Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 19 of 100
Found at i:3690389 original size:16 final size:15
Alignment explanation
Indices: 3690343--3690389 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
3690333 AAAGAAATTT
3690343 TTATATAATATTTAAA
1 TTATATAATATTT-AA
*
3690359 TTATA-AATTTATTAA
1 TTATATAATAT-TTAA
3690374 TTAATATAATATTTAA
1 TT-ATATAATATTTAA
3690390 AAAATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.31
16 14 0.54
17 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATAATATTTAA
Found at i:3698631 original size:18 final size:18
Alignment explanation
Indices: 3698608--3698653 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3698598 GATCAATAAT
*
3698608 TTCTTGAAACTTTTTGAA
1 TTCTTGAAACTTTTTAAA
*
3698626 TTCTTGACACTTTTTAAA
1 TTCTTGAAACTTTTTAAA
3698644 TTCTTTGAAA
1 TTC-TTGAAA
3698654 AACAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (18 bp):
TTCTTGAAACTTTTTAAA
Found at i:3702447 original size:114 final size:114
Alignment explanation
Indices: 3702242--3702587 Score: 611
Period size: 114 Copynumber: 3.0 Consensus size: 114
3702232 TTGGCCAAGT
* *
3702242 TTGAGTGGGTATGCTAGTGCCGGTGGATGGAGGCTGTTGAGTAATTCCAGGAGCAGATTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
3702307 CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
66 CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
*
3702356 TTGAATGGGTATGCTTGTGCCGGTGGATGGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
3702421 CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
66 CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
** * *
3702470 TTGAGTGGGTATGCTTGCACCGTTGGATTGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
1 TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
* *
3702535 CAGCAGCCATCAGAATGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
66 CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
3702584 TTGA
1 TTGA
3702588 TGCATTGCAA
Statistics
Matches: 222, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 222 1.00
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.29
Consensus pattern (114 bp):
TTGAGTGGGTATGCTTGTGCCGGTGGATGGAGGCTGTTGAGTATTTCCAGGAGCAGATTTAGCTG
CAGCAGCCATGAGAAGGGACTGTTGCTGTGCTAGGAAAGCTAGTTGTTG
Found at i:3703722 original size:48 final size:48
Alignment explanation
Indices: 3703643--3703737 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
3703633 TTATTCACAT
3703643 AAAACACATTAAGAAGAAAAACGAATAACTGTGGTTTTCTAGAAGAGC
1 AAAACACATTAAGAAGAAAAACGAATAACTGTGGTTTTCTAGAAGAGC
* *
3703691 AAAACACATTAAGAAGAAAAATGAATGACTGTGGTTTTCTAGAAGAG
1 AAAACACATTAAGAAGAAAAACGAATAACTGTGGTTTTCTAGAAGAG
3703738 TTAAAAACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (48 bp):
AAAACACATTAAGAAGAAAAACGAATAACTGTGGTTTTCTAGAAGAGC
Found at i:3707212 original size:20 final size:20
Alignment explanation
Indices: 3707150--3707216 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
3707140 TACCACAACC
*
3707150 AAACAAATTTAAAA-AAAA-
1 AAACAAATTCAAAAGAAAAT
* * * *
3707168 AAAAAAACTCTAAACGAATAT
1 AAACAAATTC-AAAAGAAAAT
3707189 AAACAAATTCAAAAGAAAAT
1 AAACAAATTCAAAAGAAAAT
3707209 AAACAAAT
1 AAACAAAT
3707217 CTTACAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 7 0.19
19 3 0.08
20 19 0.51
21 8 0.22
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.16
Consensus pattern (20 bp):
AAACAAATTCAAAAGAAAAT
Found at i:3721204 original size:15 final size:15
Alignment explanation
Indices: 3721180--3721224 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
3721170 ATCAATGTTC
3721180 CCACCTCCACCACCA
1 CCACCTCCACCACCA
* *
3721195 CCAGCTCCACCTCCA
1 CCACCTCCACCACCA
* *
3721210 CTACCGCCACCACCA
1 CCACCTCCACCACCA
3721225 TTAAACCCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.62, G:0.04, T:0.09
Consensus pattern (15 bp):
CCACCTCCACCACCA
Found at i:3739417 original size:21 final size:20
Alignment explanation
Indices: 3739393--3739431 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3739383 GAATTTGAAT
*
3739393 AATTTCAAAATGAAATTATTA
1 AATTT-AAAATCAAATTATTA
*
3739414 AATTTTAAATCAAATTAT
1 AATTTAAAATCAAATTAT
3739432 ATTTATGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
AATTTAAAATCAAATTATTA
Found at i:3750553 original size:16 final size:16
Alignment explanation
Indices: 3750492--3750553 Score: 74
Period size: 17 Copynumber: 3.9 Consensus size: 16
3750482 AAAAATGATG
*
3750492 GAAAAAATGAAAAAAT
1 GAAAAAATGAAAAAAA
3750508 GAAAAAATGGAAAAAATA
1 GAAAAAAT-GAAAAAA-A
3750526 -AAAAAATG-AAAAAA
1 GAAAAAATGAAAAAAA
*
3750540 GAAAAAGTGAAAAA
1 GAAAAAATGAAAAA
3750554 GGAGGACTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.30
16 13 0.32
17 14 0.35
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (16 bp):
GAAAAAATGAAAAAAA
Found at i:3750554 original size:8 final size:8
Alignment explanation
Indices: 3750455--3750553 Score: 98
Period size: 8 Copynumber: 12.6 Consensus size: 8
3750445 ACTATGCTTA
*
3750455 AAAAAATT
1 AAAAAATG
*
3750463 AAAAAATA
1 AAAAAATG
3750471 AAAAAATG
1 AAAAAATG
3750479 -AAAAA--
1 AAAAAATG
**
3750484 AAATGATGG
1 AAAAAAT-G
3750493 AAAAAATG
1 AAAAAATG
3750501 AAAAAATG
1 AAAAAATG
3750509 AAAAAATGG
1 AAAAAAT-G
*
3750518 AAAAAATA
1 AAAAAATG
3750526 AAAAAATG
1 AAAAAATG
3750534 AAAAAA-G
1 AAAAAATG
*
3750541 AAAAAGTG
1 AAAAAATG
3750549 AAAAA
1 AAAAA
3750554 GGAGGACTCA
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
6 3 0.04
7 11 0.14
8 49 0.64
9 13 0.17
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:3751697 original size:42 final size:42
Alignment explanation
Indices: 3751546--3751794 Score: 283
Period size: 42 Copynumber: 6.0 Consensus size: 42
3751536 GTCAATGAGT
* * * *
3751546 AATTTACTTTTC-AAAGTCGTGGTGCCT-TGTTTAGAGGAGC
1 AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* * * * * * * *
3751586 AATTTA-CTTTCCAAAGTCATGGTGCCTCTGTTTAGAGTAGT
1 AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
