTTTTAATAT
1 TTTTT-ATAA
5324646 TTTTTATAA
1 TTTTTATAA
5324655 GAAAATAGTA
Statistics
Matches: 245, Mismatches: 45, Indels: 78
0.67 0.12 0.21
Matches are distributed among these distances:
6 1 0.00
7 3 0.01
8 12 0.05
9 75 0.31
10 115 0.47
11 36 0.15
12 1 0.00
13 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5324471 original size:28 final size:28
Alignment explanation
Indices: 5324440--5324511 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
5324430 ATGGTTTCTT
*
5324440 ATATTTTTATAAGTTTATATCAA-TTTTA
1 ATATTTTTATAAGTTTA-ATAAACTTTTA
* *
5324468 ATATTATTA-ATA-TTTAATAAATCTTTTT
1 ATATTTTTATA-AGTTTAATAAA-CTTTTA
5324496 ATATTTTTATAAGTTT
1 ATATTTTTATAAGTTT
5324512 TTAAGAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.11
27 5 0.14
28 22 0.63
29 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
ATATTTTTATAAGTTTAATAAACTTTTA
Found at i:5326906 original size:64 final size:65
Alignment explanation
Indices: 5326796--5326940 Score: 242
Period size: 64 Copynumber: 2.3 Consensus size: 65
5326786 CAACCTCTAA
*
5326796 TATTTTAAAATA-A-AATAATTTACACAAAAAAGATCACTTTGACAACTTATACTTCAATTAAGT
1 TATTTTAAAATATATAAAAATTTACACAAAAAAGATCACTTTGACAACTTATACTTCAATTAAGT
* *
5326859 TATTTTAAAATATATAAAAATTTACACAAAAAA-ATCACTTTGGCAACTTATGCTTCAATTAAGT
1 TATTTTAAAATATATAAAAATTTACACAAAAAAGATCACTTTGACAACTTATACTTCAATTAAGT
5326923 TATTTTAAAATATATAAA
1 TATTTTAAAATATATAAA
5326941 CATTCCAATA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
63 12 0.16
64 48 0.62
65 17 0.22
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (65 bp):
TATTTTAAAATATATAAAAATTTACACAAAAAAGATCACTTTGACAACTTATACTTCAATTAAGT
Found at i:5338969 original size:14 final size:14
Alignment explanation
Indices: 5338935--5338969 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5338925 GCTACAATTC
*
5338935 ACTATTATGTTGTT
1 ACTATTTTGTTGTT
5338949 ACTATTTTGTTGTT
1 ACTATTTTGTTGTT
*
5338963 ATTATTT
1 ACTATTT
5338970 GGATATTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (14 bp):
ACTATTTTGTTGTT
Found at i:5339030 original size:30 final size:30
Alignment explanation
Indices: 5338994--5339056 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
5338984 ATTTATTGTA
*
5338994 TTGTTAATTTTGTTATTATTTTACAGGCAT
1 TTGTTAATTTTGTTACTATTTTACAGGCAT
*
5339024 TTGTTAATTTTGTTACTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTACAGGCAT
5339054 TTG
1 TTG
5339057 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTACAGGCAT
Found at i:5342512 original size:20 final size:21
Alignment explanation
Indices: 5342446--5342512 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
5342436 AAATATGATG
*
5342446 TTTGTATATAAATATAAATAT
1 TTTGTATATTAATATAAATAT
* **
5342467 TTGTTTATATTATATTATTGATAT
1 TT-TGTATATTA-A-TATAAATAT
5342491 TTTGTAT-TTAATATAAATAT
1 TTTGTATATTAATATAAATAT
5342511 TT
1 TT
5342513 ATATTATTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
20 9 0.25
21 3 0.08
22 10 0.28
23 5 0.14
24 9 0.25
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTGTATATTAATATAAATAT
Found at i:5362127 original size:20 final size:20
Alignment explanation
Indices: 5362090--5362128 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5362080 TTCTTAGACT
*
5362090 TTTAGCCCAACACTATATAA
1 TTTAGCCCAACACAATATAA
*
5362110 TTTAGCCCAACCCAATATA
1 TTTAGCCCAACACAATATA
5362129 CGTTTTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.28
Consensus pattern (20 bp):
TTTAGCCCAACACAATATAA
Found at i:5370491 original size:29 final size:29
Alignment explanation
Indices: 5370458--5370518 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5370448 AATAAGTCAG
* *
5370458 AAATATATATATATAATTAGTATATATAT
1 AAATATAGATATAAAATTAGTATATATAT
* *
5370487 AAATATAGATATAAAATTTGTTTATATAT
1 AAATATAGATATAAAATTAGTATATATAT
5370516 AAA
1 AAA
5370519 AAATTGTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATATAGATATAAAATTAGTATATATAT
Found at i:5370566 original size:15 final size:15
Alignment explanation
Indices: 5370546--5370576 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5370536 ATATATCAGT
5370546 ATATATGTAAAAATA
1 ATATATGTAAAAATA
*
5370561 ATATATGTAAATATA
1 ATATATGTAAAAATA
5370576 A
1 A
5370577 AATAGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
ATATATGTAAAAATA
Found at i:5371359 original size:46 final size:46
Alignment explanation
Indices: 5371221--5371365 Score: 126
Period size: 46 Copynumber: 3.2 Consensus size: 46
5371211 TAATATATAT
* *
5371221 ATATATATATACAAAACATACATAAAACAAATGTCCAAGAATGTCA
1 ATATATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
* * * * **
5371267 ATATATTATATA-TAGACATA-ATATTACT-AGAAAT-CAAGTAA--T--
1 ATATA-TATATACAAAACATACATA-AAATAAG-TGTCCAAG-AATGTCA
5371309 ATATATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
1 ATATATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
5371355 ATATATATATA
1 ATATATATATA
5371366 TATATGTAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 24
0.66 0.13 0.22
Matches are distributed among these distances:
41 6 0.08
42 16 0.22
43 9 0.12
44 2 0.03
45 8 0.11
46 26 0.36
47 6 0.08
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (46 bp):
ATATATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
Found at i:5371360 original size:42 final size:42
Alignment explanation
Indices: 5371225--5371361 Score: 102
Period size: 42 Copynumber: 3.2 Consensus size: 42
5371215 ATATATATAT
* *
5371225 ATATATACAAAACATACATAAAACAAATGTCCAAGAATGTCA
1 ATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
* * * ** *
5371267 ATATATTATATATAGACATA-ATATTACT-AGAAAT-CAAGTAATAT-A
1 ATATA-TACA-A-A-ACATACATA-AAATAAG-TGTCCAAG-AATGTCA
5371312 TATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
1 -ATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
5371355 ATATATA
1 ATATATA
5371362 TATATATATG
Statistics
Matches: 69, Mismatches: 14, Indels: 24
0.64 0.13 0.22
Matches are distributed among these distances:
42 24 0.35
43 14 0.20
44 2 0.03
45 13 0.19
46 16 0.23
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (42 bp):
ATATATACAAAACATACATAAAATAAGTGTCCAAGAATGTCA
Found at i:5377201 original size:21 final size:21
Alignment explanation
Indices: 5377159--5377206 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5377149 TTTGTTCTAC
**
5377159 CGGTAGAAGTCATGGTTGTAT
1 CGGTAGAAGTCATGGCAGTAT
5377180 CGGTAGAAGTCA-GGCAGTTAT
1 CGGTAGAAGTCATGGCAG-TAT
*
5377201 CAGTAG
1 CGGTAG
5377207 TTTTCTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (21 bp):
CGGTAGAAGTCATGGCAGTAT
Found at i:5381751 original size:24 final size:24
Alignment explanation
Indices: 5381724--5381775 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5381714 TTTAAAAAGG
* *
5381724 AATAACAAAAATTTTATACTAATA
1 AATAACAAAAATATTATACAAATA
* * *
5381748 AATATCAAATATATTATGCAAATA
1 AATAACAAAAATATTATACAAATA
5381772 AATA
1 AATA
5381776 CTGAATCTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAACAAAAATATTATACAAATA
Found at i:5381854 original size:17 final size:17
Alignment explanation
Indices: 5381832--5381866 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5381822 ATGCTACTAG
5381832 TTTGTCGATTATTGTGA
1 TTTGTCGATTATTGTGA
5381849 TTTGTCGATTATTGTGA
1 TTTGTCGATTATTGTGA
5381866 T
1 T
5381867 CAGTTCACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.23, T:0.54
Consensus pattern (17 bp):
TTTGTCGATTATTGTGA
Found at i:5381976 original size:18 final size:18
Alignment explanation
Indices: 5381939--5381977 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5381929 TCATGTACTA
**
5381939 TTCACCAATCTTGATTAG
1 TTCACCAATCTTGAAGAG
*
5381957 TTCACCATTCTTGAAGAG
