Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 21 of 56
Found at i:3721076 original size:33 final size:33
Alignment explanation
Indices: 3721039--3721101 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3721029 TACAAAAAAA
*
3721039 TTAAAAT-ACTACATCAAAATATATTGATATATT
1 TTAAAATGA-TACATCAAAATATATTAATATATT
* *
3721072 TTAAAATGATATATCTAAATATATTAATAT
1 TTAAAATGATACATCAAAATATATTAATAT
3721102 CGATGCACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (33 bp):
TTAAAATGATACATCAAAATATATTAATATATT
Found at i:3721699 original size:6 final size:6
Alignment explanation
Indices: 3721688--3721738 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
3721678 TCTCCACAGA
* * * *
3721688 AAAAAG AAAAAG AAAAA- AAAAAA AAAAAG AAGAAG AAGAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
3721735 AAAA
1 AAAA
3721739 TAACCTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.12
6 36 0.88
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3725264 original size:2 final size:2
Alignment explanation
Indices: 3725257--3725295 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3725247 GTTAAAACTT
3725257 TA 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 TA T
3725296 TTGCTAGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3725494 original size:36 final size:35
Alignment explanation
Indices: 3725437--3725531 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 35
3725427 TTTGAAATAA
*
3725437 TAATTATAAATTA-AAATAATATTTTTTATTTAA-ATT
1 TAATTATAAAATATAAATAATA---TTTATTTAATATT
3725473 TAATTATAAAATATAAA-AATATTTATTTAATATT
1 TAATTATAAAATATAAATAATATTTATTTAATATT
3725507 TAATTA-AAAA-ATAAATAATAATTTA
1 TAATTATAAAATATAAATAAT-ATTTA
3725532 AGTTAATAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
32 5 0.09
33 16 0.30
34 14 0.26
36 16 0.30
37 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TAATTATAAAATATAAATAATATTTATTTAATATT
Found at i:3726050 original size:15 final size:15
Alignment explanation
Indices: 3726025--3726072 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
3726015 GTTTATATAT
3726025 AAATATAAAATTTTA
1 AAATATAAAATTTTA
3726040 AAAT-TATAAATATTTA
1 AAATATA-AAAT-TTTA
*
3726056 ATATATAAAATTTTA
1 AAATATAAAATTTTA
3726071 AA
1 AA
3726073 GAATCAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 13 0.46
16 11 0.39
17 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATAAAATTTTA
Found at i:3726420 original size:30 final size:28
Alignment explanation
Indices: 3726386--3726488 Score: 118
Period size: 29 Copynumber: 3.5 Consensus size: 28
3726376 AATATAAGGT
3726386 TTTATTTATATATAAATTAAAAATTAAAAA
1 TTTATTTA-A-ATAAATTAAAAATTAAAAA
*
3726416 TTTATTTAAATGAAATTTTAAAAGTT-AAAA
1 TTTATTTAAAT-AAA--TTAAAAATTAAAAA
*
3726446 TTTATTTAAATAAAATAAAAATATAAAAA
1 TTTATTTAAATAAATTAAAAAT-TAAAAA
*
3726475 TTTACTTAAATAAA
1 TTTATTTAAATAAA
3726489 AACAATAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.09
28 3 0.05
29 24 0.38
30 23 0.36
31 8 0.12
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (28 bp):
TTTATTTAAATAAATTAAAAATTAAAAA
Found at i:3726459 original size:15 final size:15
Alignment explanation
Indices: 3726412--3726461 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3726402 TTAAAAATTA
3726412 AAAATTTATTTAAAT
1 AAAATTTATTTAAAT
* *
3726427 GAAA-TT-TTAAAAGTT
1 AAAATTTATTTAAA--T
3726442 AAAATTTATTTAAAT
1 AAAATTTATTTAAAT
3726457 AAAAT
1 AAAAT
3726462 AAAAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.19
14 2 0.07
15 13 0.48
16 2 0.07
17 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
AAAATTTATTTAAAT
Found at i:3726484 original size:29 final size:28
Alignment explanation
Indices: 3726386--3726502 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 28
3726376 AATATAAGGT
*
3726386 TTTATTTATATATAAATTAAAAATTAAAAA
1 TTTATTTA-A-ATAAAATAAAAATTAAAAA
* *
3726416 TTTATTTAAATGAAATTTTAAAAGTT-AAAA
1 TTTATTTAAAT-AAA--ATAAAAATTAAAAA
3726446 TTTATTTAAATAAAATAAAAATATAAAAA
1 TTTATTTAAATAAAATAAAAAT-TAAAAA
*
3726475 TTTACTTAAATAAAA-ACAATAATTAAAA
1 TTTATTTAAATAAAATA-AA-AATTAAAA
3726503 CACAAAATTG
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.08
28 4 0.05
29 32 0.42
30 26 0.34
31 8 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
TTTATTTAAATAAAATAAAAATTAAAAA
Found at i:3726999 original size:27 final size:27
Alignment explanation
Indices: 3726944--3727000 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
3726934 TCAGTTCATC
**
3726944 TTCTCTTCTCTCACTTATTTTCTGTAT
1 TTCTCTTCTCTCACTTATTTTCTAAAT
*
3726971 TTCTCTTCTCTCGCTTATTTTCTAAAT
1 TTCTCTTCTCTCACTTATTTTCTAAAT
3726998 TTC
1 TTC
3727001 ATGTGTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.12, C:0.26, G:0.04, T:0.58
Consensus pattern (27 bp):
TTCTCTTCTCTCACTTATTTTCTAAAT
Found at i:3727262 original size:21 final size:21
Alignment explanation
Indices: 3727223--3727278 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
3727213 TGATGCAGAA
**
3727223 AATATATTTTATTGATATT-TT
1 AATAT-TTTTATTTTTATTGTT
3727244 AATTATTTTTATTTTTATTGTT
1 AA-TATTTTTATTTTTATTGTT
*
3727266 TATATTTTT-TTTT
1 AATATTTTTATTTT
3727279 GTCATGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 20 0.67
22 6 0.20
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
AATATTTTTATTTTTATTGTT
Found at i:3727274 original size:15 final size:15
Alignment explanation
Indices: 3727231--3727274 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3727221 AAAATATATT
* *
3727231 TTATTGATATTTTAA
1 TTATTTATATTTTTA
*
3727246 TTATTTTTATTTTTA
1 TTATTTATATTTTTA
*
3727261 TTGTTTATATTTTT
1 TTATTTATATTTTT
3727275 TTTTGTCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (15 bp):
TTATTTATATTTTTA
Found at i:3738001 original size:23 final size:22
Alignment explanation
Indices: 3737972--3738027 Score: 85
Period size: 23 Copynumber: 2.5 Consensus size: 22
3737962 CTAACACATT
3737972 ACCTAACACACCTAATATGCTTC
1 ACCTAACACACCTAATATG-TTC
* *
3737995 ACGTAACACACCTAATATGTTT
1 ACCTAACACACCTAATATGTTC
3738017 ACCTAACACAC
1 ACCTAACACAC
3738028 TTAACAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.38, C:0.32, G:0.05, T:0.25
Consensus pattern (22 bp):
ACCTAACACACCTAATATGTTC
Found at i:3746158 original size:30 final size:30
Alignment explanation
Indices: 3746122--3746179 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3746112 GAATTTATTG
3746122 AGGTAAATAAACCATACTCAAATATAAGAA
1 AGGTAAATAAACCATACTCAAATATAAGAA
* *
3746152 AGGTAAATCAATCATACTCAAATATAAG
1 AGGTAAATAAACCATACTCAAATATAAG
3746180 GGATAGGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.22
Consensus pattern (30 bp):
AGGTAAATAAACCATACTCAAATATAAGAA
Found at i:3746960 original size:15 final size:15
Alignment explanation
Indices: 3746942--3746973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3746932 TTTTTAAAAT
*
3746942 AAATTAATTTAATTA
1 AAATTAAATTAATTA
3746957 AAATTAAATTAATTA
1 AAATTAAATTAATTA
3746972 AA
1 AA
3746974 TTTTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTAAATTAATTA
Found at i:3746966 original size:20 final size:19
Alignment explanation
Indices: 3746935--3746985 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
3746925 AATTTTATTT
*
3746935 TTAAAATAAATTAATTTAA
1 TTAAAATAAATTAATTAAA
3746954 TTAAAATTAAATTAATTAAA
1 TTAAAA-TAAATTAATTAAA
**
3746974 TTTTAATAAATT
1 TTAAAATAAATT
3746986 TTAAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAAATAAATTAATTAAA
Found at i:3747343 original size:22 final size:23
Alignment explanation
Indices: 3747303--3747347 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3747293 TTTAAAAAAT