3751627 AATTTATTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC
1 AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
*
3751668 CATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
1 AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* * *
3751710 TATTTATTTTTTTAAAGTCGTTGAGCCTTTGATTAGAGGAGC
1 AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
* *
3751752 CATTT-TTGTTTCTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
1 AATTTATT-TTTCT-AAAGTCGTTGAGCCTCTGATTAGAGGAGC
3751795 TTTGATCAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.02
40 20 0.11
41 53 0.29
42 80 0.43
43 27 0.15
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.39
Consensus pattern (42 bp):
AATTTATTTTTCTAAAGTCGTTGAGCCTCTGATTAGAGGAGC
Found at i:3751747 original size:84 final size:84
Alignment explanation
Indices: 3751545--3751795 Score: 314
Period size: 84 Copynumber: 3.0 Consensus size: 84
3751535 TGTCAATGAG
* * * * * * * * *
3751545 TAATTTACTTTTCAAAGTCGTGGTGCC-TTGTTTAGAGGAGCAATTTA-CTTTCCAAAGTCATGG
1 TAATTTATTTTTCAAAGTCGTTGAGCCTTTGATTAGAGGAGCCATTTATTTTTCTAAAGTCGTTG
* *
3751608 TGCCTCTGTTTAGAGTAG-
66 AGCCTCTGTTTAGAGGAGC
*
3751626 TAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCATTTATTTTTCTAAAGTCGTTG
1 TAATTTATTTTTCAAAGTCGTTGAGCCTTTGATTAGAGGAGCCATTTATTTTTCTAAAGTCGTTG
*
3751691 AGCCTCTGATTAGAGGAGC
66 AGCCTCTGTTTAGAGGAGC
*
3751710 T-ATTTATTTTTTTAAAGTCGTTGAGCCTTTGATTAGAGGAGCCATTT-TTGTTTCTCAAAGTCG
1 TAATTTA-TTTTTCAAAGTCGTTGAGCCTTTGATTAGAGGAGCCATTTATT-TTTCT-AAAGTCG
3751773 TTGAGCCTCTGTTTAGAGGAGC
63 TTGAGCCTCTGTTTAGAGGAGC
3751795 T
1 T
3751796 TTGATCAAAA
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
81 24 0.16
82 17 0.11
83 34 0.23
84 44 0.30
85 29 0.20
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (84 bp):
TAATTTATTTTTCAAAGTCGTTGAGCCTTTGATTAGAGGAGCCATTTATTTTTCTAAAGTCGTTG
AGCCTCTGTTTAGAGGAGC
Found at i:3752013 original size:6 final size:6
Alignment explanation
Indices: 3752002--3752052 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
3751992 TTTCTCTTCA
*
3752002 TTTTAT TTTTATTT TTTTAT TTTACAT TTTTA- TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTA--T TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTAT
3752052 T
1 T
3752053 ATTTTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 5 0.13
6 23 0.59
7 5 0.13
8 6 0.15
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:3752017 original size:26 final size:25
Alignment explanation
Indices: 3751976--3752043 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
3751966 GTAAGTCTGT
*
3751976 ATTTTTTTTTCTTTTTTT-TCTCTT-C
1 ATTTTTTTTTATTTTTTTAT-T-TTAC
3752001 ATTTTATTTTTATTTTTTTATTTTAC
1 ATTTT-TTTTTATTTTTTTATTTTAC
3752027 ATTTTTATTTTATTTTT
1 ATTTTT-TTTTATTTTT
3752044 ATTTTTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 8 0.21
26 29 0.76
27 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.79
Consensus pattern (25 bp):
ATTTTTTTTTATTTTTTTATTTTAC
Found at i:3752105 original size:12 final size:12
Alignment explanation
Indices: 3752031--3752115 Score: 52
Period size: 12 Copynumber: 7.1 Consensus size: 12
3752021 TTTTACATTT
*
3752031 TTATT-TTATTT
1 TTATTATTATTA
*
3752042 TTATTTTTATTA
1 TTATTATTATTA
3752054 TT-TTATATATGTA
1 TTATTAT-TAT-TA
* *
3752067 TATATATATTTTTC
1 T-TAT-TATTATTA
*
3752081 TT-TTCTT-TTA
1 TTATTATTATTA
3752091 TTATTATTATTA
1 TTATTATTATTA
*
3752103 TTATTATTTTTA
1 TTATTATTATTA
3752115 T
1 T
3752116 CTTAGATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
10 4 0.07
11 15 0.26
12 26 0.45
13 4 0.07
14 3 0.05
15 3 0.05
16 3 0.05
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:3753145 original size:5 final size:5
Alignment explanation
Indices: 3753123--3753264 Score: 71
Period size: 5 Copynumber: 28.2 Consensus size: 5
3753113 TATTTATTTG
* ** * * *
3753123 TTTAT TTGT-T TTTTT TTTAT TTTA- TTTAT TAGA- TTAAG TTTAT TTAAT
1 TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* * * * *
3753171 ATTCT TTTAT CTTTAT TTTATT TTTATT TTTGT TTTACT TTTCT TTT-C
1 TTTAT TTTAT -TTTAT TTTA-T TTTA-T TTTAT TTTA-T TTTAT TTTAT
*
3753219 TTTAT TTTAT TTTA- TTTA- TTTAT TTTCACT TTTAT TTTGT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT-A-T TTTAT TTTAT TTTAT T
3753265 ATTCTATTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 22
0.72 0.14 0.15
Matches are distributed among these distances:
4 18 0.17
5 62 0.58
6 22 0.21
7 4 0.04
ACGTcount: A:0.18, C:0.05, G:0.04, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:3753255 original size:30 final size:30
Alignment explanation
Indices: 3753219--3753275 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3753209 TTTTCTTTTC
3753219 TTTATTTTATTTTATTTATT-TATTTTCACT
1 TTTATTTTATTTTA-TTATTCTATTTTCACT
*
3753249 TTTATTTTGTTTTATTATTCTATTTTC
1 TTTATTTTATTTTATTATTCTATTTTC
3753276 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTTATTATTCTATTTTCACT
Found at i:3753361 original size:59 final size:58
Alignment explanation
Indices: 3753293--3753508 Score: 257
Period size: 58 Copynumber: 3.7 Consensus size: 58
3753283 AAAAAATCAA
*
3753293 AAAACAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAGTTTTC
1 AAAACAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTT-AAAAT-AAAGTTTTC
*
3753353 AAAA-AATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTT--AATAAA-TTTTC
1 AAAACAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAGTTTTC
* * * *
3753407 AAAAAAAATAAATTTTT-GAGGAAAAGTTGAAAATATCAATTTTCCTCAAAATTAAAG-TTTC
1 -AAAACAAT--ATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTTCTTAAAA-TAAAGTTTTC
*
3753468 AAAAGAATATTTTT-GAGAAAAGTTGAAAGTATCAATTTTTC
1 AAAACAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTC
3753509 CTGCAAAAAA
Statistics
Matches: 140, Mismatches: 7, Indels: 21
0.83 0.04 0.12
Matches are distributed among these distances:
54 5 0.04
55 7 0.05
56 6 0.04
57 25 0.18