1 TTCACCAATCTTGAAGAG
5381975 TTC
1 TTC
5381978 GACAAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (18 bp):
TTCACCAATCTTGAAGAG
Found at i:5382952 original size:28 final size:30
Alignment explanation
Indices: 5382900--5382956 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
5382890 AGGATATGGT
*
5382900 AAAATTATATTTTGATTTTTCAAAAATAAG
1 AAAATTATATTTTAATTTTTCAAAAATAAG
*
5382930 AAAATTA-A-TTTAATTTTTTAAAAATAA
1 AAAATTATATTTTAATTTTTCAAAAATAA
5382957 TGAATATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.68
29 1 0.04
30 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (30 bp):
AAAATTATATTTTAATTTTTCAAAAATAAG
Found at i:5391188 original size:24 final size:24
Alignment explanation
Indices: 5391161--5391212 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5391151 TTTAAAAAGG
* *
5391161 AATAACAAAAATTTTATACTAATA
1 AATAACAAAAATATTATACAAATA
* * *
5391185 AATATCAAATATATTATGCAAATA
1 AATAACAAAAATATTATACAAATA
5391209 AATA
1 AATA
5391213 CTGAATCCTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAACAAAAATATTATACAAATA
Found at i:5394978 original size:10 final size:11
Alignment explanation
Indices: 5394930--5394978 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
5394920 CTCGCACATA
5394930 ATTATTAATAT
1 ATTATTAATAT
* *
5394941 -TTTTTATTAT
1 ATTATTAATAT
*
5394951 CTTATTAATA-
1 ATTATTAATAT
5394961 ATTATTAATAT
1 ATTATTAATAT
5394972 ATT-TTAA
1 ATTATTAA
5394979 ATGACATTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTATTAATAT
Found at i:5395909 original size:4 final size:4
Alignment explanation
Indices: 5395900--5395925 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5395890 AATGAATAAT
5395900 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
5395926 TAAACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:5402806 original size:3 final size:3
Alignment explanation
Indices: 5402798--5402828 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5402788 GACTAACATA
5402798 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5402829 TGTCATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5404269 original size:42 final size:42
Alignment explanation
Indices: 5404127--5404367 Score: 238
Period size: 42 Copynumber: 5.6 Consensus size: 42
5404117 TACACTCTAT
* * * *
5404127 CCGAGTCATAAGTTCTTCCATTTACAA-ATGATCTTATGCTCCA-G
1 CCGAGACATAAG-TCTTCC-TTTA-AACATAATCTCATGCT-CATC
* * *
5404171 CCGAGACATAAGTCTTCCATTTATAA-ACAATCTTATGCTC-TAA
1 CCGAGACATAAGTCTTCC-TTTA-AACATAATCTCATGCTCAT-C
*
5404214 CCGAGATATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
* * * * *
5404256 TCGAGTCACAAGTCTTCCTTTAAACATAGTCTTATGCTCATC
1 CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
*
5404298 CCGAGACATGAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
5404340 CCGAGACATGAGTCTTCCATTTATACAT
1 CCGAGACATAAGTCTTCC-TTTAAACAT
5404368 CAAGTGATTC
Statistics
Matches: 170, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
41 2 0.01
42 107 0.63
43 50 0.29
44 11 0.06
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (42 bp):
CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
Found at i:5420870 original size:7 final size:7
Alignment explanation
Indices: 5420858--5420904 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
5420848 TTAAAATGGA
5420858 TAAAAAT
1 TAAAAAT
5420865 TAAAAA-
1 TAAAAAT
5420871 TAAAAAT
1 TAAAAAT
5420878 TAAAAAT
1 TAAAAAT
* *
5420885 TCATAAT
1 TAAAAAT
*
5420892 TAAGAAAA
1 TAA-AAAT
5420900 TAAAA
1 TAAAA
5420905 CGCCACATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
6 6 0.18
7 22 0.67
8 5 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:5420875 original size:13 final size:13
Alignment explanation
Indices: 5420857--5420884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5420847 TTTAAAATGG
5420857 ATAAAAATTAAAA
1 ATAAAAATTAAAA
5420870 ATAAAAATTAAAA
1 ATAAAAATTAAAA
5420883 AT
1 AT
5420885 TCATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
ATAAAAATTAAAA
Found at i:5422794 original size:27 final size:25
Alignment explanation
Indices: 5422763--5422812 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5422753 TATTATTTTT
5422763 TATATAAAAATAAATTAAAACATATAA
1 TATAT-AAAATAAATTAAAA-ATATAA
* *
5422790 TATATTAAATACATTAAAAATAT
1 TATATAAAATAAATTAAAAATAT
5422813 TAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 12 0.57
27 5 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
TATATAAAATAAATTAAAAATATAA
Found at i:5422991 original size:22 final size:22
Alignment explanation
Indices: 5422957--5422999 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5422947 TTTCCAAACA
5422957 ATAACAACAAAAT-AGTAGCAAT
1 ATAACAACAAAATGA-TAGCAAT
* *
5422979 ATAATAACGAAATGATAGCAA
1 ATAACAACAAAATGATAGCAA
5423000 AACAATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATGATAGCAAT
Found at i:5424299 original size:15 final size:15
Alignment explanation
Indices: 5424263--5424301 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5424253 CATATATATT
5424263 TAGATAAATATTTAA
1 TAGATAAATATTTAA
* * *
5424278 AAAATAAATATTTTA
1 TAGATAAATATTTAA
5424293 TAGATAAAT
1 TAGATAAAT
5424302 TAAATCATTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
TAGATAAATATTTAA
Found at i:5429160 original size:59 final size:60
Alignment explanation
Indices: 5429000--5429164 Score: 158
Period size: 59 Copynumber: 2.8 Consensus size: 60
5428990 CACGTCTACT
* ** * * * *
5429000 TGAGAGTTACAAGTTTGTTTTAGGACTGCTTATTAT-GTTTGGCTGATGTGGCTATCTGCA
1 TGAGAGTTTCAAGTAAGATTTAAGACTGCTTATT-TGGTTTGGCTGATGTGGATATATGCA
* * * * * * *
5429060 TGACCA-TTTCAAGGAAGATTTACGAGT-CTTATTAGGCTTGGCTGATGTGGATTTATGCA
1 TGA-GAGTTTCAAGTAAGATTTAAGACTGCTTATTTGGTTTGGCTGATGTGGATATATGCA
5429119 TGAGAGTTTCAAGTAAGATTTAAGACTGCTT-TTTGGTTTGGCTGAT
1 TGAGAGTTTCAAGTAAGATTTAAGACTGCTTATTTGGTTTGGCTGAT
5429165 CTTGGTAACT
Statistics
Matches: 82, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
58 1 0.01
59 60 0.73
60 20 0.24
61 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (60 bp):
TGAGAGTTTCAAGTAAGATTTAAGACTGCTTATTTGGTTTGGCTGATGTGGATATATGCA
Found at i:5436479 original size:31 final size:31
Alignment explanation
Indices: 5436409--5436479 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
5436399 ATTTTTTATC
**
5436409 AGAATTAAATTTATAAATTTTGTAAATGTTG
1 AGAATTAAATTTATAAATTTTGTAAAAATTG
** * *
5436440 AGGGTTAAATTTATTAATTTTTTTAAAAATT-
1 AGAATTAAATTTA-TAAATTTTGTAAAAATTG
5436471 AGAATTAAA
1 AGAATTAAA
5436480 ATAATAGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (31 bp):
AGAATTAAATTTATAAATTTTGTAAAAATTG
Found at i:5436966 original size:8 final size:8
Alignment explanation
Indices: 5436953--5436977 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5436943 TACTTTTATT
5436953 AATTTTAA
1 AATTTTAA
5436961 AATTTTAA
1 AATTTTAA
5436969 AATTTTAA
1 AATTTTAA
5436977 A
1 A
5436978 GGGCTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:5437416 original size:21 final size:21
Alignment explanation
Indices: 5437391--5437442 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5437381 TATTATAGTG
*
5437391 ATGAGATTAGA-TAATATAACA
1 ATGAGATTA-ATTAATATAAAA
*
5437412 GTGAGATTAATTAATATAAAA
1 ATGAGATTAATTAATATAAAA
5437433 ATGAGATTAA
1 ATGAGATTAA
5437443 ATTGTAGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (21 bp):
ATGAGATTAATTAATATAAAA
Found at i:5437496 original size:23 final size:23
Alignment explanation
Indices: 5437470--5437515 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5437460 AGATGAATTC
5437470 TAATGAAAAGAGAAAATAATCAT
1 TAATGAAAAGAGAAAATAATCAT
* **
5437493 TAATGACATTAGAAAATAATCAT