3747303 AATTTTTAATAAATTTAAATTTTA
1 AATTTTTAAT-AATTTAAATTTTA
3747327 AATTTTTAAT-ATTTAAATTTT
1 AATTTTTAATAATTTAAATTTT
3747348 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
24 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTTAATAATTTAAATTTTA
Found at i:3747349 original size:16 final size:16
Alignment explanation
Indices: 3747323--3747360 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3747313 AAATTTAAAT
3747323 TTTAAA-TTTTTAATA
1 TTTAAATTTTTTAATA
* *
3747338 TTTAAATTTTTTTATT
1 TTTAAATTTTTTAATA
3747354 TTTAAAT
1 TTTAAAT
3747361 AATAACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAAATTTTTTAATA
Found at i:3747490 original size:25 final size:25
Alignment explanation
Indices: 3747462--3747521 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
3747452 CCGAATCCAC
* *
3747462 TTATTATTTACA-TTAAATTCATATA
1 TTATTATTTAAATTTAAATT-AAATA
3747487 TTATTATTTAAATTTAAATTAAATA
1 TTATTATTTAAATTTAAATTAAATA
*
3747512 ATATTATTTA
1 TTATTATTTA
3747522 TTAGCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATTATTTAAATTTAAATTAAATA
Found at i:3752709 original size:2 final size:2
Alignment explanation
Indices: 3752702--3752730 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3752692 TTCACTTGAT
3752702 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3752731 AATGCAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3752778 original size:44 final size:44
Alignment explanation
Indices: 3752710--3752800 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
3752700 ATACACACAC
* *
3752710 ACACACACACACACACACACAAATGCAACAATTCTTCACTTGAT
1 ACACACACACACACACACAAAAATGCAACAATTCTTCACTTAAT
* * *
3752754 ACACACATACACACACACAAAAATGCATCAATTCTTTACTTAAT
1 ACACACACACACACACACAAAAATGCAACAATTCTTCACTTAAT
3752798 ACA
1 ACA
3752801 TATACATACA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.45, C:0.31, G:0.03, T:0.21
Consensus pattern (44 bp):
ACACACACACACACACACAAAAATGCAACAATTCTTCACTTAAT
Found at i:3755600 original size:14 final size:14
Alignment explanation
Indices: 3755577--3755651 Score: 66
Period size: 14 Copynumber: 5.4 Consensus size: 14
3755567 ATAAAATTAT
*
3755577 ATAAATTAATATAA
1 ATAAAATAATATAA
*
3755591 ATAAAATAATAAAA
1 ATAAAATAATATAA
*
3755605 ATATAATAATATAA
1 ATAAAATAATATAA
*
3755619 TATAAAA-AATAT-T
1 -ATAAAATAATATAA
*
3755632 ATAAAAT-TTATATA
1 ATAAAATAATATA-A
3755646 ATAAAA
1 ATAAAA
3755652 ATTATTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
12 9 0.18
14 35 0.71
15 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATAATATAA
Found at i:3755606 original size:24 final size:23
Alignment explanation
Indices: 3755567--3755655 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 23
3755557 ACCACATGAG
* *
3755567 ATAAAATTATATAAATTAATATAA
1 ATAAAATAATAAAAATTAATA-AA
*
3755591 ATAAAATAATAAAAATATAATAAT
1 ATAAAATAATAAAAAT-TAATAAA
*
3755615 ATAATATAA-AAAATATT-ATAAA
1 ATAAAATAATAAAA-ATTAATAAA
* *
3755637 ATTTATATAATAAAAATTA
1 A-TAAAATAATAAAAATTA
3755656 TTAATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 5 0.09
23 15 0.28
24 29 0.54
25 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAAATAATAAAAATTAATAAA
Found at i:3755615 original size:22 final size:19
Alignment explanation
Indices: 3755584--3755638 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
3755574 TATATAAATT
3755584 AATATAAATAAAATAATAAAA
1 AATAT-AATAAAAT-ATAAAA
*
3755605 ATATAATAATATAATATAAAA
1 A-AT-ATAATAAAATATAAAA
*
3755626 AATATTATAAAAT
1 AATATAATAAAAT
3755639 TTATATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 8 0.28
22 9 0.31
23 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATAATAAAATATAAAA
Found at i:3755647 original size:33 final size:33
Alignment explanation
Indices: 3755567--3755648 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
3755557 ACCACATGAG
3755567 ATAAAATTATATAA-ATTAATATAAATAAAATA
1 ATAAAATTATATAATATTAATATAAATAAAATA
* *
3755599 ATAAAAATATAATAATA-TAATATAAA-AAATATT
1 ATAAAATTAT-ATAATATTAATATAAATAAA-ATA
3755632 ATAAAATTTATATAATA
1 ATAAAA-TTATATAATA
3755649 AAAATTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 12 0.28
33 27 0.63
34 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (33 bp):
ATAAAATTATATAATATTAATATAAATAAAATA
Found at i:3756476 original size:16 final size:17
Alignment explanation
Indices: 3756443--3756477 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3756433 TTTCAATTAG
*
3756443 ATAAAATATAATATAAC
1 ATAAAATATAAAATAAC
3756460 ATAAAATA-AAAATAAC
1 ATAAAATATAAAATAAC
3756476 AT
1 AT
3756478 TATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAATATAAAATAAC
Found at i:3757040 original size:10 final size:10
Alignment explanation
Indices: 3757007--3757040 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3756997 TAATAGATCA
3757007 TTTAATATAAT
1 TTTAATA-AAT
*
3757018 TTAAATAAAT
1 TTTAATAAAT
3757028 TTTAATAAAT
1 TTTAATAAAT
3757038 TTT
1 TTT
3757041 GTTGTCGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAATAAAT
Found at i:3759730 original size:42 final size:43
Alignment explanation
Indices: 3759684--3759804 Score: 129
Period size: 50 Copynumber: 2.7 Consensus size: 43
3759674 GGATATAAAT
3759684 AAAATAATTAAAATATAATAATATAATATAAATAAATATTTTA
1 AAAATAATTAAAATATAATAATATAATATAAATAAATATTTTA
* *
3759727 AAATTTATGTAATAAAAATTATTAATATATATAA-ATATATAAATATTTTA
1 AAA---A--TAATTAAAA-TA-TAATA-ATATAATATAAATAAATATTTTA
*
3759777 AAAATAATTATAATATAATAA-ATAATAT
1 AAAATAATTAAAATATAATAATATAATAT
3759805 GAGTTATTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
41 4 0.06
42 3 0.05
43 8 0.12
44 2 0.03
45 7 0.11
46 1 0.02
47 1 0.02
48 8 0.12
49 2 0.03
50 23 0.35
51 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.40
Consensus pattern (43 bp):
AAAATAATTAAAATATAATAATATAATATAAATAAATATTTTA
Found at i:3759801 original size:18 final size:18
Alignment explanation
Indices: 3759736--3759802 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
3759726 AAAATTTATG
3759736 TAATAAA-AATTATTAATA
1 TAATAAATAATTA-TAATA
* * *
3759754 TATATAAATATATAAATATTT
1 TA-ATAAATA-AT-TATAATA
3759775 TAA-AAATAATTATAATA
1 TAATAAATAATTATAATA
3759792 TAATAAATAAT
1 TAATAAATAAT
3759803 ATGAGTTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 7 0.18
18 11 0.29
19 10 0.26
20 2 0.05
21 7 0.18
22 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAAATAATTATAATA
Found at i:3760792 original size:21 final size:22
Alignment explanation
Indices: 3760746--3760792 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3760736 TAAAAATATG
* * *
3760746 ATATTTTTATTTAGTTTGTAAT
1 ATATTTTTATTAAATTTGTAAA
3760768 ATATTTTTATTAAATTT-TAAA
1 ATATTTTTATTAAATTTGTAAA
3760789 ATAT
1 ATAT
3760793 AAATAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTTTTATTAAATTTGTAAA
Found at i:3760916 original size:30 final size:29
Alignment explanation
Indices: 3760850--3760989 Score: 83
Period size: 30 Copynumber: 4.7 Consensus size: 29
3760840 ACTTGACTTG
3760850 AAATATTATTATATTTATAAATAAT-TATTT-
1 AAATATTA--ATATTT-TAAATAATATATTTA
* *
3760880 -TA-ATTAATTTTATTAAA-AATATATTTAA
1 AAATATTAATATT-TTAAATAATATATTT-A
* *
3760908 AAATATTAATATTTTAAATAATATGTTTG
1 AAATATTAATATTTTAAATAATATATTTA
* **
3760937 AAATATTAAAAATATTTAATATTAATATACATA
1 AAATATT-AATAT-TTTAA-A-TAATATATTTA
*
3760970 AAATTGTTAATATTTTAAAT
1 AAA-TATTAATATTTTAAAT
3760990 GGTATTATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
25 3 0.04
26 13 0.15
27 1 0.01
28 4 0.05
29 14 0.16
30 21 0.25
31 6 0.07
32 6 0.07
33 14 0.16
34 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATATTAATATTTTAAATAATATATTTA
Found at i:3760930 original size:18 final size:18
Alignment explanation
Indices: 3760897--3760931 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3760887 TTTTATTAAA
3760897 AATATATTTAAAAATATT
1 AATATATTTAAAAATATT
3760915 AATAT-TTTAAATAATAT
1 AATATATTTAAA-AATAT
3760932 GTTTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATATTTAAAAATATT
Found at i:3763172 original size:27 final size:27
Alignment explanation
Indices: 3763134--3763189 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
3763124 CAAACCTCTC
*
3763134 AAAGCACATTGGGCAAATGTCTTAAGA
1 AAAGCACATTGGGCAAATGTCATAAGA
3763161 AAAGCACATTGGGCAAATGTCATAAGA
1 AAAGCACATTGGGCAAATGTCATAAGA
3763188 AA
1 AA
3763190 CTGCTGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (27 bp):
AAAGCACATTGGGCAAATGTCATAAGA
Found at i:3764012 original size:16 final size:17
Alignment explanation
Indices: 3763961--3764028 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
3763951 AAACTACGAG
* *
3763961 AAATATATATATATA-T
1 AAATAAATATAAATATT
*
3763977 ATATATAATATAAATATT
1 AAATA-AATATAAATATT
3763995 AAAATAAATA-AAAT-TT
1 -AAATAAATATAAATATT
*
3764011 AAATAAATATATATATT
1 AAATAAATATAAATATT
3764028 A
1 A
3764029 TTTTAAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 9 0.21
16 9 0.21
17 15 0.36
18 5 0.12
19 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAAATATAAATATT
Found at i:3764037 original size:18 final size:18
Alignment explanation
Indices: 3764014--3764053 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
3764004 AAAATTTAAA
3764014 TAAATAT-ATATATTATTT
1 TAAATATAAT-TATTATTT
3764032 TAAATATAATTATTATTT
1 TAAATATAATTATTATTT
3764050 TAAA
1 TAAA
3764054 AAAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATATAATTATTATTT
Found at i:3764448 original size:23 final size:23
Alignment explanation
Indices: 3764416--3764459 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3764406 ATAAAAAGAT
3764416 ATTTTTTAAATAATT-TTAATTA
1 ATTTTTTAAATAATTGTTAATTA
*
3764438 ATTTTTATAAATATTTGTTAAT
1 ATTTTT-TAAATAATTGTTAAT
3764460 CAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 8 0.42
24 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTTTTAAATAATTGTTAATTA
Found at i:3764562 original size:2 final size:2
Alignment explanation
Indices: 3764555--3764585 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3764545 ACAACTAAAC
3764555 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3764586 CTTTCGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3764625 original size:19 final size:21
Alignment explanation
Indices: 3764601--3764639 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3764591 GTAAAGTCAA
3764601 TTTAAAAG-AAAAA-ATTACT
1 TTTAAAAGTAAAAATATTACT
3764620 TTTAAAAGTAAAAATATTAC
1 TTTAAAAGTAAAAATATTAC
3764640 CTAACATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTAAAAGTAAAAATATTACT
Found at i:3765657 original size:18 final size:19
Alignment explanation
Indices: 3765625--3765662 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3765615 CATGTTAAAA
3765625 TTTTTACTATCA-TTTATT
1 TTTTTACTATCATTTTATT
3765643 TTTTTACTCAT-ATTTTATT
1 TTTTTACT-ATCATTTTATT
3765662 T
1 T
3765663 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTACTATCATTTTATT
Found at i:3767747 original size:45 final size:45
Alignment explanation
Indices: 3767685--3767795 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
3767675 ACCCACCTAA
* * * * *
3767685 GTTGCCGAAGTTGCCAGAGTTATTGA-TAGTTAAAGATCCTCCTTT
1 GTTGCCAAAGTTTCCAGAGTTATTAACT-GTCAAAGATCCTCCTTG
* * **
3767730 GTTTCCAAAGTTTCCAGAGTTGTTAACTGTCCCAGATCCTCCTTG
1 GTTGCCAAAGTTTCCAGAGTTATTAACTGTCAAAGATCCTCCTTG
3767775 GTTGCCAAAGTTTCCAGAGTT
1 GTTGCCAAAGTTTCCAGAGTT
3767796 GTTGGCCACT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (45 bp):
GTTGCCAAAGTTTCCAGAGTTATTAACTGTCAAAGATCCTCCTTG
Found at i:3767879 original size:180 final size:180
Alignment explanation
Indices: 3767554--3768329 Score: 681
Period size: 180 Copynumber: 4.3 Consensus size: 180
3767544 TCCCTGATTA
* *
3767554 CCAAAGTTGCCTGAATTGTTGATAGTTCCAGACCCTCCTTGGGTGCCAAAGTTTCCAGAGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
* * * * * * * * * * * *
3767619 -GACAGTTTCC-GGTCCACCTTGGTTACCGAAA-TTCCCGACATTATCT-GTAGTTCC-TGACCC
66 GGCCA--CTCCAGATCCACCTCGCTGACCAAAATTTCCGGA-GTT-GCTGGCAATTCCTTGA-CC
* ** * * * * *
3767679 ACCTAAGTTGCCGAAGTTGCCAGAGTTATTGATAGTTAAAGATCCTCCTTTGTTT
126 TCCTTGGTTCCCAAAGTTGCCAGAATTGTTGATAGTTAAAGATCCTCCTTGGTTT
* * * * * * *
3767734 CCAAAGTTTCCAGAGTTGTTAACTGTCCCAGATCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
* * ** *
3767799 GGCCACTCCAGTTCCACCTTGCTGAGTAAAATTTCCGGAGTTGTTGGCAATTCCTTCG-CCTCCT
66 GGCCACTCCAGATCCACCTCGCTGACCAAAATTTCCGGAGTTGCTGGCAATTCCTT-GACCTCCT
* ** *
3767863 TGGTTCCCATAGTTGCCAGAATTGTTGATAGTTACCGACCCTCCTTGGTTT
130 TGGTTCCCAAAGTTGCCAGAATTGTTGATAGTTAAAGATCCTCCTTGGTTT
* *
3767914 CCAAAGTTGCCTGAATTATTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTG
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
* * * * *
3767979 GGCTACTCCAGATCCACCTCGGTGTCCGAAATTTTCGGAGTTGCTGGCAATTCCTTGACCTCCTT
66 GGCCACTCCAGATCCACCTCGCTGACCAAAATTTCCGGAGTTGCTGGCAATTCCTTGACCTCCTT
* * ** *
3768044 GGTTCTCAAAGTTACCAGAATTGTTGATAGTTATGGTTCCTCCTTGGTTT
131 GGTTCCCAAAGTTGCCAGAATTGTTGATAGTTAAAGATCCTCCTTGGTTT
* *
3768094 CCGAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCATTGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCA--G-AGTT
* * * * ** * **** *
3768159 GTTGG-TAGTTCCAGATCCAGCTTGCTCG-CCAAAACCTCC-GACGTTGTTGTTTTTTCC-CGAT
63 GTTGGCCA-CTCCAGATCCACCTCGCT-GACCAAAATTTCCGGA-GTTGCTGGCAATTCCTTGA-
* * * * * ** * *
3768220 CCTTCTTGGTTTCCAATGTTGCCTGAATTGTTGATGGTTACTGATCCCCCTTGGTTA
124 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGATAGTTAAAGATCCTCCTTGGTTT
* * *
3768277 CCAAAGTTGCCTGAATTGTTGACAGTTCCTGACCCCCCTTGGTTACCAAAGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTT
3768330 GCCTGAATTG
Statistics
Matches: 487, Mismatches: 95, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
179 5 0.01
180 331 0.68
181 10 0.02
182 8 0.02
183 132 0.27
184 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (180 bp):
CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
GGCCACTCCAGATCCACCTCGCTGACCAAAATTTCCGGAGTTGCTGGCAATTCCTTGACCTCCTT
GGTTCCCAAAGTTGCCAGAATTGTTGATAGTTAAAGATCCTCCTTGGTTT
Found at i:3767906 original size:45 final size:45
Alignment explanation
Indices: 3767857--3768389 Score: 263
Period size: 45 Copynumber: 11.8 Consensus size: 45
3767847 AATTCCTTCG
* *
3767857 CCTCCTTGGTTCCCATAGTTGCCAGAATTGTTGATAGTTACC-GAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTT-CCAGAC
* * *
3767902 CCTCCTTGGTTTCCAAAGTTGCCTGAATTATTGACAGTTCCAGAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
* * * * * * *
3767947 CCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTGGGCTA-CTCCAGAT
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGAC-AGTTCCAGAC
* * * ** * * * * * *
3767992 CCACCTCGGTGTCCGAAA-TTTTCGGAGTTGCTGGCAATTCCTTGA-
1 CCTCCTTGGT-TCCCAAAGTTGCCAGAATTGTTGACAGTTCC-AGAC
* * * *** **
3768037 CCTCCTTGGTTCTCAAAGTTACCAGAATTGTTGATAGTTATGGTT
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
* * *
3768082 CCTCCTTGGTTTCCGAAGTTGCCTGAATTGTTGACAGTTCCAGAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
* * ** ** *
3768127 CCTCCTTGGTTGCCAAAGTTTCCATTGTTGTTGTTGGTAGTTCCAGAT
1 CCTCCTTGGTTCCCAAAGTTGCCA--G-AATTGTTGACAGTTCCAGAC
** * ** * **** * *
3768175 CCAGCTT-GCTCGCCAAAACCT-CC-GACGTTGTTGTTTTTTCCCGAT
1 CCTCCTTGGTTC-CC-AAAGTTGCCAGA-ATTGTTGACAGTTCCAGAC