58 39 0.28
59 37 0.26
60 13 0.09
61 8 0.06
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (58 bp):
AAAACAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAGTTTTC
Found at i:3755338 original size:15 final size:16
Alignment explanation
Indices: 3755318--3755369 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
3755308 TATAAACTAT
3755318 TTATTATTAT-TGTT-G
1 TTATTATTATGT-TTAG
3755333 TTATTATTATGTTTAG
1 TTATTATTATGTTTAG
*
3755349 TTATTATT-T-TTTAT
1 TTATTATTATGTTTAG
3755363 TTATTAT
1 TTATTAT
3755370 ATTGTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.32
15 13 0.38
16 10 0.29
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (16 bp):
TTATTATTATGTTTAG
Found at i:3755763 original size:19 final size:18
Alignment explanation
Indices: 3755735--3755770 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
3755725 TCTCAGCATC
3755735 AAAAAAAAAAAGAAAAAG
1 AAAAAAAAAAAGAAAAAG
3755753 AAAAGAAAAAAAGAAAAA
1 AAAA-AAAAAAAGAAAAA
3755771 AATTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAAAG
Found at i:3756579 original size:14 final size:13
Alignment explanation
Indices: 3756552--3756591 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
3756542 TTAAATTTGA
3756552 AAAAAGTAATAAAT
1 AAAAA-TAATAAAT
*
3756566 TAAAATAATGAAAT
1 AAAAATAAT-AAAT
3756580 AAAAATAATAAA
1 AAAAATAATAAA
3756592 AATGTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAAAATAATAAAT
Found at i:3756916 original size:17 final size:17
Alignment explanation
Indices: 3756894--3756926 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3756884 ATTTTATTCT
*
3756894 TATTTTTTATTTTTTTG
1 TATTTTGTATTTTTTTG
3756911 TATTTTGTATTTTTTT
1 TATTTTGTATTTTTTT
3756927 TCTTTTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (17 bp):
TATTTTGTATTTTTTTG
Found at i:3757291 original size:11 final size:11
Alignment explanation
Indices: 3757277--3757301 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3757267 TGGCTTTTTT
3757277 TTTTTGAAAAA
1 TTTTTGAAAAA
3757288 TTTTTGAAAAA
1 TTTTTGAAAAA
3757299 TTT
1 TTT
3757302 CCAAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTTTGAAAAA
Found at i:3757978 original size:14 final size:15
Alignment explanation
Indices: 3757952--3757998 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3757942 ATTTAGTTTC
*
3757952 AAACAAAAAAATATA
1 AAACATAAAAATATA
* *
3757967 AAATAT-AAAATAAA
1 AAACATAAAAATATA
3757981 AAACATAAAAATATA
1 AAACATAAAAATATA
3757996 AAA
1 AAA
3757999 ATTTTGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACATAAAAATATA
Found at i:3757981 original size:22 final size:22
Alignment explanation
Indices: 3757956--3757998 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3757946 AGTTTCAAAC
3757956 AAAAAA-ATATAAAATATAAAAT
1 AAAAAACATA-AAAATATAAAAT
3757978 AAAAAACATAAAAATATAAAA
1 AAAAAACATAAAAATATAAAA
3757999 ATTTTGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAAAACATAAAAATATAAAAT
Found at i:3757996 original size:8 final size:8
Alignment explanation
Indices: 3757958--3758000 Score: 56
Period size: 7 Copynumber: 5.8 Consensus size: 8
3757948 TTTCAAACAA
3757958 AAAAATAT
1 AAAAATAT
3757966 -AAAATAT
1 AAAAATAT
3757973 -AAAATA-
1 AAAAATAT
*
3757979 AAAAACAT
1 AAAAATAT
3757987 AAAAATAT
1 AAAAATAT
3757995 AAAAAT
1 AAAAAT
3758001 TTTGGAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAATAT
Found at i:3762112 original size:22 final size:22
Alignment explanation
Indices: 3762084--3762132 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3762074 TGATCCTTTG
3762084 GTTTTGAACCCTTTAAACACAT
1 GTTTTGAACCCTTTAAACACAT
**
3762106 GTTTTGAGTCCTTTAAACACAT
1 GTTTTGAACCCTTTAAACACAT
3762128 GTTTT
1 GTTTT
3762133 AAGCCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (22 bp):
GTTTTGAACCCTTTAAACACAT
Found at i:3762373 original size:9 final size:9
Alignment explanation
Indices: 3762351--3762383 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3762341 AGTGAAAGAG
3762351 GAAAAAAA-
1 GAAAAAAAT
3762359 GAAAAAGAAT
1 GAAAAA-AAT
3762369 GAAAAAAAT
1 GAAAAAAAT
3762378 GAAAAA
1 GAAAAA
3762384 TGAAAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 11 0.48
10 6 0.26
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:3762381 original size:34 final size:34
Alignment explanation
Indices: 3762331--3762406 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
3762321 ACGGATGAAA
* *
3762331 AATGAGAAAAAGTGAAAGAGGAAA-AAAAGAAAAAG
1 AATGA-AAAAAATGAAAAAGGAAAGAAAA-AAAAAG
* *
3762366 AATGAAAAAAATGAAAAATGAAAGAATAAAAAAG
1 AATGAAAAAAATGAAAAAGGAAAGAAAAAAAAAG
3762400 -ATGAAAA
1 AATGAAAA
3762407 TGAGAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 7 0.19
34 21 0.58
35 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (34 bp):
AATGAAAAAAATGAAAAAGGAAAGAAAAAAAAAG
Found at i:3762382 original size:24 final size:24
Alignment explanation
Indices: 3762361--3762406 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3762351 GAAAAAAAGA
3762361 AAAAGAATGAAAAAA-ATGAAAAAT
1 AAAAGAAT-AAAAAAGATGAAAAAT
*
3762385 GAAAGAATAAAAAAGATGAAAA
1 AAAAGAATAAAAAAGATGAAAA
3762407 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (24 bp):
AAAAGAATAAAAAAGATGAAAAAT
Found at i:3762383 original size:20 final size:18
Alignment explanation
Indices: 3762351--3762397 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 18
3762341 AGTGAAAGAG
*
3762351 GAAAAAAAGAAAAAGAAT
1 GAAAAAAAGAAAAAGAAA
3762369 GAAAAAAATGAAAAATGAAA
1 GAAAAAAA-GAAAAA-GAAA
3762389 GAATAAAAA
1 GAA-AAAAA
3762398 AGATGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
20 6 0.24
21 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (18 bp):
GAAAAAAAGAAAAAGAAA
Found at i:3762422 original size:24 final size:24
Alignment explanation
Indices: 3762370--3762422 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3762360 AAAAAGAATG
*
3762370 AAAAAAATGAAAAATGAAAGAATA
1 AAAAAAATGAAAAATGAAAGAAAA
* *