1 TAATGAAAAGAGAAAATAATCAT
5437516 CAAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.26
Consensus pattern (23 bp):
TAATGAAAAGAGAAAATAATCAT
Found at i:5440969 original size:12 final size:11
Alignment explanation
Indices: 5440946--5440980 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5440936 TGATAGAGGC
5440946 AGAGAAGAAAA
1 AGAGAAGAAAA
5440957 AGAGAATGAAAA
1 AGAGAA-GAAAA
*
5440969 AGAAAAGAAAA
1 AGAGAAGAAAA
5440980 A
1 A
5440981 AAGGAAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (11 bp):
AGAGAAGAAAA
Found at i:5442809 original size:26 final size:26
Alignment explanation
Indices: 5442748--5442811 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
5442738 TGGAAGTTGT
* *
5442748 TAGCAGTAGTTATTGGTTAAGGTTAT
1 TAGCAGCAGTTATTGGTTAAGGTTAA
* * *
5442774 TATCATCAGTTGTTGGTTAA-GTTAGA
1 TAGCAGCAGTTATTGGTTAAGGTTA-A
5442800 TAGCAGCAGTTA
1 TAGCAGCAGTTA
5442812 ATGCTGATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (26 bp):
TAGCAGCAGTTATTGGTTAAGGTTAA
Found at i:5447396 original size:26 final size:25
Alignment explanation
Indices: 5447364--5447432 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
5447354 GCTGGAATGG
5447364 AAGTTGTTAATAGAAGTTGTTGGTT
1 AAGTTGTTAATAGAAGTTGTTGGTT
*
5447389 AAGGTTGTT-ATCATCAA-TTGTTGGTT
1 AA-GTTGTTAAT-A-GAAGTTGTTGGTT
* *
5447415 AAGTTGTTAGTAGCAGTT
1 AAGTTGTTAATAGAAGTT
5447433 AATGCTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
24 1 0.03
25 13 0.37
26 19 0.54
27 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.26, T:0.43
Consensus pattern (25 bp):
AAGTTGTTAATAGAAGTTGTTGGTT
Found at i:5448135 original size:22 final size:22
Alignment explanation
Indices: 5448107--5448149 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5448097 CTTTAAAGCA
5448107 TCAATGTTGCGACAACCAACTC
1 TCAATGTTGCGACAACCAACTC
*
5448129 TCAATGTTGCGACATCCAACT
1 TCAATGTTGCGACAACCAACT
5448150 TCGAACCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (22 bp):
TCAATGTTGCGACAACCAACTC
Found at i:5454760 original size:21 final size:21
Alignment explanation
Indices: 5454736--5454784 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5454726 CTCAAGTACG
*
5454736 GGTAGAAGCATGATTTGTTTC
1 GGTAGAAGCATGATTTGTATC
* *
5454757 GGTAGAAGCCTTATTTGTATC
1 GGTAGAAGCATGATTTGTATC
5454778 GGTAGAA
1 GGTAGAA
5454785 TTGTCATAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.35
Consensus pattern (21 bp):
GGTAGAAGCATGATTTGTATC
Found at i:5458747 original size:19 final size:19
Alignment explanation
Indices: 5458706--5458750 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5458696 GATTCTTAAA
5458706 ATTTAAAAATAAAAAACCT
1 ATTTAAAAATAAAAAACCT
*
5458725 -TTTAAAAAGTAAAAAA-TT
1 ATTTAAAAA-TAAAAAACCT
5458743 ATTTAAAA
1 ATTTAAAA
5458751 GTTCATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
ATTTAAAAATAAAAAACCT
Found at i:5460634 original size:3 final size:3
Alignment explanation
Indices: 5460626--5460666 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5460616 TTTTGGTGTT
5460626 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5460667 GAAGAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5464424 original size:24 final size:28
Alignment explanation
Indices: 5464376--5464428 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 28
5464366 TCCTTTATCT
5464376 TTTACTTTCAATATATACATATATTAAA
1 TTTACTTTCAATATATACATATATTAAA
5464404 TTTA-TTT-AATATATA-AT-TATTAAA
1 TTTACTTTCAATATATACATATATTAAA
5464428 T
1 T
5464429 AAAGTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 8 0.32
27 3 0.12
28 4 0.16
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTACTTTCAATATATACATATATTAAA
Found at i:5464436 original size:24 final size:26
Alignment explanation
Indices: 5464385--5464447 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 26
5464375 TTTTACTTTC
** *
5464385 AATATATACATATATTAAATTTATTT
1 AATATATACATATATTAAATAAAGTT
5464411 AATATATA-AT-TATTAAATAAAGTT
1 AATATATACATATATTAAATAAAGTT
5464435 AAT-TA-ACATATAT
1 AATATATACATATAT
5464448 ATACATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.03
23 4 0.12
24 17 0.53
25 2 0.06
26 8 0.25
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATATACATATATTAAATAAAGTT
Found at i:5465361 original size:24 final size:25
Alignment explanation
Indices: 5465317--5465378 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
5465307 TTCAAATAAT
*
5465317 TTTTAATTTTATAAGTTATAAAT-A
1 TTTTAATTTTATAAGTAATAAATCA
* *
5465341 TTTTAATTTTGA-ATGTAATAATTCA
1 TTTTAATTTT-ATAAGTAATAAATCA
*
5465366 TTTTATTTTTATA
1 TTTTAATTTTATA
5465379 GGATGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 19 0.61
25 12 0.39
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTTAATTTTATAAGTAATAAATCA
Found at i:5466256 original size:67 final size:67
Alignment explanation
Indices: 5466148--5466284 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
5466138 TTATTTTACA
5466148 AGGGAATGGATTCAAACTTGAAACCTTAATTTAATTTCCATGCTTTAATAGTTATCAATTAACCA
1 AGGGAATGGATTCAAACTTGAAACCTTAATTTAATTTCCATGCTTTAATAGTTATCAATTAACCA
5466213 CT
66 CT
5466215 AGGGAATGGATTCAAACTTGAAACCTTAATTTAATTTCCATGCTTTAATAGTTATCAATTAACCA
1 AGGGAATGGATTCAAACTTGAAACCTTAATTTAATTTCCATGCTTTAATAGTTATCAATTAACCA
5466280 CT
66 CT
5466282 AGG
1 AGG
5466285 TTATTGCCTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (67 bp):
AGGGAATGGATTCAAACTTGAAACCTTAATTTAATTTCCATGCTTTAATAGTTATCAATTAACCA
CT
Found at i:5468698 original size:16 final size:17
Alignment explanation
Indices: 5468667--5468700 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5468657 GAATTTTTCA
5468667 AGTTTGGATCTGTTACG
1 AGTTTGGATCTGTTACG
5468684 AGTTTGGAT-TGTTACG
1 AGTTTGGATCTGTTACG
5468700 A
1 A
5468701 ACTTCGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (17 bp):
AGTTTGGATCTGTTACG
Found at i:5470497 original size:31 final size:31
Alignment explanation
Indices: 5470462--5470524 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
5470452 AAACCTAGAG
* *
5470462 ACTTAAAT-AAAAGTTTTCAAATAGTTTAGTA
1 ACTTAAATGAAAA-CTTTCAAATAATTTAGTA
5470493 ACTTAAATGAAAACTTTCAAATAATTTAGTA
1 ACTTAAATGAAAACTTTCAAATAATTTAGTA
5470524 A
1 A
5470525 TCATTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCAAATAATTTAGTA
Found at i:5474190 original size:12 final size:12
Alignment explanation
Indices: 5474154--5474190 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5474144 CAGATAAAGG
5474154 TAGTGGAATCCA
1 TAGTGGAATCCA
* *
5474166 CAGTGGAACCCA
1 TAGTGGAATCCA
5474178 TAGTGGAATCCA
1 TAGTGGAATCCA
5474190 T
1 T
5474191 GGCTAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (12 bp):
TAGTGGAATCCA
Found at i:5476093 original size:13 final size:13
Alignment explanation
Indices: 5476075--5476099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5476065 TAAAATCTAC
5476075 CAAAAACAAAAAA
1 CAAAAACAAAAAA
5476088 CAAAAACAAAAA
1 CAAAAACAAAAA
5476100 GGTCTATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAACAAAAAA
Found at i:5483077 original size:20 final size:20
Alignment explanation
Indices: 5483052--5483141 Score: 92
Period size: 20 Copynumber: 4.4 Consensus size: 20
5483042 AATGAAGAAG
5483052 TGCCCTTGTTTGCACTTCGA
1 TGCCCTTGTTTGCACTTCGA
* *
5483072 TGCCCTTGTTTGCAGTTCAA
1 TGCCCTTGTTTGCACTTCGA
* * * *
5483092 TGCCCCTATTTGCACTTTGG
1 TGCCCTTGTTTGCACTTCGA
5483112 TGCCCTTGTCTTGCATCTAT-GA
1 TGCCCTTGT-TTGCA-CT-TCGA
5483134 TGCCCTTG
1 TGCCCTTG
5483142 AAATGAAGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 39 0.70
21 5 0.09
22 11 0.20
23 1 0.02
ACGTcount: A:0.11, C:0.29, G:0.20, T:0.40
Consensus pattern (20 bp):