* * * * ** * *
3768220 CCTTCTTGGTTTCCAATGTTGCCTGAATTGTTGATGGTTACTGATC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGA-C
* * *
3768266 CC-CCTTGGTTACCAAAGTTGCCTGAATTGTTGACAGTTCCTGAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
* * * *
3768310 CCCCCTTGGTTACCAAAGTTGCCTGAATTGTTGACAGTTCCCGAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
* * * *
3768355 CCCCCTTGGTTACCAAAGTTGCCTGAATTATTGAC
1 CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGAC
3768390 TGTGGCTGAC
Statistics
Matches: 377, Mismatches: 93, Indels: 36
0.75 0.18 0.07
Matches are distributed among these distances:
44 15 0.04
45 317 0.84
46 14 0.04
47 3 0.01
48 24 0.06
49 4 0.01
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (45 bp):
CCTCCTTGGTTCCCAAAGTTGCCAGAATTGTTGACAGTTCCAGAC
Found at i:3767953 original size:90 final size:90
Alignment explanation
Indices: 3767554--3768389 Score: 368
Period size: 90 Copynumber: 9.3 Consensus size: 90
3767544 TCCCTGATTA
* * * * *
3767554 CCAAAGTTGCCTGAATTGTTGATAGTTCCAGACCCTCCTTGGGTGCCAAAGTTTCCAGAGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTGTT
* * ** *
3767619 GACAGTTTCCGGTCCACCTTGGTTA
66 GATAGTTACCGACCCACCTTGGTTT
* * * * * ** * * *
3767644 CCGAAA-TT-CCCGACATTATCTG-TAGTTCCTGACCCACCTAAGTTGCCGAAGTTGCCAGAGTT
1 CC-AAAGTTGCCTGA-ATTGT-TGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATT
* ** * * *
3767706 ATTGATAGTTAAAGATCCTCCTTTGTTT
63 GTTGATAGTTACCGACCCACCTTGGTTT
* * * * * * * * * *
3767734 CCAAAGTTTCCAGAGTTGTTAACTGTCCCAGATCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTGTT
** * ** * **
3767799 GGCCA-CT-CCAGTTCCACCTTGCTGA
66 -GATAGTTACC-GACCCACCTTGGTTT
** * * * * * * ** *
3767824 GTAAAATTTCCGGAGTTGTTGGCAATTCC-TTCGCCTCCTTGGTTCCCATAGTTGCCAGAATTGT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGAC-CCTCCTTGGTTCCCAAAGTTGCCAGAATTGT
*
3767888 TGATAGTTACCGACCCTCCTTGGTTT
65 TGATAGTTACCGACCCACCTTGGTTT
* * * *
3767914 CCAAAGTTGCCTGAATTATTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCAGAGTTGTG
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTGT-
* * * * * *
3767979 GGCTA-CT-CCAGATCCACCTCGGTGT
65 TGATAGTTACC-GACCCACCTTGGTTT
** * * * * * * * *
3768004 CCGAAA-TTTTCGGAGTTGCTGGCAATTCCTTGA-CCTCCTTGGTTCTCAAAGTTACCAGAATTG
1 CC-AAAGTTGCCTGAATTGTTGACAGTTCC-AGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTG
** ** *
3768067 TTGATAGTTATGGTTCCTCCTTGGTTT
64 TTGATAGTTACCGACCCACCTTGGTTT
* * * **
3768094 CCGAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTGCCAAAGTTTCCATTGTTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCA--G-AATT
* * * * **
3768159 GTTGGTAGTT-CCAGATCCAGCTTGCTCG
63 GTTGATAGTTACC-GACCCACCTTGGTTT
** * **** * * * * * *
3768187 CCAAAACCT-CC-GACGTTGTTGTTTTTTCCCGATCCTTCTTGGTTTCCAATGTTGCCTGAATTG
1 CC-AAAGTTGCCTGA-ATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTG
* * *
3768250 TTGATGGTTACTGATCCC-CCTTGGTTA
64 TTGATAGTTACCGA-CCCACCTTGGTTT
* * * *
3768277 CCAAAGTTGCCTGAATTGTTGACAGTTCCTGACCCCCCTTGGTTACCAAAGTTGCCTGAATTGTT
1 CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTGTT
* * * *
3768342 GACAGTTCCCGACCCCCCTTGGTTA
66 GATAGTTACCGACCCACCTTGGTTT
*
3768367 CCAAAGTTGCCTGAATTATTGAC
1 CCAAAGTTGCCTGAATTGTTGAC
3768390 TGTGGCTGAC
Statistics
Matches: 536, Mismatches: 179, Indels: 62
0.69 0.23 0.08
Matches are distributed among these distances:
89 26 0.05
90 421 0.79
91 28 0.05
92 3 0.01
93 55 0.10
94 3 0.01
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34
Consensus pattern (90 bp):
CCAAAGTTGCCTGAATTGTTGACAGTTCCAGACCCTCCTTGGTTCCCAAAGTTGCCAGAATTGTT
GATAGTTACCGACCCACCTTGGTTT
Found at i:3769459 original size:16 final size:16
Alignment explanation
Indices: 3769438--3769488 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
3769428 AATAGATTAT
*
3769438 TTTTATATTTAAGTTA
1 TTTTATATTTAAGTCA
* *
3769454 TTTTATGTTTAGGTCA
1 TTTTATATTTAAGTCA
*
3769470 TTTTA-ATTTTGAGTCA
1 TTTTATA-TTTAAGTCA
3769486 TTT
1 TTT
3769489 AGAGTTTGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.61
Consensus pattern (16 bp):
TTTTATATTTAAGTCA
Found at i:3770174 original size:17 final size:18
Alignment explanation
Indices: 3770148--3770196 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 18
3770138 TTAAACCCAT
3770148 TTATTATTAAAATATTAA
1 TTATTATTAAAATATTAA
3770166 TTA-TATT--AATA-TAA
1 TTATTATTAAAATATTAA
3770180 TTATTATTAAAATATTA
1 TTATTATTAAAATATTA
3770197 GTTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
17 8 0.30
18 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTATTAAAATATTAA
Found at i:3770299 original size:15 final size:15
Alignment explanation
Indices: 3770270--3770327 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
3770260 TTATTTATCA
3770270 TTAA-ATTAATAATTT
1 TTAATATTAAT-ATTT
3770285 TTAATATTAATATTT
1 TTAATATTAATATTT
** *
3770300 CAAATAGTAATA-TT
1 TTAATATTAATATTT
3770314 TTAATGA-TAATATT
1 TTAAT-ATTAATATT
3770328 AATGCTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.29
15 19 0.54
16 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATTAATATTT
Found at i:3770358 original size:18 final size:19
Alignment explanation
Indices: 3770323--3770359 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3770313 TTTAATGATA
3770323 ATATTAATGCTAAAATATT
1 ATATTAATGCTAAAATATT
*
3770342 ATATTAATG-TTAAATATT
1 ATATTAATGCTAAAATATT
3770360 TAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATTAATGCTAAAATATT
Found at i:3770565 original size:30 final size:28
Alignment explanation
Indices: 3770525--3770609 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
3770515 AAATGAAATT
3770525 AATATT-TATTAATTATTATTAAAATAA
1 AATATTATATTAATTATTATTAAAATAA
3770552 ATACTATTATATT-ATATATTATTAAAATATA
1 A-A-TATTATATTAAT-TATTATTAAAATA-A
*
3770583 AATA-TATATTTAA-TAATATTAAAATAA
1 AATATTATA-TTAATTATTATTAAAATAA
3770610 CTAGCAAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
27 2 0.04
28 17 0.34
29 10 0.20
30 19 0.38
31 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
AATATTATATTAATTATTATTAAAATAA
Found at i:3770582 original size:15 final size:15
Alignment explanation
Indices: 3770538--3770582 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
3770528 ATTTATTAAT
*
3770538 TATTATTAAAATAAA
1 TATTATTAAAATATA
* * *
3770553 TACTATTATATTATA
1 TATTATTAAAATATA
3770568 TATTATTAAAATATA
1 TATTATTAAAATATA
3770583 AATATATATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTATTAAAATATA
Found at i:3773520 original size:2 final size:2
Alignment explanation
Indices: 3773513--3773552 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3773503 CCAAATAGTT
3773513 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
3773553 GAGACGAATT
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:3774633 original size:23 final size:23
Alignment explanation
Indices: 3774607--3774662 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3774597 AATAAAACCT
*
3774607 AAACCTATTTAAACCTAAATTAA
1 AAACCTATTTAAACCTAAACTAA
* * * *
3774630 AAACTTATCTAAATCTAAACTAG
1 AAACCTATTTAAACCTAAACTAA
3774653 AAACCTATTT
1 AAACCTATTT
3774663 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (23 bp):
AAACCTATTTAAACCTAAACTAA
Found at i:3775326 original size:12 final size:12
Alignment explanation
Indices: 3775309--3775336 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3775299 ATATTGAAAA
3775309 TTATTATTATTT
1 TTATTATTATTT
3775321 TTATTATTATTT
1 TTATTATTATTT
3775333 TTAT
1 TTAT
3775337 CAAAATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:3776762 original size:12 final size:12
Alignment explanation