3762394 AAAAAGATG-AAAATGAGAGAAAA
1 AAAAAAATGAAAAATGAAAGAAAA
*
3762417 AGAAAA
1 AAAAAA
3762423 CTCAGATTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (24 bp):
AAAAAAATGAAAAATGAAAGAAAA
Found at i:3769329 original size:25 final size:23
Alignment explanation
Indices: 3769293--3769385 Score: 109
Period size: 25 Copynumber: 4.0 Consensus size: 23
3769283 ATGAAATTTT
*
3769293 AAATTTTCAAATTAGAATCTTTGA
1 AAATTTTCAAATGAGAATCTTT-A
3769317 AACATTTTCAAATGAGAATCTTT-
1 AA-ATTTTCAAATGAGAATCTTTA
* *
3769340 AAGTCTT-AAATGAGAATCTTTA
1 AAATTTTCAAATGAGAATCTTTA
3769362 AGATATTTTCAAATGAGAATCTTT
1 A-A-ATTTTCAAATGAGAATCTTT
3769386 GAGTTTTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
21 14 0.24
22 4 0.07
23 3 0.05
24 5 0.08
25 33 0.56
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (23 bp):
AAATTTTCAAATGAGAATCTTTA
Found at i:3769352 original size:21 final size:21
Alignment explanation
Indices: 3769326--3769687 Score: 210
Period size: 21 Copynumber: 16.7 Consensus size: 21
3769316 AAACATTTTC
3769326 AAATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTTTAAGTCTT
*
3769347 AAATGAGAATCTTTAAGATATTTT
1 AAATGAGAATCTTTAAG---TCTT
*
3769371 CAAATGAGAATCTTTGAGT-TT
1 -AAATGAGAATCTTTAAGTCTT
* *
3769392 ---T--CAATTTTTAAGTCTT
1 AAATGAGAATCTTTAAGTCTT
* * *
3769408 CAAATAAGAATATTTGAGTCTT
1 -AAATGAGAATCTTTAAGTCTT
*
3769430 AAATGAGAATCTTTAAGATATTTTT
1 AAATGAGAATCTTTAAG----TCTT
* *
3769455 AAATGAGAATTTTTAAGACATTTT
1 AAATGAGAATCTTTAAG---TCTT
*
3769479 AAATGA-AACCTTTGAA-TCTT
1 AAATGAGAATCTTT-AAGTCTT
*
3769499 CAAATGAAAATCTTTAAGT-TT
1 -AAATGAGAATCTTTAAGTCTT
3769520 CAAATGAGAATC-TTAAGT-TT
1 -AAATGAGAATCTTTAAGTCTT
*
3769540 CAAATGAGAATCTTGAA-TCTT
1 -AAATGAGAATCTTTAAGTCTT
* * * *
3769561 AAATGAAAAT-TTAAAAAAAATCCT
1 AAATGAGAATCTT----TAAGTCTT
*
3769585 CAATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTTTAAGTCTT
3769606 CAAATGAGAATCTTTAAGTCTT
1 -AAATGAGAATCTTTAAGTCTT
*
3769628 AAATGAAAATCTTTAAGAAATCTT
1 AAATGAGAATCTTTAAG---TCTT
* *
3769652 CAAATGAGAATCTTTGAGTTTT
1 -AAATGAGAATCTTTAAGTCTT
*
3769674 AAATAAGAATCTTT
1 AAATGAGAATCTTT
3769688 GAGTTTTGAG
Statistics
Matches: 273, Mismatches: 36, Indels: 64
0.73 0.10 0.17
Matches are distributed among these distances:
15 9 0.03
16 2 0.01
17 1 0.00
19 2 0.01
20 34 0.12
21 93 0.34
22 43 0.16
23 7 0.03
24 30 0.11
25 52 0.19
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
AAATGAGAATCTTTAAGTCTT
Found at i:3769357 original size:46 final size:44
Alignment explanation
Indices: 3769301--3769666 Score: 228
Period size: 46 Copynumber: 8.3 Consensus size: 44
3769291 TTAAATTTTC
* *
3769301 AAATTAGAATCTTTGAAACATTTTCAAATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTTT-AAA-ATCTTCAAATGAGAATCTTTAAGTCTT
* *
3769347 AAATGAGAATCTTTAAGATATTTTCAAATGAGAATCTTTGAGT-TT
1 AAATGAGAATCTTTAA-A-ATCTTCAAATGAGAATCTTTAAGTCTT
* * * * * *
3769392 ---T--CAAT-TTTTAAGTCTTCAAATAAGAATATTTGAGTCTT
1 AAATGAGAATCTTTAAAATCTTCAAATGAGAATCTTTAAGTCTT
* * * *
3769430 AAATGAGAATCTTTAAGATATTTTTAAATGAGAATTTTTAAGACATTTT
1 AAATGAGAATCTTTAA-A-ATCTTCAAATGAGAATCTTTAAG---TCTT
* * *
3769479 AAATGA-AACCTTT-GAATCTTCAAATGAAAATCTTTAAGT-TT
1 AAATGAGAATCTTTAAAATCTTCAAATGAGAATCTTTAAGTCTT
* *
3769520 CAAATGAGAATC-TT-AAGT-TTCAAATGAGAATCTTGAA-TCTT
1 -AAATGAGAATCTTTAAAATCTTCAAATGAGAATCTTTAAGTCTT
* * *
3769561 AAATGAAAAT-TTAAAAAAAATCCTC-AATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTT---TAAAATCTTCAAATGAGAATCTTTAAGTCTT
* *
3769606 CAAATGAGAATCTTT-AAGTCTT-AAATGAAAATCTTTAAGAAATCTT
1 -AAATGAGAATCTTTAAAATCTTCAAATGAGAATCTTTAAG---TCTT
3769652 CAAATGAGAATCTTT
1 -AAATGAGAATCTTT
3769667 GAGTTTTAAA
Statistics
Matches: 252, Mismatches: 39, Indels: 58
0.72 0.11 0.17
Matches are distributed among these distances:
37 20 0.08
38 3 0.01
39 4 0.02
40 14 0.06
41 22 0.09
42 12 0.05
43 26 0.10
44 21 0.08
45 30 0.12
46 83 0.33
47 2 0.01
48 6 0.02
49 9 0.04
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (44 bp):
AAATGAGAATCTTTAAAATCTTCAAATGAGAATCTTTAAGTCTT
Found at i:3769483 original size:24 final size:25
Alignment explanation
Indices: 3769428--3769516 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 25
3769418 TATTTGAGTC
*
3769428 TTAAATGAGAATCTTTAAGATATTT
1 TTAAATGAGAATCTTTAAGACATTT
*
3769453 TTAAATGAGAATTTTTAAGACA-TT
1 TTAAATGAGAATCTTTAAGACATTT
* *
3769477 TTAAATGA-AACCTTT--GA-ATCT
1 TTAAATGAGAATCTTTAAGACATTT
* *
3769498 TCAAATGAAAATCTTTAAG
1 TTAAATGAGAATCTTTAAG
3769517 TTTCAAATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.02
21 10 0.19
22 6 0.11
23 5 0.09
24 11 0.21
25 20 0.38
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (25 bp):
TTAAATGAGAATCTTTAAGACATTT
Found at i:3769696 original size:28 final size:28
Alignment explanation
Indices: 3769664--3769745 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
3769654 AATGAGAATC
* *
3769664 TTTGAGTTTTAAATAAGAATCTTTGAGT
1 TTTGAGTTTCAAATGAGAATCTTTGAGT
*
3769692 TTTGAGTTTCAAATGAGAATCTTTAAGT
1 TTTGAGTTTCAAATGAGAATCTTTGAGT
*
3769720 TTTGAGTTTCAAATGATAATCTTTGA
1 TTTGAGTTTCAAATGAGAATCTTTGA
3769746 TGTATGAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (28 bp):
TTTGAGTTTCAAATGAGAATCTTTGAGT
Found at i:3770364 original size:43 final size:43
Alignment explanation
Indices: 3770294--3770573 Score: 370
Period size: 43 Copynumber: 6.6 Consensus size: 43
3770284 GATTGTTAAT
* *
3770294 GAGCAATTTA-TTTTTCAAAGTTATGGTTGCCTCTATTTAGAT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
*
3770336 GAGCATTTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
* * *
3770379 GAGTAATTTATTTTTTCAAAGTTGT-GTTACCTTTATTTAGAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
*
3770421 GAGCAATTTATTTTTTTCAAAGTTGT-GTTACCTCTATTTAGAG
1 GAGCAATTTA-TTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
* * * *
3770464 GAACAATTTATTTTTCCAAAGTTGTGGTTGCCTCTATCTAGAT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
* * ** * *