TGCCCTTGTTTGCACTTCGA
Found at i:5490011 original size:40 final size:40
Alignment explanation
Indices: 5489966--5490104 Score: 244
Period size: 40 Copynumber: 3.5 Consensus size: 40
5489956 CTTCATGGCT
*
5489966 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACTTAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACTGAG
*
5490006 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACCGAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACTGAG
5490046 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTA-TCGAG
1 TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACT-GAG
5490086 TCATAAGTCTTCCTTTTAA
1 TCATAAGTCTTCCTTTTAA
5490105 AAAAAAAAAC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (40 bp):
TCATAAGTCTTCCTTTTAATCACTCTTATGCTCTACTGAG
Found at i:5495274 original size:24 final size:24
Alignment explanation
Indices: 5495234--5495445 Score: 109
Period size: 24 Copynumber: 8.3 Consensus size: 24
5495224 AATGTATATA
* * *
5495234 TAAGCTTACGAGAGTAAATGTATG
1 TAAGCTGACGAGCGTAAACGTATG
* ** *
5495258 CAAGCTGGTGAGCGTAAACGCATATATT
1 TAAGCTGACGAGCGTAAACG----TATG
* *
5495286 TAAGCTGACGAGCTTAAACGTGTG
1 TAAGCTGACGAGCGTAAACGTATG
* ** * *
5495310 CAAGCTGGTGAGCGTAAATGCATATATA
1 TAAGCTGACGAGCGTAAA--C--GTATG
* *
5495338 TAAGCTGATGAGCGTAAACGTGTG
1 TAAGCTGACGAGCGTAAACGTATG
* * *
5495362 TAAGCTGGCGAGCGTAAACACATATATA
1 TAAGCTGACGAGCGT-AA-AC--GTATG
*
5495390 TATAGCTGACAAGCGTAAACGTATG
1 TA-AGCTGACGAGCGTAAACGTATG
*
5495415 CAAGCTGACGAGCGTAAACGTATG
1 TAAGCTGACGAGCGTAAACGTATG
*
5495439 AAAGCTG
1 TAAGCTG
5495446 GTGAGTGTAA
Statistics
Matches: 138, Mismatches: 37, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
24 72 0.52
25 6 0.04
26 4 0.03
27 2 0.01
28 43 0.31
29 11 0.08
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (24 bp):
TAAGCTGACGAGCGTAAACGTATG
Found at i:5495290 original size:52 final size:52
Alignment explanation
Indices: 5495228--5495434 Score: 270
Period size: 52 Copynumber: 4.0 Consensus size: 52
5495218 AAATTAAATG
* * * *
5495228 TATATATAAGCTTACGAGAGTAAATGTATGCAAGCTGGTGAGCGTAAACGCA
1 TATATATAAGCTGACGAGCGTAAACGTATGCAAGCTGGCGAGCGTAAACGCA
* * * * *
5495280 TATATTTAAGCTGACGAGCTTAAACGTGTGCAAGCTGGTGAGCGTAAATGCA
1 TATATATAAGCTGACGAGCGTAAACGTATGCAAGCTGGCGAGCGTAAACGCA
* * * *
5495332 TATATATAAGCTGATGAGCGTAAACGTGTGTAAGCTGGCGAGCGTAAACACA
1 TATATATAAGCTGACGAGCGTAAACGTATGCAAGCTGGCGAGCGTAAACGCA
* *
5495384 TATATATATAGCTGACAAGCGTAAACGTATGCAAGCTGACGAGCGTAAACG
1 TATATATA-AGCTGACGAGCGTAAACGTATGCAAGCTGGCGAGCGTAAACG
5495435 TATGAAAGCT
Statistics
Matches: 134, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 98 0.73
53 36 0.27
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (52 bp):
TATATATAAGCTGACGAGCGTAAACGTATGCAAGCTGGCGAGCGTAAACGCA
Found at i:5497723 original size:28 final size:27
Alignment explanation
Indices: 5497687--5497741 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
5497677 GAACTAGACT
5497687 TCATTATTTTATTTTAATTAGAATAAG
1 TCATTATTTTATTTTAATTAGAATAAG
*
5497714 TCATCTATTTTATTTTGATTAGAATAAG
1 TCAT-TATTTTATTTTAATTAGAATAAG
5497742 GTGTTCAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (27 bp):
TCATTATTTTATTTTAATTAGAATAAG
Found at i:5507374 original size:21 final size:21
Alignment explanation
Indices: 5507348--5507412 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
5507338 GTCTACTAAG
5507348 TAGTTAATTTTATAGTAATAT
1 TAGTTAATTTTATAGTAATAT
* * * *
5507369 TAGTT-ATATGTCTACT-A-AG
1 TAGTTAAT-TTTATAGTAATAT
5507388 TAGTTAATTTTATAGTAATAT
1 TAGTTAATTTTATAGTAATAT
5507409 TAGT
1 TAGT
5507413 GATAAATGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 11 0.34
20 6 0.19
21 15 0.47
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.49
Consensus pattern (21 bp):
TAGTTAATTTTATAGTAATAT
Found at i:5507378 original size:40 final size:40
Alignment explanation
Indices: 5507333--5507412 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5507323 GTCTTCTTGA
5507333 TATATGTCTACTAAGTAGTTAATTTTATAGTAATATTAGT
1 TATATGTCTACTAAGTAGTTAATTTTATAGTAATATTAGT
5507373 TATATGTCTACTAAGTAGTTAATTTTATAGTAATATTAGT
1 TATATGTCTACTAAGTAGTTAATTTTATAGTAATATTAGT
5507413 GATAAATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (40 bp):
TATATGTCTACTAAGTAGTTAATTTTATAGTAATATTAGT
Found at i:5508463 original size:20 final size:20
Alignment explanation
Indices: 5508440--5508478 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5508430 GTTACATAAA
*
5508440 TAGATGCATTGTTATATATT
1 TAGATACATTGTTATATATT
**
5508460 TAGATATTTTGTTATATAT
1 TAGATACATTGTTATATAT
5508479 ATTATATAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (20 bp):
TAGATACATTGTTATATATT
Found at i:5508809 original size:20 final size:20
Alignment explanation
Indices: 5508786--5508823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5508776 TATATAAATT
5508786 GATACGTTATTATATATTGA
1 GATACGTTATTATATATTGA
**
5508806 GATATTTTATTATATATT
1 GATACGTTATTATATATT
5508824 ATATAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATACGTTATTATATATTGA
Found at i:5511955 original size:24 final size:23
Alignment explanation
Indices: 5511927--5511971 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
5511917 GTTGGATCCA
*
5511927 AATTAAATTTAAAAAGATAATTTG
1 AATTAAATCTAAAAA-ATAATTTG
*
5511951 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
5511972 CCCTAATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:5513031 original size:15 final size:16
Alignment explanation
Indices: 5513002--5513050 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
5512992 TTTCTCAATA
*
5513002 TTTTTCAATTCTTTTT
1 TTTTTCAATTTTTTTT
5513018 TTTTTC-ATTTTTTTT
1 TTTTTCAATTTTTTTT
* *
5513033 CTTTTCGACTTTTTTTT
1 TTTTTC-AATTTTTTTT
5513050 T
1 T
5513051 CTAAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.48
16 6 0.22
17 8 0.30
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTCAATTTTTTTT
Found at i:5513993 original size:6 final size:6
Alignment explanation
Indices: 5513982--5514018 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
5513972 GTGTATAATT
*
5513982 AAAATA AAAATA AAAAT- AAAATA AAAATG AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
5514019 TATACTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:5514001 original size:17 final size:17
Alignment explanation
Indices: 5513981--5514018 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
5513971 AGTGTATAAT
5513981 TAAAATAAAAATAAAAA
1 TAAAATAAAAATAAAAA
*
5513998 TAAAATAAAAATGAAAA
1 TAAAATAAAAATAAAAA
5514015 TAAA
1 TAAA
5514019 TATACTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAATAAAAATAAAAA
Found at i:5514052 original size:10 final size:10
Alignment explanation
Indices: 5514039--5514071 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5514029 TTTTTTGAAC
5514039 TTTTCAATTT
1 TTTTCAATTT
*
5514049 TTTT-ATTTT
1 TTTTCAATTT
5514058 TTTTCAATTT
1 TTTTCAATTT
5514068 TTTT
1 TTTT
5514072 TAAAAACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCAATTT
Found at i:5514095 original size:4 final size:4
Alignment explanation
Indices: 5514086--5514117 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
5514076 AACATGAAAG
5514086 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
5514118 AATAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:5516524 original size:17 final size:17
Alignment explanation
Indices: 5516502--5516575 Score: 78
Period size: 17 Copynumber: 4.2 Consensus size: 17
5516492 CCATTCTAAG
*
5516502 TTTAAATTAATTTTGAA
1 TTTAAATTAATTTTAAA
*
5516519 TTTAAATTTATTTTAAA
1 TTTAAATTAATTTTAAA
* *
5516536 TTTAAATTTTGATTTAAAA
1 TTTAAA--TTAATTTTAAA