Indices: 3776745--3776770 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3776735 ATTGATGGGT
3776745 TTTTTTTTTTTC
1 TTTTTTTTTTTC
3776757 TTTTTTTTTTTC
1 TTTTTTTTTTTC
3776769 TT
1 TT
3776771 GGGTTAAATT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:3780752 original size:2 final size:2
Alignment explanation
Indices: 3780745--3780772 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3780735 TTAATAATAA
3780745 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
3780773 TTAAAGAAGT
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:3780957 original size:3 final size:3
Alignment explanation
Indices: 3780949--3780987 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3780939 TCAAGGTATC
*
3780949 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3780988 GAAGTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3781317 original size:23 final size:24
Alignment explanation
Indices: 3781272--3781325 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
3781262 AATAATACAA
*
3781272 AAAT-TTAATTTAAAAATAATTAT
1 AAATATTAATATAAAAATAATTAT
*
3781295 AAATATTAATATAAAAA-ATTTAT
1 AAATATTAATATAAAAATAATTAT
*
3781318 TAATATTA
1 AAATATTA
3781326 TTAAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATTAATATAAAAATAATTAT
Found at i:3781491 original size:3 final size:3
Alignment explanation
Indices: 3781456--3781503 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
3781446 TATGATTAAA
* *
3781456 AAT AAA AAT AAT -AT AGT AAT AA- AAT AGAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
3781500 AAT A
1 AAT A
3781504 TTTGTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3786783 original size:6 final size:6
Alignment explanation
Indices: 3786766--3786805 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
3786756 TCACACTATA
*
3786766 ATATTAT ATATTT ATATTT ATATTT ATACTT ATATATT AT
1 ATATT-T ATATTT ATATTT ATATTT ATATTT ATAT-TT AT
3786806 TATAATGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 21 0.70
7 9 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (6 bp):
ATATTT
Found at i:3786786 original size:14 final size:13
Alignment explanation
Indices: 3786766--3786803 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
3786756 TCACACTATA
3786766 ATATTATATATTT
1 ATATTATATATTT
3786779 ATATT-TATATTT
1 ATATTATATATTT
3786791 ATACTTATATATT
1 ATA-TTATATATT
3786804 ATTATAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 7 0.30
14 6 0.26
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATTATATATTT
Found at i:3793554 original size:4 final size:4
Alignment explanation
Indices: 3793547--3793572 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3793537 AAAAAAAAAA
3793547 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
3793573 GACCATCCTT
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:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3797134 original size:3 final size:3
Alignment explanation
Indices: 3797126--3797160 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3797116 TTCTTTGCTG
* *
3797126 TTA TTA TTA TTA TTA TTA CTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3797161 TTGAACGCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3798041 original size:1 final size:1
Alignment explanation
Indices: 3798035--3798059 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3798025 GAAAATTTCC
3798035 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3798060 GTGAAGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3801496 original size:20 final size:20
Alignment explanation
Indices: 3801471--3801527 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 20
3801461 AAACATAATT
3801471 TTTAATAATTTAAATTATTA
1 TTTAATAATTTAAATTATTA
3801491 TTTAATAA--TAAATT-TTA
1 TTTAATAATTTAAATTATTA
*
3801508 TTT--TTATTTAAATTTATTA
1 TTTAATAATTTAAA-TTATTA
3801527 T
1 T
3801528 AAAAAGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 2 0.06
17 10 0.31
18 8 0.25
19 4 0.12
20 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATAATTTAAATTATTA
Found at i:3801508 original size:17 final size:19
Alignment explanation
Indices: 3801471--3801510 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3801461 AAACATAATT
3801471 TTTAATAATTTAAATTATTA
1 TTTAATAA-TTAAATTATTA
3801491 TTTAATAA-TAAATT-TTA
1 TTTAATAATTAAATTATTA
3801508 TTT
1 TTT
3801511 TTATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 6 0.30
20 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATAATTAAATTATTA
Found at i:3802421 original size:3 final size:3
Alignment explanation
Indices: 3802413--3802457 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3802403 ACAAAGTGTA
3802413 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3802458 AATATTAGGC
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):
TAT
Found at i:3803436 original size:19 final size:19
Alignment explanation
Indices: 3803381--3803438 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
3803371 CTATTATTAC
*
3803381 AAAAATTTATGATTTTT-A
1 AAAAATATATGATTTTTAA
** *
3803399 AAAAATATAAAATTATTAA
1 AAAAATATATGATTTTTAA
*
3803418 AAAAATATGTGATTTTTAA
1 AAAAATATATGATTTTTAA
3803437 AA
1 AA
3803439 TTTATGAATG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAATATATGATTTTTAA
Found at i:3809790 original size:2 final size:2
Alignment explanation
Indices: 3809783--3809817 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3809773 GATTTCACAA
3809783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3809818 CACACACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3811858 original size:1 final size:1
Alignment explanation
Indices: 3811854--3811908 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
3811844 AATGTGGGGG
* * * * * *
3811854 AAAAAAACAAAAAAACAAAAAAACAAAAAACAAAAAACAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3811909 GAAGAAGAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:3811867 original size:7 final size:7
Alignment explanation
Indices: 3811855--3811901 Score: 69
Period size: 7 Copynumber: 6.6 Consensus size: 7
3811845 ATGTGGGGGA
3811855 AAAAAAC
1 AAAAAAC
3811862 AAAAAAAC
1 -AAAAAAC
3811870 AAAAAAAC
1 -AAAAAAC
3811878 AAAAAAC
1 AAAAAAC
3811885 AAAAAAC
1 AAAAAAC
3811892 AAAAAA-
1 AAAAAAC
3811898 AAAA
1 AAAA
3811902 GAAAAAAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 4 0.10
7 20 0.51
8 15 0.38
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:3811906 original size:23 final size:23
Alignment explanation
Indices: 3811854--3811906 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
3811844 AATGTGGGGG
3811854 AAAAAAACAAAAAAACAAAAAAA
1 AAAAAAACAAAAAAACAAAAAAA
*
3811877 CAAAAAAC-AAAAAACAAAAAAA
1 AAAAAAACAAAAAAACAAAAAAA
3811899 AAAGAAAA
1 AAA-AAAA
3811907 AAGAAGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAAAAACAAAAAAACAAAAAAA
Found at i:3811908 original size:8 final size:8
Alignment explanation
Indices: 3811854--3811898 Score: 76
Period size: 8 Copynumber: 5.9 Consensus size: 8
3811844 AATGTGGGGG
3811854 AAAAAAAC
1 AAAAAAAC
3811862 AAAAAAAC
1 AAAAAAAC
3811870 AAAAAAAC
1 AAAAAAAC
3811878 -AAAAAAC
1 AAAAAAAC
3811885 -AAAAAAC
1 AAAAAAAC
3811892 AAAAAAA
1 AAAAAAA
3811899 AAAGAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 14 0.39
8 22 0.61
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:3821773 original size:24 final size:24
Alignment explanation
Indices: 3821741--3821798 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3821731 TATGATCTAG
* *
3821741 TTTTTTTTTCTTTTTAAAAAATAA
1 TTTTATTTTATTTTTAAAAAATAA