3770507 GAACAATTTATTTTTCCAAAGTT-AAGTTGCCTCTGTTTAGAA
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
3770549 GAGCAATTTATTTTTTCAAAGTTGT
1 GAGCAATTTATTTTTTCAAAGTTGT
3770574 TTCACCTTTA
Statistics
Matches: 212, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
42 82 0.39
43 130 0.61
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (43 bp):
GAGCAATTTATTTTTTCAAAGTTGTGGTTGCCTCTATTTAGAG
Found at i:3770455 original size:85 final size:85
Alignment explanation
Indices: 3770294--3770590 Score: 377
Period size: 85 Copynumber: 3.5 Consensus size: 85
3770284 GATTGTTAAT
* * *
3770294 GAGCAATTTA-TTTTTCAAAGTTATGGTTGCCTCTATTTAGATGAGCATTTTATTTTTTCAAAGT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTACCTCTATTTAGATGAGCAATTTATTTTTTCAAAGT
3770358 TGTGGTTGCCTCTATTTAGAG
66 TGT-GTTGCCTCTATTTAGAG
* * *
3770379 GAGTAATTTATTTTTTCAAAGTTGT-GTTACCTTTATTTAGAGGAGCAATTTATTTTTTTCAAAG
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTACCTCTATTTAGATGAGCAATTTA-TTTTTTCAAAG
*
3770443 TTGTGTTACCTCTATTTAGAG
65 TTGTGTTGCCTCTATTTAGAG
* * * * * *
3770464 GAACAATTTATTTTTCCAAAGTTGTGGTTGCCTCTATCTAGATGAACAATTTATTTTTCCAAAGT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTTACCTCTATTTAGATGAGCAATTTATTTTTTCAAAGT
** * *
3770529 TAAGTTGCCTCTGTTTAGAA
66 TGTGTTGCCTCTATTTAGAG
*
3770549 GAGCAATTTATTTTTTCAAAGTTGT--TTCACCTTTATTTAGAT
1 GAGCAATTTATTTTTTCAAAGTTGTGGTT-ACCTCTATTTAGAT
3770591 AAGCTTTATT
Statistics
Matches: 182, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
83 2 0.01
84 11 0.06
85 119 0.65
86 50 0.27
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (85 bp):
GAGCAATTTATTTTTTCAAAGTTGTGGTTACCTCTATTTAGATGAGCAATTTATTTTTTCAAAGT
TGTGTTGCCTCTATTTAGAG
Found at i:3770474 original size:128 final size:127
Alignment explanation
Indices: 3770294--3770589 Score: 389
Period size: 128 Copynumber: 2.3 Consensus size: 127
3770284 GATTGTTAAT
* * * * * *
3770294 GAGCAATTTA-TTTTTCAAAGTTATGGTTGCCTCTATTTAGATGAGCATTTTATTTTTTCAAAGT
1 GAGCAATTTATTTTTTCAAAGTTGT-GTTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGT
* ** * ** * *
3770358 TGTGGTTGCCTCTATTTAGAGGAGTAATTTATTTTTTCAAAGTTGTGTTACCTTTATTTAGAG
65 TGTGGTTGCCTCTATCTAGAGGAACAATTTATTTTTCCAAAGTTAAGTTACCTCTATTTAGAA
3770421 GAGCAATTTATTTTTTTCAAAGTTGTGTTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGT
1 GAGCAATTTA-TTTTTTCAAAGTTGTGTTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGT
* * *
3770486 TGTGGTTGCCTCTATCTAGATGAACAATTTATTTTTCCAAAGTTAAGTTGCCTCTGTTTAGAA
65 TGTGGTTGCCTCTATCTAGAGGAACAATTTATTTTTCCAAAGTTAAGTTACCTCTATTTAGAA
*
3770549 GAGCAATTTATTTTTTCAAAGTTGT-TTCACCTTTATTTAGA
1 GAGCAATTTATTTTTTCAAAGTTGTGTT-ACCTCTATTTAGA
3770590 TAAGCTTTAT
Statistics
Matches: 148, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
126 2 0.01
127 37 0.25
128 96 0.65
129 13 0.09
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (127 bp):
GAGCAATTTATTTTTTCAAAGTTGTGTTACCTCTATTTAGAGGAACAATTTATTTTTCCAAAGTT
GTGGTTGCCTCTATCTAGAGGAACAATTTATTTTTCCAAAGTTAAGTTACCTCTATTTAGAA
Found at i:3771239 original size:19 final size:20
Alignment explanation
Indices: 3771217--3771261 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3771207 AAACTTGAAT
3771217 TTTTTGAAG-ATTTTTTCAA
1 TTTTTGAAGTATTTTTTCAA
* *
3771236 TTTTTGACGTGTTTTTTCAA
1 TTTTTGAAGTATTTTTTCAA
*
3771256 ATTTTG
1 TTTTTG
3771262 GTAGAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (20 bp):
TTTTTGAAGTATTTTTTCAA
Found at i:3771844 original size:7 final size:8
Alignment explanation
Indices: 3771825--3771867 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
3771815 ATTTATTTTC
*
3771825 AAATAAAA
1 AAATATAA
3771833 AAATAT-A
1 AAATATAA
3771840 AAATATAA
1 AAATATAA
*
3771848 AAACATAA
1 AAATATAA
3771856 AAATATAA
1 AAATATAA
3771864 AAAT
1 AAAT
3771868 TTTGAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATATAA
Found at i:3771849 original size:15 final size:16
Alignment explanation
Indices: 3771825--3771867 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
3771815 ATTTATTTTC
*
3771825 AAATAAAAAAATAT-A
1 AAATATAAAAATATAA
*
3771840 AAATATAAAAACATAA
1 AAATATAAAAATATAA
3771856 AAATATAAAAAT
1 AAATATAAAAAT
3771868 TTTGAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATATAAAAATATAA
Found at i:3788914 original size:53 final size:54
Alignment explanation
Indices: 3788827--3788928 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
3788817 TTTTTTTTAC
*
3788827 TTTACAATGTTTATTTCTAAATTTTTCACTATTTGAG-TATATTTAGAAAAAAA
1 TTTACAATGTTTATTTCTAAATTTTTCACTATTTGAGTTAAATTTAGAAAAAAA
* * *
3788880 TTTACAA-GTTTTATTTTTAAATTTTTTA-TCATTTGGGTTAAATTTAGAA
1 TTTACAATG-TTTATTTCTAAATTTTTCACT-ATTTGAGTTAAATTTAGAA
3788929 TCTAAAGTCT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 2 0.05
53 30 0.71
54 10 0.24
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (54 bp):
TTTACAATGTTTATTTCTAAATTTTTCACTATTTGAGTTAAATTTAGAAAAAAA
Found at i:3790790 original size:18 final size:19
Alignment explanation
Indices: 3790759--3790795 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3790749 AACAACATAA
3790759 ATAAAATAATAAAT-AAAT
1 ATAAAATAATAAATGAAAT
3790777 ATAAAAT-ATAAAATGAAAT
1 ATAAAATAAT-AAATGAAAT
3790796 GAGTAACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.12
18 11 0.65
19 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (19 bp):
ATAAAATAATAAATGAAAT
Found at i:3791777 original size:5 final size:5
Alignment explanation
Indices: 3791767--3791798 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
3791757 ATATCTTTAT
3791767 TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA
3791799 TACATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:3795495 original size:12 final size:12
Alignment explanation
Indices: 3795456--3795498 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3795446 TTAATATAAT
*
3795456 ATATATAATTAA
1 ATATATAATTTA
* *
3795468 ATAAATAATATA
1 ATATATAATTTA