5516555 TTTAAATTTAA-TTTAAA
1 TTTAAA-TTAATTTTAAA
5516572 TTTA
1 TTTA
5516576 GACTTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
17 30 0.61
18 4 0.08
19 15 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:5516528 original size:6 final size:6
Alignment explanation
Indices: 5516502--5516575 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
5516492 CCATTCTAAG
* * * **
5516502 TTTAAA -TTAAT TTTGAA TTTAAA TTT-AT TTTAAA TTTAAA TTTTGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5516548 TTTAAAA TTTAAA TTT-AA TTTAAA TTTA
1 TTT-AAA TTTAAA TTTAAA TTTAAA TTTA
5516576 GACTTATATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 13 0.24
6 37 0.69
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:5516533 original size:11 final size:11
Alignment explanation
Indices: 5516502--5516575 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
5516492 CCATTCTAAG
* *
5516502 TTTAAATTAAT
1 TTTAATTTAAA
5516513 TTTGAATTTAAA
1 TTT-AATTTAAA
*
5516525 TTTATTTTAAA
1 TTTAATTTAAA
**
5516536 TTTAAATTTTGA
1 TTT-AATTTAAA
5516548 TTTAAAATTTAAA
1 TTT--AATTTAAA
5516561 TTTAATTTAAA
1 TTTAATTTAAA
5516572 TTTA
1 TTTA
5516576 GACTTATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
11 25 0.48
12 17 0.33
13 10 0.19
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5516546 original size:30 final size:31
Alignment explanation
Indices: 5516502--5516574 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
5516492 CCATTCTAAG
*
5516502 TTTAAA-TT-AATTTTGAATTT-AAATTT-AT
1 TTTAAATTTAAATTTTG-ATTTAAAATTTAAA
5516530 TTTAAATTTAAATTTTGATTTAAAATTTAAA
1 TTTAAATTTAAATTTTGATTTAAAATTTAAA
5516561 TTT-AATTTAAATTT
1 TTTAAATTTAAATTT
5516575 AGACTTATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 6 0.15
29 6 0.15
30 24 0.60
31 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTAAATTTAAATTTTGATTTAAAATTTAAA
Found at i:5518595 original size:30 final size:29
Alignment explanation
Indices: 5518560--5518775 Score: 193
Period size: 30 Copynumber: 7.2 Consensus size: 29
5518550 CAAGAAATGG
*
5518560 TATTTTAACCTCAAAACTTTTTGAAAATTA
1 TATTTTAACC-CAAAACTTTTTCAAAATTA
* * *
5518590 CATTTTAACCACTAAACTTTTCCAAAATTA
1 TATTTTAACC-CAAAACTTTTTCAAAATTA
*
5518620 TATTTTAACCCTAAAACTTTCT-ATAAATTA
1 TATTTTAACCC-AAAACTTTTTCA-AAATTA
* * *
5518650 CATTTTAACCCTTAAACTTTTCCAAAATTA
1 TATTTTAACCC-AAAACTTTTTCAAAATTA
*
5518680 TATTTTAACCCCAAAACTTTTT-ATATATTA
1 TATTTTAA-CCCAAAACTTTTTCA-AAATTA
* * * * *
5518710 CATTTTGATCCCTAAACTTTTCCAACATTA
1 TATTTT-AACCCAAAACTTTTTCAAAATTA
* *
5518740 TATTTTGACCCCAAAACTTTTTAAAAATTA
1 TATTTT-AACCCAAAACTTTTTCAAAATTA
5518770 TATTTT
1 TATTTT
5518776 TACTCCCGAA
Statistics
Matches: 151, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
29 3 0.02
30 142 0.94
31 6 0.04
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (29 bp):
TATTTTAACCCAAAACTTTTTCAAAATTA
Found at i:5518626 original size:60 final size:59
Alignment explanation
Indices: 5518560--5518775 Score: 308
Period size: 60 Copynumber: 3.6 Consensus size: 59
5518550 CAAGAAATGG
*
5518560 TATTTTAACCTCAAAACTTTTTGA-AAATTACATTTTAACCACTAAACTTTTCCAAAATTA
1 TATTTTAACCCCAAAACTTTTT-ATAAATTACATTTTAACC-CTAAACTTTTCCAAAATTA
* *
5518620 TATTTTAACCCTAAAACTTTCTATAAATTACATTTTAACCCTTAAACTTTTCCAAAATTA
1 TATTTTAACCCCAAAACTTTTTATAAATTACATTTTAACCC-TAAACTTTTCCAAAATTA
* * *
5518680 TATTTTAACCCCAAAACTTTTTATATATTACATTTTGATCCCTAAACTTTTCCAACATTA
1 TATTTTAACCCCAAAACTTTTTATAAATTACATTTT-AACCCTAAACTTTTCCAAAATTA
* * *
5518740 TATTTTGACCCCAAAACTTTTTAAAAATTATATTTT
1 TATTTTAACCCCAAAACTTTTTATAAATTACATTTT
5518776 TACTCCCGAA
Statistics
Matches: 141, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
59 2 0.01
60 135 0.96
61 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (59 bp):
TATTTTAACCCCAAAACTTTTTATAAATTACATTTTAACCCTAAACTTTTCCAAAATTA
Found at i:5518715 original size:90 final size:90
Alignment explanation
Indices: 5518561--5518775 Score: 229
Period size: 90 Copynumber: 2.4 Consensus size: 90
5518551 AAGAAATGGT
* * * * *
5518561 ATTTTAACCTCAAAACTTTTTGAAAATTACATTTTAACCACTAAACTTTTCCAAAATTATATTTT
1 ATTTTAACCCCAAAACTTTTTAAAAATTATATTTTAACCACAAAACTTTTCCAAAATTACATTTT
*
5518626 -AACCCTAAAAC-TTTCTATAAATTAC
66 GAACCCT-AAACTTTTCCA-AAATTAC
** ** * * *
5518651 ATTTTAACCCTTAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTT-TATATATTACATTT
1 ATTTTAACCCCAAAACTTTTTAAAAATTATATTTTAACCACAAAACTTTTCCA-AAATTACATTT
* * *
5518715 TGATCCCTAAACTTTTCCAACATTAT
65 TGAACCCTAAACTTTTCCAAAATTAC
*
5518741 ATTTTGACCCCAAAACTTTTTAAAAATTATATTTT
1 ATTTTAACCCCAAAACTTTTTAAAAATTATATTTT
5518776 TACTCCCGAA
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
89 1 0.01
90 91 0.89
91 10 0.10
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.42
Consensus pattern (90 bp):
ATTTTAACCCCAAAACTTTTTAAAAATTATATTTTAACCACAAAACTTTTCCAAAATTACATTTT
GAACCCTAAACTTTTCCAAAATTAC
Found at i:5528168 original size:115 final size:115
Alignment explanation
Indices: 5528008--5528266 Score: 428
Period size: 115 Copynumber: 2.3 Consensus size: 115
5527998 CAAGCGAGGC
* *
5528008 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAAGTCAAGCGCTCAACGCGAGCAAATTTTT
1 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAAGTCAAGCGCTCAACGCGAGCAAATCTTC
*
5528073 GAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
66 AAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
*
5528123 GGTCATCTTTCTGATGAGATACAGAGAAGAATACCAAGTCAAGCGCTCAACGCGAGCAAATCTTC
1 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAAGTCAAGCGCTCAACGCGAGCAAATCTTC
* * * *
5528188 AAACTCATCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGTAATAAAAT
66 AAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
* *
5528238 GGTTAGCTTCCTGATGAGATACAGAGAAG
1 GGTCATCTTCCTGATGAGATACAGAGAAG
5528267 TAGACCAGAT
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 133 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (115 bp):
GGTCATCTTCCTGATGAGATACAGAGAAGAATACCAAGTCAAGCGCTCAACGCGAGCAAATCTTC
AAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
Found at i:5528801 original size:18 final size:18
Alignment explanation
Indices: 5528778--5528844 Score: 75
Period size: 17 Copynumber: 3.7 Consensus size: 18
5528768 TCATTCTAAG
*
5528778 TTTAAATTAATTTTTGAA
1 TTTAAATTAATTTTTAAA
*
5528796 TTTAAATTTA-TTTTAAA
1 TTTAAATTAATTTTTAAA
*
5528813 TTTAAATT-TTTTTTAAAA
1 TTTAAATTAATTTTT-AAA
5528831 TTTAAATTTAATTT
1 TTTAAA-TTAATTT
5528845 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 18 0.44
18 18 0.44
19 2 0.05
20 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
TTTAAATTAATTTTTAAA
Found at i:5528812 original size:11 final size:11
Alignment explanation
Indices: 5528794--5528880 Score: 67
Period size: 11 Copynumber: 8.1 Consensus size: 11
5528784 TTAATTTTTG
5528794 AATTTAAATTT
1 AATTTAAATTT
*
5528805 ATTTTAAATTT
1 AATTTAAATTT
**
5528816 AAATTT-TTTTT
1 -AATTTAAATTT
5528827 AAAATTTAAATTT
1 --AATTTAAATTT
5528840 AATTTAAATTT
1 AATTTAAATTT
* *
5528851 -TTTTTAA---
1 AATTTAAATTT
5528858 AATTTAAATTT
1 AATTTAAATTT
5528869 AATTTAAATTT
1 AATTTAAATTT
5528880 A
1 A
5528881 GACTTATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
8 5 0.08
10 5 0.08
11 36 0.61
12 10 0.17
13 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:5528818 original size:35 final size:35
Alignment explanation
Indices: 5528778--5528880 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 35
5528768 TCATTCTAAG
* *
5528778 TTTAAATTAATTTTT-GAATTTAAATTTATTTTAAA
1 TTTAAATT-ATTTTTAAAATTTAAATTTAATTTAAA
*
5528813 TTTAAATTTTTTTTAAAATTTAAATTTAATTTAAA
1 TTTAAATTATTTTTAAAATTTAAATTTAATTTAAA