*
3821765 TTTTATTTTATTTTTTAAAAATAA
1 TTTTATTTTATTTTTAAAAAATAA
* *
3821789 CTTAATTTTA
1 TTTTATTTTA
3821799 GGATAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATTTTATTTTTAAAAAATAA
Found at i:3822799 original size:17 final size:17
Alignment explanation
Indices: 3822773--3822818 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3822763 AATTATATTA
3822773 CAAATCATATTATTTAAT
1 CAAAT-ATATTATTTAAT
*
3822791 CAAATATA-TATTTTAT
1 CAAATATATTATTTAAT
*
3822807 AAAATAT-TTATT
1 CAAATATATTATT
3822819 ATATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 17 0.68
17 3 0.12
18 5 0.20
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (17 bp):
CAAATATATTATTTAAT
Found at i:3825302 original size:15 final size:15
Alignment explanation
Indices: 3825253--3825305 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
3825243 AAAAAAATTA
3825253 ATAAA-ATATTAAAT
1 ATAAATATATTAAAT
* * *
3825267 A-AAATATTTTTATT
1 ATAAATATATTAAAT
*
3825281 ATTAATATATTAAAT
1 ATAAATATATTAAAT
3825296 ATAAATATAT
1 ATAAATATAT
3825306 ATATATATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
13 3 0.10
14 8 0.28
15 18 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATATATTAAAT
Found at i:3825834 original size:29 final size:29
Alignment explanation
Indices: 3825751--3825844 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 29
3825741 ATCGAAATTT
*
3825751 ATATAAATATATAATATT-TTAAATATA-A
1 ATATAAATATATAA-ATTATAAAATATACA
* * * **
3825779 TTAT-GATATATAAAAATATATGA-ATACA
1 ATATAAATATAT-AAATTATAAAATATACA
3825807 ATATAAATATATAAATTATAAAATATACCTA
1 ATATAAATATATAAATTATAAAATATA-C-A
3825838 ATATAAA
1 ATATAAA
3825845 GTCGGAAGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
27 11 0.23
28 19 0.40
29 9 0.19
30 1 0.02
31 8 0.17
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (29 bp):
ATATAAATATATAAATTATAAAATATACA
Found at i:3826414 original size:22 final size:22
Alignment explanation
Indices: 3826383--3826424 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3826373 TATAGATTAC
* *
3826383 ATATATATATATATGTAAAAAT
1 ATATACATATATATATAAAAAT
3826405 ATATACATATATATATAAAA
1 ATATACATATATATATAAAA
3826425 TAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATACATATATATATAAAAAT
Found at i:3826430 original size:28 final size:28
Alignment explanation
Indices: 3826380--3826437 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
3826370 TAATATAGAT
* *
3826380 TACATATATATATATATGTAAAAATATA
1 TACATATATATATAAATGAAAAAATATA
3826408 TACATATATATATAAAAT-AAAAAATATA
1 TACATATATATAT-AAATGAAAAAATATA
3826436 TA
1 TA
3826438 TAATATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (28 bp):
TACATATATATATAAATGAAAAAATATA
Found at i:3827452 original size:28 final size:29
Alignment explanation
Indices: 3827421--3827484 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3827411 ATTTGATCTT
* * *
3827421 AAAAATTATTAAATT-TTTTTATAATTAA
1 AAAAATTATTAAATTAATATTACAATTAA
* *
3827449 AAAAAATATTATATTAATATTACAATTAA
1 AAAAATTATTAAATTAATATTACAATTAA
3827478 AAAAATT
1 AAAAATT
3827485 TAAATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAAATTATTAAATTAATATTACAATTAA
Found at i:3827453 original size:29 final size:29
Alignment explanation
Indices: 3827421--3827494 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 29
3827411 ATTTGATCTT
* * * *
3827421 AAAAATTATTAAATT-TTTTTATAATTAA
1 AAAAAATATTAAATTAATATTACAATTAA
*
3827449 AAAAAATATTATATTAATATTACAATT-A
1 AAAAAATATTAAATTAATATTACAATTAA
*
3827477 AAAAAAT-TTAAATAAATA
1 AAAAAATATTAAATTAATA
3827495 ATTATTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 9 0.24
28 21 0.55
29 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAAAATATTAAATTAATATTACAATTAA
Found at i:3829086 original size:14 final size:14
Alignment explanation
Indices: 3829063--3829101 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3829053 TTCAATTTTT
3829063 ATATTATTAAATTTA
1 ATATT-TTAAATTTA
* *
3829078 ATATTTTAATTTTT
1 ATATTTTAAATTTA
3829092 ATATTTTAAA
1 ATATTTTAAA
3829102 GTTTTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTTAAATTTA
Found at i:3829389 original size:29 final size:26
Alignment explanation
Indices: 3829328--3829394 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
3829318 TTTGTTATAA
* *
3829328 TTTTTAAAATATAAAAATTAAAATTT
1 TTTTTAAAATATAAAAACTAAAACTT
3829354 TAATTTTAATAATATAAAAACTAAAGTACTTT
1 T--TTTTAA-AATATAAAAACTAAA--AC-TT
3829386 TTTTTAAAA
1 TTTTTAAAA
3829395 AAAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
26 1 0.03
28 6 0.18
29 16 0.48
30 6 0.18
31 1 0.03
32 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (26 bp):
TTTTTAAAATATAAAAACTAAAACTT
Found at i:3834407 original size:4 final size:4
Alignment explanation
Indices: 3834398--3834423 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3834388 TTCATCATTG
3834398 GGCA GGCA GGCA GGCA GGCA GGCA GG
1 GGCA GGCA GGCA GGCA GGCA GGCA GG
3834424 GCCAGCCTAC
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:0.23, C:0.23, G:0.54, T:0.00
Consensus pattern (4 bp):
GGCA
Found at i:3834751 original size:47 final size:44
Alignment explanation
Indices: 3834700--3834788 Score: 108
Period size: 47 Copynumber: 2.0 Consensus size: 44
3834690 AATTATTATT
*
3834700 TATTAAT-TAAAAAATATTTTATTTAAAATTTAATTATAAAAAATATA
1 TATTAATAT-AAAAATAATTT-TTTAAAATTTAA--ATAAAAAATATA
**
3834747 TATTAATATAAAAATAATTTTTTAATTTTTAAATAAAAAATA
1 TATTAATATAAAAATAATTTTTTAAAATTTAAATAAAAAATA
3834789 AATTTTTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
44 10 0.26
46 10 0.26
47 17 0.45
48 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
TATTAATATAAAAATAATTTTTTAAAATTTAAATAAAAAATATA
Found at i:3836325 original size:17 final size:17
Alignment explanation
Indices: 3836295--3836335 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
3836285 TCTAAAAAAT
3836295 ATAAT-AAT-AAATATCA
1 ATAATAAATAAAATAT-A
3836311 ATAA-AAATAAAATATA
1 ATAATAAATAAAATATA
3836327 ATAATAAAT
1 ATAATAAAT
3836336 TTTAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAATAAATAAAATATA
Found at i:3836327 original size:13 final size:13
Alignment explanation
Indices: 3836290--3836334 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
3836280 TTTACTCTAA
3836290 AAAATATAATAAT
1 AAAATATAATAAT
*
3836303 AAATATCAATAAAAAT
1 AAA-AT--ATAATAAT
3836319 AAAATATAATAAT
1 AAAATATAATAAT
3836332 AAA
1 AAA
3836335 TTTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 13 0.48
14 2 0.07
15 2 0.07
16 10 0.37
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:3836982 original size:2 final size:2
Alignment explanation
Indices: 3836977--3837002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3836967 CAAAAAAATC
3836977 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
3837003 CAACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3837996 original size:24 final size:24
Alignment explanation
Indices: 3837956--3838001 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3837946 ATTTACTTAT
3837956 AAAATTTTAAAATTTATATTAATAA
1 AAAATTTTAAAATTTAT-TTAATAA
*
3837981 AAAATTTTAATA-TTATTTAAT
1 AAAATTTTAAAATTTATTTAAT
3838002 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATTTTAAAATTTATTTAATAA
Found at i:3838026 original size:28 final size:26
Alignment explanation
Indices: 3837995--3838050 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
3837985 TTTTAATATT
3837995 ATTTAATTTAAATTTAAAT-AATATATAA
1 ATTTAATTTAAA--T-AATCAATATATAA
*
3838023 ATTTATTTTAAATAATCAATATATAA
1 ATTTAATTTAAATAATCAATATATAA
3838049 AT
1 AT