3795480 ATATATAATTTA
1 ATATATAATTTA
3795492 ATATATA
1 ATATATA
3795499 TAGTCAAGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATAATTTA
Found at i:3797709 original size:25 final size:23
Alignment explanation
Indices: 3797655--3797712 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
3797645 ATCTCATAAC
* * *
3797655 ATAAAAATTAATAAAAAAATGTT
1 ATAAAAAATAATAAAAAAAAGTA
3797678 ATGAAAAAATATATAAAAAAAAGTAA
1 AT-AAAAAATA-ATAAAAAAAAGT-A
3797704 ATAAAAAAT
1 ATAAAAAAT
3797713 TCAAACATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.07
24 7 0.24
25 18 0.62
26 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (23 bp):
ATAAAAAATAATAAAAAAAAGTA
Found at i:3798430 original size:16 final size:16
Alignment explanation
Indices: 3798409--3798440 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3798399 TCTTCCCCTT
3798409 AGTTTGTCAATTTTGC
1 AGTTTGTCAATTTTGC
*
3798425 AGTTTGTCCATTTTGC
1 AGTTTGTCAATTTTGC
3798441 TCTTTATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
AGTTTGTCAATTTTGC
Found at i:3804805 original size:187 final size:184
Alignment explanation
Indices: 3804543--3805164 Score: 464
Period size: 187 Copynumber: 3.4 Consensus size: 184
3804533 CAACTTATTG
* * * * **
3804543 AAGGCGTTTTATAATAAAAGATGCCTTTAATAA-T-TCAAAAATTTTTTTTTTG-AAAAATTATT
1 AAGGCATTTTATAGTAGAAGACGCCTTTAATAATTATC-AAAA--TTTTTAGTGAAAAAATT-TT
* *
3804605 GAAGGC-ATTGTTATGTACAACCGCTTTCACTAATTATCTACAAACTATAATAGGAATTATTAAA
62 GAAGGCGTTTGTTAT-TACAACCGCCTTCACTAATTAT-TACAAACTATAATAGGAATTATTAAA
* *
3804669 GGTATTTTTCATAAATATACGCCTTCAATAACCGTGTTAGAATTTTTTAGGAGGTATATAA
125 GGTATTTTTC-TGAATATACGCCTTCAATAACCGTGTTAGAATTTATTAGGAGGTATATAA
* * * * *
3804730 AAGGTATTTTATAGTAGAAGACGCCTTTAATAATTTTTAAAATTTTTAGTGAAAAAATTTTAAAA
1 AAGGCATTTTATAGTAGAAGACGCCTTTAATAATTATCAAAATTTTTAGTGAAAAAATTTTGAAG
* * * * * * * *
3804795 GCGTTTGTTATTAACAAACGCCTTCAGTTATGGATTACTAAGTTTAA-AGGTA-TATTAAAGGTG
66 GCGTTTGTTATT-ACAACCGCCTTCACTAAT-TATTACAAACTATAATAGGAATTATTAAAGGT-
** * * * **
3804858 CCTTTTC-GAATAAACGCCTTCCATAACC--------A-TCATT---A--TATATTG
128 ATTTTTCTGAATATACGCCTTCAATAACCGTGTTAGAATTTATTAGGAGGTATATAA
* * * * * * *
3804900 AAGGCGTGTCATAATAAAAGACGCCTTTAATAATCTATCAAAATTTTT--TTAGAGAAATTATTG
1 AAGGCATTTTATAGTAGAAGACGCCTTTAATAAT-TATCAAAATTTTTAGTGA-AAAAATT-TTG
* * * *
3804963 AAGGCG-TTGTTATCTATAACTGCCTTCACTAATTATTTACAAACTATGATAGAAATTATTAAAG
63 AAGGCGTTTGTTAT-TACAACCGCCTTCACTAATTA-TTACAAACTATAATAGGAATTATTAAAG
* * * * * *
3805027 GCATATTTCTTGAATATACGCTTTCAATAACCGTGTTAGAATTTGTTAGGTGGTATATAT
126 GTATTTTTC-TGAATATACGCCTTCAATAACCGTGTTAGAATTTATTAGGAGGTATATAA
* * ** *
3805087 AAGGCATTTTACAGTAGAAGACGCTTTTAATAATTCCCAAAATTTTTAGTGAAAAATTTTTGAAG
1 AAGGCATTTTATAGTAGAAGACGCCTTTAATAATTATCAAAATTTTTAGTGAAAAAATTTTGAAG
3805152 GCGTTTGTTATTA
66 GCGTTTGTTATTA
3805165 ACAAATGCCT
Statistics
Matches: 325, Mismatches: 77, Indels: 67
0.69 0.16 0.14
Matches are distributed among these distances:
169 3 0.01
170 68 0.21
171 26 0.08
172 10 0.03
173 18 0.06
175 3 0.01
176 1 0.00
181 1 0.00
182 3 0.01
184 18 0.06
185 10 0.03
186 45 0.14
187 109 0.34
188 9 0.03
189 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (184 bp):
AAGGCATTTTATAGTAGAAGACGCCTTTAATAATTATCAAAATTTTTAGTGAAAAAATTTTGAAG
GCGTTTGTTATTACAACCGCCTTCACTAATTATTACAAACTATAATAGGAATTATTAAAGGTATT
TTTCTGAATATACGCCTTCAATAACCGTGTTAGAATTTATTAGGAGGTATATAA
Found at i:3804960 original size:357 final size:357
Alignment explanation
Indices: 3804538--3805422 Score: 1148
Period size: 357 Copynumber: 2.5 Consensus size: 357
3804528 TATAACAACT
* * * *
3804538 TATTGAAGGCGTTTTATAATAAAAGATGCCTTTAATAA--TTCAAAAATTTTTTTTTTGAAAAAT
1 TATTGAAGGCGTGTCATAATAAAAGATGCCTTTAATAATCTTC-AAAA-TTTTTTTTAGAGAAAT
* * * * * *
3804601 TATTGAAGGCATTGTTATGTACAACCGCTTTCACTAATTATCTACAAACTATAATAGGAATTATT
64 TATTGAAGGCATTGTTATCTATAACCGCCTTCACTAATTATATACAAACTATGATAGAAATTATT
* * *
3804666 AAAGGTATTTTTCATAAATATACGCCTTCAATAACCGTGTTAGAATTTTTTAGGAGGTATATAAA
129 AAAGGCATATTTCATAAATATACGCCTTCAATAACCGTGTTAGAATTTGTTAGGAGGTATATAAA
* * ***
3804731 AGGTATTTTATAGTAGAAGACGCCTTTAATAATTTTTAAAATTTTTAGTGAAAAAATTTTAAAAG
194 AGGCATTTTACAGTAGAAGACGCCTTTAATAATTCCCAAAATTTTTAGTGAAAAAATTTTAAAAG
* *
3804796 CGTTTGTTATTAACAAACGCCTTCAGTTATGGATTACTAAGTTTAAAGGTATATTAAAGGTGCCT
259 CGTTTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGCTGCCT
* * *
3804861 TTTCGAATAAACGCCTTCCATAACCATCATTATA
324 TTTAGAATAAACACCTTCCATAACCATCATGATA
*
3804895 TATTGAAGGCGTGTCATAATAAAAGACGCCTTTAATAATCTATCAAAA-TTTTTTTAGAGAAATT
1 TATTGAAGGCGTGTCATAATAAAAGATGCCTTTAATAATCT-TCAAAATTTTTTTTAGAGAAATT
* * *
3804959 ATTGAAGGCGTTGTTATCTATAACTGCCTTCACTAATTATTTACAAACTATGATAGAAATTATTA
65 ATTGAAGGCATTGTTATCTATAACCGCCTTCACTAATTATATACAAACTATGATAGAAATTATTA
* * * * *
3805024 AAGGCATATTTCTTGAATATACGCTTTCAATAACCGTGTTAGAATTTGTTAGGTGGTATATATAA
130 AAGGCATATTTCATAAATATACGCCTTCAATAACCGTGTTAGAATTTGTTAGGAGGTATATAAAA
* * * *
3805089 GGCATTTTACAGTAGAAGACGCTTTTAATAATTCCCAAAATTTTTAGTGAAAAATTTTTGAAGGC
195 GGCATTTTACAGTAGAAGACGCCTTTAATAATTCCCAAAATTTTTAGTGAAAAAATTTTAAAAGC
* * *
3805154 GTTTGTTATTAACAAATGCCTTTAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGCTGCCTT
260 GTTTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGCTGCCTT
** *
3805219 TTAGAATAAACACCTTCCATAACCATTGTGGTA
325 TTAGAATAAACACCTTCCATAACCATCATGATA
* * * *
3805252 TATTGAAGGCATGTCATAATAAAAAATACCTTTAATAATCCGTCAAAATTTTTTTTA-AGAAAAT
1 TATTGAAGGCGTGTCATAATAAAAGATGCCTTTAATAAT-CTTCAAAATTTTTTTTAGAG-AAAT
* * * * * * *
3805316 TATTAAAGGCATTATTATCTGTAATCACCTTCACTAATTATATACAAACTGTGACAGAAATTATT
64 TATTGAAGGCATTGTTATCTATAACCGCCTTCACTAATTATATACAAACTATGATAGAAATTATT
* * ** ** * *
3805381 AAAGGCGTCTTTTTTGGATATATGCCTTCAATAACCATGTTA
129 AAAGGCATATTTCATAAATATACGCCTTCAATAACCGTGTTA
3805423 AAAATTGTGT
Statistics
Matches: 459, Mismatches: 63, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
357 349 0.76
358 103 0.22
359 5 0.01