5528848 --T---TT-TTTTTAAAATTTAAATTTAATTTAAA
1 TTTAAATTATTTTTAAAATTTAAATTTAATTTAAA
5528877 TTTA
1 TTTA
5528881 GACTTATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
29 26 0.43
30 2 0.03
31 1 0.02
33 1 0.02
34 5 0.08
35 26 0.43
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTAAATTATTTTTAAAATTTAAATTTAATTTAAA
Found at i:5528845 original size:18 final size:16
Alignment explanation
Indices: 5528794--5528880 Score: 83
Period size: 17 Copynumber: 5.4 Consensus size: 16
5528784 TTAATTTTTG
5528794 AATTTAAATTTATTTTA
1 AATTTAAATTTA-TTTA
*
5528811 AATTTAAATTTTTTTTAA
1 AATTTAAA-TTTATTT-A
5528829 AATTTAAATTTAATTTA
1 AATTTAAATTT-ATTTA
*
5528846 AATTT---TTT-TTAA
1 AATTTAAATTTATTTA
5528858 AATTTAAATTTAATTTA
1 AATTTAAATTT-ATTTA
5528875 AATTTA
1 AATTTA
5528881 GACTTATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.14
14 3 0.05
15 3 0.05
17 29 0.50
18 15 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:5528879 original size:29 final size:29
Alignment explanation
Indices: 5528811--5528879 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
5528801 ATTTATTTTA
5528811 AATTTAAATTTTTTTTAAAATTTAAATTT
1 AATTTAAATTTTTTTTAAAATTTAAATTT
5528840 AATTTAAATTTTTTTTAAAATTTAAATTT
1 AATTTAAATTTTTTTTAAAATTTAAATTT
5528869 AATTTAAATTT
1 AATTTAAATTT
5528880 AGACTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
AATTTAAATTTTTTTTAAAATTTAAATTT
Found at i:5529606 original size:3 final size:3
Alignment explanation
Indices: 5529598--5529640 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
5529588 TTTTACATTG
**
5529598 AAT AAT AAT AATT GTT AAGT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AA-T AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
5529641 ATATTAGTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 30 0.88
4 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5530880 original size:30 final size:30
Alignment explanation
Indices: 5530846--5531190 Score: 283
Period size: 30 Copynumber: 11.5 Consensus size: 30
5530836 CTAAACTATC
**
5530846 CAAAAATGGTATTTTAACCCTAAAACTTTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
5530876 CAAAAATTATATTTTAACCCCT-AAACTTTT
1 CAAAAATTATATTTTAA-CCCTAAAACTTTT
** * * *
5530906 CCTAAATTGTATTTAAACCCCAAAACTTTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
* * * * *
5530936 TATAAATTACATTTTAACCCTTAAATTTTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
* *
5530966 CCAAAATTATATTTTAACCCCAAAAC-TTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
* *
5530995 CTATAAATTACATTTTAACCCT-AAACTTTT
1 C-AAAAATTATATTTTAACCCTAAAACTTTT
* *
5531025 CCAAAATTATATTTTAACCCCAAAAC-TTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
* *
5531054 CTATAAATTACATTTTAACCCCT-AAACTTTT
1 C-AAAAATTATATTTTAA-CCCTAAAACTTTT
*** *
5531085 TTGAAATTATATTTTGACCCTAAGAA-TTTT
1 CAAAAATTATATTTTAACCCTAA-AACTTTT
* * * * * **
5531115 TATAAATTACATTTTTACTCTCGAACTTCTT
1 CAAAAATTATATTTTAACCCTAAAACTT-TT
5531146 C-AAAATTATATTTTAACCCTAAAAC-TTT
1 CAAAAATTATATTTTAACCCTAAAACTTTT
*
5531174 CTAAAAATTACATTTTA
1 C-AAAAATTATATTTTA
5531191 CTCCCGAACT
Statistics
Matches: 247, Mismatches: 54, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
28 3 0.01
29 38 0.15
30 192 0.78
31 14 0.06
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (30 bp):
CAAAAATTATATTTTAACCCTAAAACTTTT
Found at i:5530931 original size:60 final size:60
Alignment explanation
Indices: 5530855--5531190 Score: 421
Period size: 60 Copynumber: 5.6 Consensus size: 60
5530845 CCAAAAATGG
* * * * *
5530855 TATTTTAACCCTAAAACTTT-TCAAAAATTATATTTTAACCCCTAAACTTTTCCTAAATTG
1 TATTTTAACCCCAAAACTTTCT-ATAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
* * * *
5530915 TATTTAAACCCCAAAACTTTTTATAAATTACATTTTAACCCTTAAATTTTTCCAAAATTA
1 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
5530975 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAA-CCCTAAACTTTTCCAAAATTA
1 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
***
5531034 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAACCCCTAAACTTTTTTGAAATTA
1 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
* * * * * *
5531094 TATTTTGACCCTAAGAA-TTTTTATAAATTACATTTTTA-CTCTCGAACTTCTT-CAAAATTA
1 TATTTTAACCCCAA-AACTTTCTATAAATTACATTTTAACCCCT-AAACTT-TTCCAAAATTA
* *
5531154 TATTTTAACCCTAAAACTTTCTAAAAATTACATTTTA
1 TATTTTAACCCCAAAACTTTCTATAAATTACATTTTA
5531191 CTCCCGAACT
Statistics
Matches: 243, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
59 62 0.26
60 176 0.72
61 5 0.02
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (60 bp):
TATTTTAACCCCAAAACTTTCTATAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
Found at i:5531152 original size:179 final size:179
Alignment explanation
Indices: 5530855--5531190 Score: 473
Period size: 179 Copynumber: 1.9 Consensus size: 179
5530845 CCAAAAATGG
* * *
5530855 TATTTTAACCCTAAAACTTTTCAAAAATTATATTTTAACCCCTAAACTTTTCCTAAATTGTATTT
1 TATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCCTAAACTTTTCCTAAATTATATTT
* *
5530920 AAACCCCAAAACTTTTTATAAATTACATTTTAACCCTTAAATTTTTCCAAAATTATATTTTAACC
66 AAACCCCAAAACTTTTTATAAATTACATTTTAACCCTGAAATTCTTCCAAAATTATATTTTAACC
*
5530985 CCAAAACTTTCTATAAATTACATTTTAACCCTAAACTTTTCCAAAATTA
131 CCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTTCCAAAATTA
* *
5531034 TATTTTAACCCCAAAAC-TTTCTATAAATTACATTTTAACCCCTAAACTTTT-TTGAAATTATAT
1 TATTTTAACCCCAAAACTTTTC-AAAAATTACATTTTAACCCCTAAACTTTTCCT-AAATTATAT
** * * * *
5531097 TTTGACCCTAAGAA-TTTTTATAAATTACATTTTTACTCTCGAACTTCTT-CAAAATTATATTTT
64 TTAAACCCCAA-AACTTTTTATAAATTACATTTTAACCCT-GAAATTCTTCCAAAATTATATTTT
*
5531160 AACCCTAAAACTTTCTAAAAATTACATTTTA
127 AACCCCAAAACTTTCTAAAAATTACATTTTA
5531191 CTCCCGAACT
Statistics
Matches: 138, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
178 5 0.04
179 125 0.91
180 8 0.06
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (179 bp):
TATTTTAACCCCAAAACTTTTCAAAAATTACATTTTAACCCCTAAACTTTTCCTAAATTATATTT
AAACCCCAAAACTTTTTATAAATTACATTTTAACCCTGAAATTCTTCCAAAATTATATTTTAACC
CCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTTCCAAAATTA
Found at i:5531648 original size:96 final size:96
Alignment explanation
Indices: 5531483--5531664 Score: 251
Period size: 96 Copynumber: 1.9 Consensus size: 96
5531473 AAAACTTTAA
* * * **
5531483 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAATTTTGCGCCTTAACTTACTAGGTGCGATT
1 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
5531548 TTTCTTCAAATCGAAATAATCGAATATCCTT
66 TTTCTTCAAATCGAAATAATCGAATATCCTT
*
5531579 AATCGAGGCAATGTT-TTCTTATCTTCG-GTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAA
1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAA
** *
5531642 CCTTTCTTTGAATCGAGATAATC
64 CCTTTCTTCAAATCGAAATAATC
5531665 AAACACCCTT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 2 0.03
96 69 0.92
97 4 0.05
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATATCCTT
Found at i:5532604 original size:10 final size:10
Alignment explanation
Indices: 5532582--5532611 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
5532572 TAAAAATGCA
5532582 AATAATAAAAT
1 AATAAT-AAAT
5532593 AATAATAAAT
1 AATAATAAAT
5532603 AATAATAAA
1 AATAATAAA
5532612 ATGGCTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAATAAAT
Found at i:5533717 original size:25 final size:25
Alignment explanation
Indices: 5533664--5533710 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
5533654 GTTGGATCCA
5533664 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
5533689 AATTAAA-TCTAAATA-ATAATTT
1 AATTAAATTCTAAAAAGATAATTT