3838051 ATTCAATTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 12 0.46
28 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAATTTAAATAATCAATATATAA
Found at i:3838132 original size:2 final size:2
Alignment explanation
Indices: 3838125--3838153 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3838115 AAGAGGCAGT
3838125 GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3838154 TCTGGCAGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3839074 original size:13 final size:13
Alignment explanation
Indices: 3839058--3839106 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3839048 TTTAATTTAA
*
3839058 TAAAATAATATAT
1 TAAAATAATATTT
*
3839071 TAAATATAAAATTT
1 TAAA-ATAATATTT
* *
3839085 TTAATTAATATTT
1 TAAAATAATATTT
3839098 TAAAATAAT
1 TAAAATAAT
3839107 GAATAGAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATAATATTT
Found at i:3846921 original size:20 final size:20
Alignment explanation
Indices: 3846876--3846918 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3846866 AAAATATTTT
*
3846876 AAAATTTTTTTTATAAGTGA
1 AAAATATTTTTTATAAGTGA
*
3846896 AAAATATTTTTTATTA-TGA
1 AAAATATTTTTTATAAGTGA
3846915 AAAA
1 AAAA
3846919 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AAAATATTTTTTATAAGTGA
Found at i:3847371 original size:7 final size:7
Alignment explanation
Indices: 3847361--3847440 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
3847351 GGGTTTAAGA
3847361 TTAAAAT
1 TTAAAAT
3847368 TTAAAAT
1 TTAAAAT
**
3847375 TTATCAT
1 TTAAAAT
*
3847382 TTAAGAT
1 TTAAAAT
*
3847389 TTAATAT
1 TTAAAAT
3847396 TTAAAAT
1 TTAAAAT
3847403 TTAAAAT
1 TTAAAAT
**
3847410 TTATGAT
1 TTAAAAT
* *
3847417 TTCATAT
1 TTAAAAT
*
3847424 TCAAAAT
1 TTAAAAT
*
3847431 TTAAGAT
1 TTAAAAT
3847438 TTA
1 TTA
3847441 GATTTAGTAT
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (7 bp):
TTAAAAT
Found at i:3847401 original size:28 final size:28
Alignment explanation
Indices: 3847354--3847452 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 28
3847344 ATTTTTAGGG
* **
3847354 TTTAAGA-TTAAAATTTAAAATTTATCA
1 TTTAAGATTTAATATTTAAAATTTAAAA
3847381 TTTAAGATTTAATATTTAAAATTTAAAA
1 TTTAAGATTTAATATTTAAAATTTAAAA
* * * *
3847409 TTTATGATTTCATATTCAAAATTTAAGA
1 TTTAAGATTTAATATTTAAAATTTAAAA
*
3847437 TTT-AGATTTAGTATTT
1 TTTAAGATTTAATATTT
3847453 TAATAAAATA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.27
28 44 0.73
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTAAGATTTAATATTTAAAATTTAAAA
Found at i:3848015 original size:30 final size:29
Alignment explanation
Indices: 3847965--3848021 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
3847955 ATTAATTAAA
* *
3847965 AAATAATTATATATATTTATTATATTTTT
1 AAATAATTATATAAATTTATTAAATTTTT
*
3847994 AAATTATTATTATAAATTTATTAAATTT
1 AAATAATTA-TATAAATTTATTAAATTT
3848022 ATATATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATAATTATATAAATTTATTAAATTTTT
Found at i:3848778 original size:17 final size:16
Alignment explanation
Indices: 3848739--3848772 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3848729 TGAGGAAACT
*
3848739 GAAAAGAAAAAGAAAA
1 GAAAGGAAAAAGAAAA
3848755 GAAAGGAAAAA-AAAA
1 GAAAGGAAAAAGAAAA
3848770 GAA
1 GAA
3848773 GAAGGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAGGAAAAAGAAAA
Found at i:3853218 original size:18 final size:18
Alignment explanation
Indices: 3853192--3853263 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
3853182 AATGGGTGAA
*
3853192 TATTTATATAATATAAAT
1 TATTAATATAATATAAAT
*
3853210 TATTAATATATTA-AAATT
1 TATTAATATAATATAAA-T
3853228 TATATAATATATAATATAAA-
1 TAT-T-A-ATATAATATAAAT
*
3853248 TATAAATATAA-ATAAA
1 TATTAATATAATATAAA
3853264 AGTTATTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
16 5 0.11
17 9 0.20
18 16 0.36
19 1 0.02
20 4 0.09
21 7 0.16
22 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTAATATAATATAAAT
Found at i:3853237 original size:17 final size:17
Alignment explanation
Indices: 3853193--3853237 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3853183 ATGGGTGAAT
3853193 ATTTATATAATA-TAAA
1 ATTTATATAATATTAAA
*
3853209 TTATTA-AT-ATATTAAA
1 AT-TTATATAATATTAAA
3853225 ATTTATATAATAT
1 ATTTATATAATAT
3853238 ATAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTATATAATATTAAA
Found at i:3853251 original size:6 final size:6
Alignment explanation
Indices: 3853228--3853261 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
3853218 TATTAAAATT
3853228 TATATAA TATATAA TATAAA TATAAA TATAAA TA
1 TATA-AA TATA-AA TATAAA TATAAA TATAAA TA
3853262 AAAGTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 16 0.59
7 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TATAAA
Found at i:3853281 original size:57 final size:58
Alignment explanation
Indices: 3853196--3853309 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 58
3853186 GGTGAATATT
3853196 TATATAATATAAATTATTAATATATTAAAATTTATATAATATATAATATAAATATAAA
1 TATATAATATAAATTATTAATATATTAAAATTTATATAATATATAATATAAATATAAA
* * *
3853254 TATA-AATA-AAAGTTATTAGTATTTTAAAATTTATATAATATATAATTTAAATATAA
1 TATATAATATAAA-TTATTAATATATTAAAATTTATATAATATATAATATAAATATAA
3853310 TGATGATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 3 0.06
57 45 0.87
58 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (58 bp):
TATATAATATAAATTATTAATATATTAAAATTTATATAATATATAATATAAATATAAA
Found at i:3853347 original size:19 final size:18
Alignment explanation
Indices: 3853323--3853361 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
3853313 TGATATAAAA
3853323 ATAAATAAATTTATATTAT
1 ATAAATAAATTTA-ATTAT
3853342 ATAAATAAATTTAATTAT
1 ATAAATAAATTTAATTAT
3853360 AT
1 AT
3853362 TTTATCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATAAATTTAATTAT
Found at i:3853366 original size:25 final size:23
Alignment explanation
Indices: 3853316--3853374 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
3853306 ATAATGATGA
*
3853316 TATAAAAATAAATAAATTTATAT
1 TATATAAATAAATAAATTTATAT
* *
3853339 TATATAAATAAATTTAATTATATTT
1 TATATAAATAAA-TAAATT-TATAT
*
3853364 TATCTAAATAA
1 TATATAAATAA
3853375 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 11 0.37
24 5 0.17
25 14 0.47
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATAAATAAATAAATTTATAT
Found at i:3857250 original size:9 final size:9
Alignment explanation
Indices: 3857232--3857334 Score: 56
Period size: 9 Copynumber: 11.2 Consensus size: 9
3857222 TTAATTTAAA
3857232 ATATTTTAT
1 ATATTTTAT
3857241 AT-TTTATAT
1 ATATTT-TAT
*
3857250 AAATTTTA-
1 ATATTTTAT
*
3857258 ATATATTA-
1 ATATTTTAT
3857266 ATAATTTATAAT
1 AT-ATTT-T-AT
*
3857278 ATATATTTAAA
1 ATAT-TTT-AT
3857289 ATATTTTAT
1 ATATTTTAT
*
3857298 AT-TTATAT
1 ATATTTTAT
3857306 -TA-TTTAT
1 ATATTTTAT
3857313 ATTATTTTATT
1 A-TATTTTA-T
3857324 ATATTTTAT
1 ATATTTTAT
3857333 AT
1 AT
3857335 TATATTTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
7 5 0.07
8 16 0.22
9 19 0.26
10 18 0.24
11 12 0.16
12 4 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTTTAT
Found at i:3857314 original size:22 final size:22
Alignment explanation
Indices: 3857289--3857394 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
3857279 TATATTTAAA
3857289 ATATTTTATATTTATATTATTT
1 ATATTTTATATTTATATTATTT
*
3857311 ATATTATTTTA-TTATA-T-TTT
1 ATATT-TTATATTTATATTATTT
* *
3857331 ATATTATAT-TTTA-ATTTTTT
1 ATATTTTATATTTATATTATTT
* *
3857351 -TAATGTCATATTTATATTATTT
1 AT-ATTTTATATTTATATTATTT
*
3857373 TTATTTTATATTTAATATTATT
1 ATATTTTATATTT-ATATTATT
3857395 AAGTTTAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
18 1 0.02
19 7 0.11
20 15 0.23