360 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (357 bp):
TATTGAAGGCGTGTCATAATAAAAGATGCCTTTAATAATCTTCAAAATTTTTTTTAGAGAAATTA
TTGAAGGCATTGTTATCTATAACCGCCTTCACTAATTATATACAAACTATGATAGAAATTATTAA
AGGCATATTTCATAAATATACGCCTTCAATAACCGTGTTAGAATTTGTTAGGAGGTATATAAAAG
GCATTTTACAGTAGAAGACGCCTTTAATAATTCCCAAAATTTTTAGTGAAAAAATTTTAAAAGCG
TTTGTTATTAACAAACGCCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTAAAGCTGCCTTT
TAGAATAAACACCTTCCATAACCATCATGATA
Found at i:3811614 original size:24 final size:24
Alignment explanation
Indices: 3811587--3811632 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3811577 TTTTATTATT
3811587 TATGTATGTTTAAGACTATTGTAA
1 TATGTATGTTTAAGACTATTGTAA
3811611 TATGTATGTTTAAGACTATTGT
1 TATGTATGTTTAAGACTATTGT
3811633 GTTGTTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (24 bp):
TATGTATGTTTAAGACTATTGTAA
Found at i:3815699 original size:8 final size:8
Alignment explanation
Indices: 3815646--3815700 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
3815636 AAAAACTTAG
3815646 GGTTTGGAA
1 GGTTTGG-A
*
3815655 GGTTTTGA
1 GGTTTGGA
*
3815663 GGTTTTGA
1 GGTTTGGA
3815671 GGTTT-GA
1 GGTTTGGA
*
3815678 GGATTTAG-
1 GG-TTTGGA
3815686 GGTTTGGA
1 GGTTTGGA
3815694 GGTTTGG
1 GGTTTGG
3815701 TTTAGGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 8 0.20
8 26 0.63
9 7 0.17
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (8 bp):
GGTTTGGA
Found at i:3815745 original size:14 final size:14
Alignment explanation
Indices: 3815701--3815754 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
3815691 GGAGGTTTGG
*
3815701 TTTAGGGTTTTGTAT
1 TTTAGGGTTTT-AAT
* *
3815716 TTTGGGGTTTGAAAT
1 TTTAGGGTTT-TAAT
3815731 TTTAGGGTTTTAAT
1 TTTAGGGTTTTAAT
*
3815745 TTTAAGGTTT
1 TTTAGGGTTT
3815755 CAAGAGTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTTAAT
Found at i:3815867 original size:30 final size:30
Alignment explanation
Indices: 3815828--3815907 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
3815818 GATTTTAAGA
*
3815828 TTTGAAGGGTTTAAGATTTCGATTTCAGGGT
1 TTTG-AGGGTTTAGGATTTCGATTTCAGGGT
* *
3815859 TTTGAGGGTTTAGGGCTTT-GATTTTAGGGT
1 TTTGAGGGTTTA-GGATTTCGATTTCAGGGT
* *
3815889 TTAGATGGTTTAGGATTTC
1 TTTGAGGGTTTAGGATTTC
3815908 AAATTTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
29 5 0.12
30 28 0.68
31 8 0.20
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (30 bp):
TTTGAGGGTTTAGGATTTCGATTTCAGGGT
Found at i:3815953 original size:21 final size:23
Alignment explanation
Indices: 3815911--3815957 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
3815901 GGATTTCAAA
*
3815911 TTTTAATGTTTAGAGGTTTAAGG
1 TTTTAATGTTTAGAGATTTAAGG
3815934 TTTTAAT-TTTA-AGATTTAAGG
1 TTTTAATGTTTAGAGATTTAAGG
3815955 TTT
1 TTT
3815958 CGAGGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (23 bp):
TTTTAATGTTTAGAGATTTAAGG
Found at i:3815972 original size:36 final size:37
Alignment explanation
Indices: 3815912--3815987 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
3815902 GATTTCAAAT
* *
3815912 TTTAATGTTTAGAGGTTTAAGGTTTT-AATTTTAAGA
1 TTTAAGGTTTAGAGGTTTAAGGTTTTGAAATTTAAGA
* ** *
3815948 TTTAAGGTTTCGAGGTTTTGGGTTTTGAAATTTAGGA
1 TTTAAGGTTTAGAGGTTTAAGGTTTTGAAATTTAAGA
3815985 TTT
1 TTT
3815988 TGATTTTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 22 0.67
37 11 0.33
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.50
Consensus pattern (37 bp):
TTTAAGGTTTAGAGGTTTAAGGTTTTGAAATTTAAGA
Found at i:3816123 original size:9 final size:9
Alignment explanation
Indices: 3816105--3816152 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
3816095 CAGGTTTCAA
3816105 TTTT-AGGG
1 TTTTGAGGG
3816113 TTTTGAGGG
1 TTTTGAGGG
*
3816122 TTTTGA-GA
1 TTTTGAGGG
3816130 TTTT-AGGG
1 TTTTGAGGG
3816138 TTTTG-GGG
1 TTTTGAGGG
3816146 ATTTTGA
1 -TTTTGA
3816153 CAGTTTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 1 0.03
8 17 0.52
9 15 0.45
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (9 bp):
TTTTGAGGG
Found at i:3816133 original size:25 final size:25
Alignment explanation
Indices: 3816104--3816152 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3816094 TCAGGTTTCA
3816104 ATTTTAGGGTTTTGAGGG-TTTTGAG
1 ATTTTAGGGTTTTG-GGGATTTTGAG
3816129 ATTTTAGGGTTTTGGGGATTTTGA
1 ATTTTAGGGTTTTGGGGATTTTGA
3816153 CAGTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (25 bp):
ATTTTAGGGTTTTGGGGATTTTGAG
Found at i:3816453 original size:3 final size:3
Alignment explanation
Indices: 3816447--3816494 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
3816437 TTGTATAAAC
*
3816447 TTA TTA TTG TTA TTA TTA TTA TTTA GTTA TTTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA
3816494 T
1 T
3816495 AAGGTCTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 28 0.72
4 9 0.23
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3817793 original size:24 final size:23
Alignment explanation
Indices: 3817761--3817809 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3817751 ATTTAATATT
* *
3817761 TAATTATAAAACTAAATGATAAAA
1 TAATAATAAAACTAAA-AATAAAA
*
3817785 TAATAATAAAAGTAAAAATAAAA
1 TAATAATAAAACTAAAAATAAAA
3817808 TA
1 TA
3817810 GTGGGCTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (23 bp):
TAATAATAAAACTAAAAATAAAA
Found at i:3818087 original size:15 final size:14
Alignment explanation
Indices: 3818069--3818099 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3818059 TTCCTTTCTC
*
3818069 TTTTTTTTTTGGTT
1 TTTTTTTTTTTGTT
3818083 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
3818097 TTT
1 TTT
3818100 AGGTTTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:3819037 original size:22 final size:22
Alignment explanation
Indices: 3819009--3819176 Score: 133
Period size: 22 Copynumber: 7.6 Consensus size: 22
3818999 ACTTTTTCAA
* *
3819009 CTAATCTAAGCTTATGTGTCAG
1 CTAATCTGAGCTTATGTGCCAG
3819031 CTAATCTGAGCTTATGTGCCAG
1 CTAATCTGAGCTTATGTGCCAG