5533711 CCTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:5533793 original size:13 final size:13
Alignment explanation
Indices: 5533772--5533805 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5533762 TAAATAATAT
5533772 AATAATAATCCTA
1 AATAATAATCCTA
*
5533785 AATATTAATCCTA
1 AATAATAATCCTA
*
5533798 AAAAATAA
1 AATAATAA
5533806 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:5538847 original size:14 final size:15
Alignment explanation
Indices: 5538814--5538851 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5538804 TATTAAACTA
5538814 AAAATAAAACAAAGT
1 AAAATAAAACAAAGT
* *
5538829 AAAATAATATAAA-T
1 AAAATAAAACAAAGT
5538843 AAAATAAAA
1 AAAATAAAA
5538852 ATATTGTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAATAAAACAAAGT
Found at i:5548976 original size:2 final size:2
Alignment explanation
Indices: 5548969--5549005 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5548959 TGTTGATTCG
5548969 TA 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 TA T
5549006 GAAAAGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5553750 original size:25 final size:26
Alignment explanation
Indices: 5553704--5553764 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
5553694 CGAGTTAATC
5553704 ATTTATATATATAAATAAATTTAAAT
1 ATTTATATATATAAATAAATTTAAAT
* ** *
5553730 ATTTATAT-TTTAAATCGATTTTAAT
1 ATTTATATATATAAATAAATTTAAAT
*
5553755 AATTATATAT
1 ATTTATATAT
5553765 GAATTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTTATATATATAAATAAATTTAAAT
Found at i:5557608 original size:21 final size:21
Alignment explanation
Indices: 5557579--5557634 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
5557569 AATAGTGCAG
*
5557579 ACTTATACCGATACAAGTGAC-T
1 ACTTCTACCGATACAAGT--CTT
* *
5557601 -CTTCTACCTAAACAAGTCTT
1 ACTTCTACCGATACAAGTCTT
5557621 ACTTCTACCGATAC
1 ACTTCTACCGATAC
5557635 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 25 0.93
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCTT
Found at i:5561637 original size:36 final size:36
Alignment explanation
Indices: 5561589--5561658 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
5561579 CTCCCAAACT
*
5561589 TGATTAATGCAATCATACTTACACCGGTGTAAGTTA
1 TGATTAAAGCAATCATACTTACACCGGTGTAAGTTA
5561625 TGATTAAAGCAATCATACTTACACCGGTGTAAGT
1 TGATTAAAGCAATCATACTTACACCGGTGTAAGT
5561659 AAGTTGTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (36 bp):
TGATTAAAGCAATCATACTTACACCGGTGTAAGTTA
Found at i:5565049 original size:20 final size:21
Alignment explanation
Indices: 5565014--5565079 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
5565004 AGATGATTAC
*
5565014 ATATAAAATTATAATAAAATAT
1 ATATAAAA-TAAAATAAAATAT
**
5565036 ATATAAAA-AAAAT-ATCTA-
1 ATATAAAATAAAATAAAATAT
*
5565054 ATATAAAATTAAATATAAATAT
1 ATATAAAATAAAATA-AAATAT
5565076 ATAT
1 ATAT
5565080 TTTTTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 4 0.12
21 3 0.09
22 12 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATATAAAATAAAATAAAATAT
Found at i:5565590 original size:20 final size:20
Alignment explanation
Indices: 5565565--5565605 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5565555 AATAAGCATA
*
5565565 TTATGATGTATTTGAGACAT
1 TTATGATGTATTTGAAACAT
5565585 TTATGATGTATTTGAAACAT
1 TTATGATGTATTTGAAACAT
5565605 T
1 T
5565606 GTTTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (20 bp):
TTATGATGTATTTGAAACAT
Found at i:5566598 original size:16 final size:16
Alignment explanation
Indices: 5566574--5566607 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5566564 TTTGGATTTT
* *
5566574 AAAATTTTAAAATTAA
1 AAAAATTTAAAAATAA
5566590 AAAAATTTAAAAATAA
1 AAAAATTTAAAAATAA
5566606 AA
1 AA
5566608 GATAAATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTTAAAAATAA
Found at i:5566897 original size:20 final size:20
Alignment explanation
Indices: 5566874--5566918 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5566864 AATTTTTTAA
* * *
5566874 ATTTTTTTGAGATTTTTTCT
1 ATTTTTTTAAAATTTTTACT
*
5566894 ATTTGTTTAAAATTTTTACT
1 ATTTTTTTAAAATTTTTACT
5566914 ATTTT
1 ATTTT
5566919 ATGATATTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (20 bp):
ATTTTTTTAAAATTTTTACT
Found at i:5567279 original size:6 final size:6
Alignment explanation
Indices: 5567268--5567299 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5567258 ATAATAGATG
5567268 TACATA TACATA TACATA TACATA TACATA TA
1 TACATA TACATA TACATA TACATA TACATA TA
5567300 ATCATGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:5567980 original size:20 final size:20
Alignment explanation
Indices: 5567909--5568002 Score: 54
Period size: 20 Copynumber: 4.8 Consensus size: 20
5567899 AAAATTATTA
* *
5567909 TTTTATAAAAATTTT--AAC
1 TTTTATAAATATTTTAGAAT
* * * *
5567927 TTATATATATATATTAGATT
1 TTTTATAAATATTTTAGAAT
*
5567947 TTTTTTACAA-ATTTTAGAAT
1 TTTTATA-AATATTTTAGAAT
*
5567967 TTTTATAAATATTTT-TAAT
1 TTTTATAAATATTTTAGAAT
5567986 TTTTGA-AAATTATTTTA
1 TTTT-ATAAA-TATTTTA
5568003 AATATTTTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
18 11 0.20
19 12 0.21
20 32 0.57
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTATAAATATTTTAGAAT
Found at i:5567995 original size:19 final size:20
Alignment explanation
Indices: 5567964--5568001 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5567954 CAAATTTTAG
5567964 AATTTTTATAAA-TATTTTT
1 AATTTTTATAAATTATTTTT
5567983 AATTTTTGA-AAATTATTTT
1 AATTTTT-ATAAATTATTTT
5568002 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTTATAAATTATTTTT
Found at i:5567996 original size:29 final size:30
Alignment explanation
Indices: 5567964--5568021 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
5567954 CAAATTTTAG
5567964 AATT-TTTATAAATA-TTTTTAATTTTTGAA
1 AATTATTT-TAAATATTTTTTAATTTTTGAA
5567993 AATTATTTTAAATATTTTTTTAATTTTTG
1 AATTATTTTAAATA-TTTTTTAATTTTTG
5568022 TTAAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTATTTTAAATATTTTTTAATTTTTGAA
Found at i:5570197 original size:69 final size:69
Alignment explanation
Indices: 5570086--5570225 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 69
5570076 ACACTAATCG
*
5570086 CAAGTAAACTAATAGTCCACTCAAACCCACTCTCATACAAAATATCAGCACGTGATAAGATTGGA
1 CAAGTAAACTAATAGTCCACTCAAACCCACCCTCATACAAAATATCAGCACGTGATAAGATTGGA
5570151 GACT
66 GACT
* * * *
5570155 CAAGTAAACTCATAGTCCACTCAAACTCACCCTTATATAAAATATCAGCACGTGATAAGATTGGA
1 CAAGTAAACTAATAGTCCACTCAAACCCACCCTCATACAAAATATCAGCACGTGATAAGATTGGA
5570220 GACT
66 GACT
5570224 CA
1 CA
5570226 CATATGACAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (69 bp):
CAAGTAAACTAATAGTCCACTCAAACCCACCCTCATACAAAATATCAGCACGTGATAAGATTGGA
GACT
Found at i:5572292 original size:20 final size:20
Alignment explanation
Indices: 5572267--5572307 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5572257 AATCTTATTT
5572267 TGTTTTTTGTAATTCCTCCA
1 TGTTTTTTGTAATTCCTCCA
5572287 TGTTTTTTGTAATTCCTCCA
1 TGTTTTTTGTAATTCCTCCA
5572307 T
1 T
5572308 ACATATCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (20 bp):
TGTTTTTTGTAATTCCTCCA
Found at i:5576966 original size:18 final size:18
Alignment explanation
Indices: 5576943--5576977 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5576933 TGATTGAAAA
* *
5576943 ATTAATTTAGTTAATTTG
1 ATTAATTAAATTAATTTG
5576961 ATTAATTAAATTAATTT
1 ATTAATTAAATTAATTT
5576978 AATAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTAATTAAATTAATTTG
Found at i:5577592 original size:11 final size:11
Alignment explanation
Indices: 5577566--5577620 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
5577556 AAAACAATTC
5577566 TAAAAA-AT-T
1 TAAAAATATAT
5577575 TAAAAATATAT