21 5 0.08
22 25 0.38
23 13 0.20
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (22 bp):
ATATTTTATATTTATATTATTT
Found at i:3857317 original size:20 final size:20
Alignment explanation
Indices: 3857294--3857394 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3857284 TTAAAATATT
3857294 TTATATTTATATTATTTATA
1 TTATATTTATATTATTTATA
3857314 TTAT-TTTAT-TATATTTTATA
1 TTATATTTATAT-TA-TTTATA
*
3857334 TTATATTT-TAATT-TTTTTAA
1 TTATATTTAT-ATTATTTAT-A
*
3857354 TGTCATATTTATATTATTTTTATT
1 T-T-ATATTTATATTA--TTTATA
3857378 TTATATTTAATATTATT
1 TTATATTT-ATATTATT
3857395 AAGTTTAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
18 1 0.02
19 11 0.17
20 17 0.26
21 7 0.11
22 16 0.25
23 8 0.12
24 1 0.02
25 4 0.06
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (20 bp):
TTATATTTATATTATTTATA
Found at i:3857379 original size:5 final size:5
Alignment explanation
Indices: 3857290--3857386 Score: 54
Period size: 5 Copynumber: 18.4 Consensus size: 5
3857280 ATATTTAAAA
* * *
3857290 TATTT TATATT TATAT TA-TT TATAT TATTT TATTA TATTT TATATT ATATTT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT -TATTT
* * * *
3857342 TAATTT T-TTT AATGT CATATT TATAT TATTTT TATTT TATATT TA
1 T-ATTT TATTT TATTT TAT-TT TATTT TA-TTT TATTT TAT-TT TA
3857387 ATATTATTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
4 6 0.09
5 36 0.51
6 25 0.36
7 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (5 bp):
TATTT
Found at i:3857575 original size:20 final size:18
Alignment explanation
Indices: 3857529--3857576 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
3857519 TAAAATTAAC
*
3857529 ATATTTATTATATTTATT
1 ATATTTTTTATATTTATT
* *
3857547 AAATATTTTATATTTATATT
1 ATATTTTTTATA-TT-TATT
3857567 ATATTTTTTA
1 ATATTTTTTA
3857577 CAAATAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 9 0.39
19 2 0.09
20 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATTTTTTATATTTATT
Found at i:3858290 original size:3 final size:3
Alignment explanation
Indices: 3858284--3858326 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3858274 TATGAAGTAG
3858284 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3858327 GTTTTAATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3859897 original size:18 final size:19
Alignment explanation
Indices: 3859870--3859910 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3859860 TTTTTTAAAG
*
3859870 AAAAGTTTA-TAGTTTTTT
1 AAAAGGTTATTAGTTTTTT
*
3859888 AAAAGGTTATTATTTTTTT
1 AAAAGGTTATTAGTTTTTT
3859907 AAAA
1 AAAA
3859911 TTATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (19 bp):
AAAAGGTTATTAGTTTTTT
Found at i:3868825 original size:4 final size:4
Alignment explanation
Indices: 3868816--3868869 Score: 81
Period size: 4 Copynumber: 13.5 Consensus size: 4
3868806 TAGATATGGA
* *
3868816 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
3868864 GTAT AT
1 ATAT AT
3868870 TTATGTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:3868827 original size:6 final size:6
Alignment explanation
Indices: 3868816--3868869 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
3868806 TAGATATGGA
* *
3868816 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATGTAT GTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
3868864 GTATAT
1 ATATAT
3868870 TTATGTCAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:3868831 original size:10 final size:10
Alignment explanation
Indices: 3868816--3868869 Score: 81
Period size: 10 Copynumber: 5.4 Consensus size: 10
3868806 TAGATATGGA
3868816 ATATATATAT
1 ATATATATAT
3868826 ATATATATAT
1 ATATATATAT
3868836 ATATATATAT
1 ATATATATAT
*
3868846 ATATATATGT
1 ATATATATAT
* *
3868856 ATGTATATGT
1 ATATATATAT
3868866 ATAT
1 ATAT
3868870 TTATGTCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:3871823 original size:20 final size:23
Alignment explanation
Indices: 3871792--3871835 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
3871782 AAGAGTGATC
3871792 TTTTTAAGGAGG-ATTGAT-TTT
1 TTTTTAAGGAGGAATTGATATTT
3871813 TTTTTAA-GAGGAATTGATATTT
1 TTTTTAAGGAGGAATTGATATTT
3871835 T
1 T
3871836 ATAAGGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (23 bp):
TTTTTAAGGAGGAATTGATATTT
Found at i:3871834 original size:23 final size:21
Alignment explanation
Indices: 3871792--3871843 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3871782 AAGAGTGATC
3871792 TTTTTAAGGAGGATTGATTTT
1 TTTTTAAGGAGGATTGATTTT
*
3871813 TTTTTAA-GAGGAATTGA-TAT
1 TTTTTAAGGAGG-ATTGATTTT
*
3871833 TTTATAAGGAG
1 TTTTTAAGGAG
3871844 TTATCACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
TTTTTAAGGAGGATTGATTTT
Found at i:3872437 original size:2 final size:2
Alignment explanation
Indices: 3872432--3872468 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3872422 GTGTGTGTCC
3872432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3872469 GTGCAACACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3873430 original size:2 final size:2
Alignment explanation
Indices: 3873423--3873469 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3873413 GCACACCAAA
3873423 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3873465 AG AG A
1 AG AG A
3873470 ATAGGTAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3874201 original size:18 final size:19
Alignment explanation
Indices: 3874168--3874203 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3874158 AATGATGATG
3874168 CCAACTGATAGCCATCCAA
1 CCAACTGATAGCCATCCAA
*
3874187 CCAACT-ATAGTCATCCA
1 CCAACTGATAGCCATCCA
3874204 TCACTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.36, G:0.08, T:0.19
Consensus pattern (19 bp):
CCAACTGATAGCCATCCAA
Found at i:3879743 original size:23 final size:21
Alignment explanation
Indices: 3879702--3879743 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3879692 TTTATAATTA
*
3879702 TTTTTAATTATAAATTTATTT
1 TTTTTAATTATAAAATTATTT
3879723 TTTTTAAATTGATAAAATTAT
1 TTTTT-AATT-ATAAAATTAT
3879744 ATTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTAATTATAAAATTATTT
Found at i:3880272 original size:26 final size:25
Alignment explanation
Indices: 3880194--3880272 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 25
3880184 TTTTAAATGT
* * *
3880194 AAAAATTAAAAT-TTTTATATGATA
1 AAAAATTAATATATATTATATAATA
3880218 AAAAA-TACATA-ATA-TATATAAATA
1 AAAAATTA-ATATATATTATAT-AATA
*
3880242 TAAAATTAATATATATTATATAATTA
1 AAAAATTAATATATATTATATAA-TA
3880268 AAAAA
1 AAAAA
3880273 AGAGTCAGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
23 7 0.16
24 18 0.42
25 7 0.16
26 11 0.26
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (25 bp):
AAAAATTAATATATATTATATAATA
Found at i:3881942 original size:2 final size:2
Alignment explanation
Indices: 3881935--3881963 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3881925 AACCCAACAC
3881935 AG AG 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 AG AG A
3881964 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3882968 original size:1 final size:1
Alignment explanation
Indices: 3882964--3882990 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3882954 CTTAATTGAG
3882964 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3882991 CCAATTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3889671 original size:3 final size:3
Alignment explanation
Indices: 3889663--3889702 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3889653 TAACTAAATT
*
3889663 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3889703 ACCCTTGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Done.