1 TAAAAATATAT
*
5577586 TAAAAATA-AA
1 TAAAAATATAT
*
5577596 TATAAAT-T-T
1 TAAAAATATAT
5577605 TAAAAATATAT
1 TAAAAATATAT
5577616 TAAAA
1 TAAAA
5577621 TTTATGTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 12 0.32
10 10 0.27
11 15 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:5577619 original size:18 final size:19
Alignment explanation
Indices: 5577585--5577624 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5577575 TAAAAATATA
*
5577585 TTAAAAATAAATATAAATT
1 TTAAAAATAAATATAAAAT
*
5577604 TTAAAAATATAT-TAAAAT
1 TTAAAAATAAATATAAAAT
5577622 TTA
1 TTA
5577625 TGTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAAAATAAATATAAAAT
Found at i:5577754 original size:60 final size:60
Alignment explanation
Indices: 5577629--5577755 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
5577619 AATTTATGTT
* ** * * *
5577629 AAAAAATTCAACAAATTTGGGCCTTGATGTTTACAAAAATTTTCATTTGAGTTCTAATTC
1 AAAAAATTCAACAAATTTGGCCCTCAATATTTACAAAAATTTTCATTTGAGTCCTAACTC
**
5577689 AAAAAATTCAATTAATTTGGCCCTCAATATTTA-AAAAATTTGTCAATTT-AGTCCTAACTC
1 AAAAAATTCAACAAATTTGGCCCTCAATATTTACAAAAATTT-TC-ATTTGAGTCCTAACTC
*
5577749 TAAAAAT
1 AAAAAAT
5577756 AAAAAAAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 8 0.14
60 44 0.79
61 4 0.07
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (60 bp):
AAAAAATTCAACAAATTTGGCCCTCAATATTTACAAAAATTTTCATTTGAGTCCTAACTC
Found at i:5581242 original size:16 final size:16
Alignment explanation
Indices: 5581207--5581244 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5581197 GAAATAGGAC
*
5581207 TGTAATGGAAAATATA
1 TGTAATGGAAAAAATA
5581223 TGTAATGGAATAAAAT-
1 TGTAATGGAA-AAAATA
5581239 TGTAAT
1 TGTAAT
5581245 TAGTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (16 bp):
TGTAATGGAAAAAATA
Found at i:5582676 original size:24 final size:23
Alignment explanation
Indices: 5582649--5582703 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5582639 TATATATATG
**
5582649 AAATTGCATTTGATTTTGTATCT
1 AAATTGCATGGGATTTTGTATCT
*
5582672 AAAATTGTATGGGATTTTGTATCT
1 -AAATTGCATGGGATTTTGTATCT
*
5582696 GAATTGCA
1 AAATTGCA
5582704 ACTGCATACG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (23 bp):
AAATTGCATGGGATTTTGTATCT
Found at i:5586557 original size:29 final size:29
Alignment explanation
Indices: 5586481--5586704 Score: 158
Period size: 29 Copynumber: 7.7 Consensus size: 29
5586471 AACACTCAAG
* * **
5586481 GGGTAAAAATAGAATTTTTAGACA-TCTGG
1 GGGTAAAAATGGAATTTTTAGAAAGT-TCA
*
5586510 GGGT-AAAATGTAATTTTTAGAAAGTTCA
1 GGGTAAAAATGGAATTTTTAGAAAGTTCA
* *
5586538 GGGTCAAAAATGGAA-TTTTAGGAAATTTAA
1 GGGT-AAAAATGGAATTTTTA-GAAAGTTCA
* *
5586568 GGGT-AAAATGGTAATTTTTGGAAAGGTCA
1 GGGTAAAAATGG-AATTTTTAGAAAGTTCA
* *
5586597 GGGTTAAAAATGGAATTTTT-GGAAGTTCGG
1 GGG-TAAAAATGGAATTTTTAGAAAGTTC-A
*
5586627 GGGT-AAAATGGTAATTTTTGGAGAA-TTC-
1 GGGTAAAAATGG-AATTTTTAGA-AAGTTCA
* * *
5586655 GAGGTCAAAAGTGGAATTTTTAGAAATTTGA
1 G-GGT-AAAAATGGAATTTTTAGAAAGTTCA
*
5586686 GGGTAAAAATGTAATTTTT
1 GGGTAAAAATGGAATTTTT
5586705 GGAGAATTTG
Statistics
Matches: 157, Mismatches: 21, Indels: 34
0.74 0.10 0.16
Matches are distributed among these distances:
28 36 0.23
29 53 0.34
30 52 0.33
31 16 0.10
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTAGAAAGTTCA
Found at i:5586606 original size:59 final size:58
Alignment explanation
Indices: 5586510--5586724 Score: 247
Period size: 59 Copynumber: 3.6 Consensus size: 58
5586500 AGACATCTGG
* *
5586510 GGGTAAAATGTAATTTTTAGAAAGTTCAGGGTCAAAAATGGAATTTTAGGAAATTTAA
1 GGGTAAAATGTAATTTTTGGAAAGTTCAGGGTCAAAAATGGAATTTTAGGAAATTTGA
* * * * * *
5586568 GGGTAAAATGGTAATTTTTGGAAAGGTCAGGGTTAAAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAAT-GTAATTTTTGGAAAGTTCAGGGTCAAAAATGGAATTTTAGGAAATTTGA
*
5586627 GGGTAAAATGGTAATTTTTGGAGAA-TTC-GAGGTCAAAAGTGGAATTTTTA-GAAATTTGA
1 GGGTAAAAT-GTAATTTTTGGA-AAGTTCAG-GGTCAAAAATGGAA-TTTTAGGAAATTTGA
* *
5586686 GGGTAAAAATGTAATTTTTGGAGAATTTGAGGGTCAAAA
1 GGGT-AAAATGTAATTTTTGGA-AAGTTCAGGGTCAAAA
5586725 TATGATTTCT
Statistics
Matches: 134, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
58 10 0.07
59 102 0.76
60 21 0.16
61 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGGAAAGTTCAGGGTCAAAAATGGAATTTTAGGAAATTTGA
Found at i:5586715 original size:30 final size:29
Alignment explanation
Indices: 5586481--5586725 Score: 185
Period size: 30 Copynumber: 8.3 Consensus size: 29
5586471 AACACTCAAG
* * * *
5586481 GGGTAAAAATAG-AATTTTTAGACATCTGG
1 GGGTAAAAAT-GTAATTTTTGGAAATTTGA
* * *
5586510 GGGT-AAAATGTAATTTTTAGAAAGTTCA
1 GGGTAAAAATGTAATTTTTGGAAATTTGA
* * *
5586538 GGGTCAAAAATGGAATTTTAGGAAATTTAA
1 GGGT-AAAAATGTAATTTTTGGAAATTTGA
** *
5586568 GGGT-AAAATGGTAATTTTTGGAAAGGTCA
1 GGGTAAAAAT-GTAATTTTTGGAAATTTGA
* * * *
5586597 GGGTTAAAAATGGAATTTTTGGAAGTTCGG
1 GGG-TAAAAATGTAATTTTTGGAAATTTGA
*
5586627 GGGT-AAAATGGTAATTTTTGGAGAATTCGA
1 GGGTAAAAAT-GTAATTTTTGGA-AATTTGA
* * *
5586657 -GGTCAAAAGTGGAATTTTTAGAAATTTGA
1 GGGT-AAAAATGTAATTTTTGGAAATTTGA
5586686 GGGTAAAAATGTAATTTTTGGAGAATTTGA
1 GGGTAAAAATGTAATTTTTGGA-AATTTGA
*
5586716 GGGTCAAAAT
1 GGGTAAAAAT
5586726 ATGATTTCTG
Statistics
Matches: 171, Mismatches: 33, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 31 0.18
29 57 0.33
30 73 0.43
31 9 0.05
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAATTTGA
Found at i:5587927 original size:2 final size:2
Alignment explanation
Indices: 5587920--5587955 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5587910 AAAATATTTA
5587920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5587956 TTATTACATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5588715 original size:11 final size:10
Alignment explanation
Indices: 5588679--5588737 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
5588669 GGACATTATT
5588679 AATTTAAATA
1 AATTTAAATA
*
5588689 AATTTAGACTTA
1 AATTTA-A-ATA
5588701 AATTTATAATA
1 AATTTA-AATA
5588712 AATTTAAAT-
1 AATTTAAATA
*
5588721 --TTCAAATA
1 AATTTAAATA
5588729 AATTTAAAT
1 AATTTAAAT
5588738 TCTGTTGGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
7 6 0.15
10 15 0.38
11 9 0.23
12 9 0.23
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (10 bp):
AATTTAAATA
Found at i:5588720 original size:17 final size:17
Alignment explanation
Indices: 5588698--5588738 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
5588688 AAATTTAGAC
5588698 TTAAATTT-ATAATAAAT
1 TTAAATTTCA-AATAAAT
5588715 TTAAATTTCAAATAAAT
1 TTAAATTTCAAATAAAT
5588732 TTAAATT
1 TTAAATT
5588739 CTGTTGGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTTCAAATAAAT
Found at i:5589366 original size:48 final size:48
Alignment explanation
Indices: 5589303--5589416 Score: 228
Period size: 48 Copynumber: 2.4 Consensus size: 48
5589293 CCGCTTCTCT
5589303 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCA
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCA
5589351 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCA
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCA
5589399 GTATCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCT
5589417 TAGGTTTGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (48 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTTTCA
Found at i:5590795 original size:23 final size:21
Alignment explanation
Indices: 5590753--5590792 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5590743 ATTACTAATT
5590753 AATATATATATATAATATTAG
1 AATATATATATATAATATTAG
5590774 AATATA-ATAATATAA-ATTA
1 AATATATAT-ATATAATATTA
5590793 TTATTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AATATATATATATAATATTAG
Done.