*
3819053 CTAAAT-T-AGACTTATATGCCAG
1 CT-AATCTGAG-CTTATGTGCCAG
* * *
3819075 CTAAACTGGGCTTATATGCCAG
1 CTAATCTGAGCTTATGTGCCAG
* * *
3819097 CTAAACTGAGCTTACGTACCAG
1 CTAATCTGAGCTTATGTGCCAG
* * * *
3819119 CTAATCTGGGTTTATGTGTCAA
1 CTAATCTGAGCTTATGTGCCAG
* * * * *
3819141 CTAAACTGGGCTTACGTGCTAA
1 CTAATCTGAGCTTATGTGCCAG
*
3819163 CTAAACTGAGCTTA
1 CTAATCTGAGCTTA
3819177 AAACTCCATT
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
21 4 0.03
22 112 0.93
23 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (22 bp):
CTAATCTGAGCTTATGTGCCAG
Found at i:3819088 original size:44 final size:44
Alignment explanation
Indices: 3819017--3819159 Score: 153
Period size: 44 Copynumber: 3.2 Consensus size: 44
3819007 AACTAATCTA
* * *
3819017 AGCTTATGTGTCAGCTAATCTGAGCTTATGTGCCAGCTAAA-TT
1 AGCTTATGTGCCAGCTAATCTGGGCTTATGTGCCAGCTAAACTG
* * *
3819060 AGACTTATATGCCAGCTAAACTGGGCTTATATGCCAGCTAAACTG
1 AG-CTTATGTGCCAGCTAATCTGGGCTTATGTGCCAGCTAAACTG
* * * * *
3819105 AGCTTACGTACCAGCTAATCTGGGTTTATGTGTCAACTAAACTG
1 AGCTTATGTGCCAGCTAATCTGGGCTTATGTGCCAGCTAAACTG
* *
3819149 GGCTTACGTGC
1 AGCTTATGTGC
3819160 TAACTAAACT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 2 0.02
44 77 0.94
45 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
AGCTTATGTGCCAGCTAATCTGGGCTTATGTGCCAGCTAAACTG
Found at i:3819495 original size:31 final size:31
Alignment explanation
Indices: 3819452--3819518 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
3819442 TAAAAGAGAC
*
3819452 ATAATTTTTTATACAAGCTC-ACAGATGAAAT
1 ATAAGTTTTTATACAAGCTCGA-AGATGAAAT
3819483 ATAAGTTTTTATACAAGCTCGAAGATGAAAT
1 ATAAGTTTTTATACAAGCTCGAAGATGAAAT
3819514 ATAAG
1 ATAAG
3819519 CTCATAGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (31 bp):
ATAAGTTTTTATACAAGCTCGAAGATGAAAT
Found at i:3820233 original size:19 final size:18
Alignment explanation
Indices: 3820186--3820250 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 18
3820176 TTTCAACCCA
*
3820186 TTCATTTTTTTCCTTTTCT
1 TTCATTTTCTTCCTTTT-T
*
3820205 TT--TGTTCTTCCTTTCTT
1 TTCATTTTCTTCCTTT-TT
3820222 TTCATTTTCTTCCTTTTT
1 TTCATTTTCTTCCTTTTT
*
3820240 TTCCTTTTCTT
1 TTCATTTTCTT
3820251 TTGCATTCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.33
18 13 0.33
19 13 0.33
ACGTcount: A:0.03, C:0.23, G:0.02, T:0.72
Consensus pattern (18 bp):
TTCATTTTCTTCCTTTTT
Found at i:3820247 original size:18 final size:19
Alignment explanation
Indices: 3820209--3820250 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
3820199 TTTTCTTTTG
3820209 TTCTTCCTTTCTTTTCATT
1 TTCTTCCTTTCTTTTCATT
*
3820228 TTCTTCCTTT-TTTTCCTT
1 TTCTTCCTTTCTTTTCATT
3820246 TTCTT
1 TTCTT
3820251 TTGCATTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCTTCCTTTCTTTTCATT
Found at i:3821652 original size:18 final size:18
Alignment explanation
Indices: 3821629--3821672 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3821619 CTCAAAACTT
**
3821629 TTTTTTTTGTCTTTTATC
1 TTTTTTTTCACTTTTATC
* *
3821647 TTTTTTCTCACTTTTTTC
1 TTTTTTTTCACTTTTATC
3821665 TTTTTTTT
1 TTTTTTTT
3821673 TAGGTATTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTTTCACTTTTATC
Found at i:3823111 original size:46 final size:46
Alignment explanation
Indices: 3823053--3823146 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 46
3823043 CCTTCATAGC
* * *
3823053 TTGAATTCTTTC-TTCTAAAAGACTATATCTTCTTTGTTCATTTAGA
1 TTGAATTCTTTCTTTC-AAAAAACTATACCTTCTTTATTCATTTAGA
*
3823099 TTGAATTTTTTCTTTCAAAAAACTATACCTTCTTTATTCATTTAGA
1 TTGAATTCTTTCTTTCAAAAAACTATACCTTCTTTATTCATTTAGA
3823145 TT
1 TT
3823147 CCCTCGCTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 40 0.93
47 3 0.07
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (46 bp):
TTGAATTCTTTCTTTCAAAAAACTATACCTTCTTTATTCATTTAGA
Found at i:3826570 original size:22 final size:22
Alignment explanation
Indices: 3826544--3826591 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3826534 ATTTATTTAT
3826544 TTAATCTTGATATTATTGCGAA
1 TTAATCTTGATATTATTGCGAA
*
3826566 TTAATCTTGATATTATTGTGAA
1 TTAATCTTGATATTATTGCGAA
3826588 TTAA
1 TTAA
3826592 AGATATGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (22 bp):
TTAATCTTGATATTATTGCGAA
Found at i:3826814 original size:21 final size:21
Alignment explanation
Indices: 3826788--3826828 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3826778 AATGATTTTT
3826788 GGGTTTCAGATTTAAGGTTTG
1 GGGTTTCAGATTTAAGGTTTG
** *
3826809 GGGTTTTGGATTTTAGGTTT
1 GGGTTTCAGATTTAAGGTTT
3826829 TAAAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (21 bp):
GGGTTTCAGATTTAAGGTTTG
Found at i:3826880 original size:18 final size:19
Alignment explanation
Indices: 3826859--3826897 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3826849 GGTTTTGAGG
*
3826859 TTTTGAGGATT-TAAGGTT
1 TTTTAAGGATTCTAAGGTT
*
3826877 TTTTAAGGGTTCTAAGGTT
1 TTTTAAGGATTCTAAGGTT
3826896 TT
1 TT
3826898 GATTTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.21, C:0.03, G:0.26, T:0.51
Consensus pattern (19 bp):
TTTTAAGGATTCTAAGGTT
Found at i:3826916 original size:22 final size:23
Alignment explanation
Indices: 3826877--3827033 Score: 94
Period size: 22 Copynumber: 7.0 Consensus size: 23
3826867 ATTTAAGGTT
*
3826877 TTTTAAGGGTTCTA-AGGTTT-TGA
1 TTTTAA-GGTT-TAGAGGTTTAAGA
*
3826900 TTTTAGGGTTTAGAGGTTT-AG-
1 TTTTAAGGTTTAGAGGTTTAAGA
** * * *
3826921 GCTGAAGGTTTAAAGGTTTAGGA
1 TTTTAAGGTTTAGAGGTTTAAGA
* * * *
3826944 -TTTCATGTTTTGGGGTTTAAGA
1 TTTTAAGGTTTAGAGGTTTAAGA
* * *
3826966 TTTTAAGGTTTTGAGGGTTTAGGG
1 TTTTAAGGTTTAGA-GGTTTAAGA
*
3826990 TTTTAAGGGTTTAG-GGTTT-TGA
1 TTTTAA-GGTTTAGAGGTTTAAGA
3827012 TTTTAAGGTTTAGAGGTTTAAG
1 TTTTAAGGTTTAGAGGTTTAAG
3827034 GTTTCTGATT
Statistics
Matches: 101, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
21 23 0.23
22 38 0.38
23 21 0.21
24 13 0.13
25 6 0.06
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.45
Consensus pattern (23 bp):
TTTTAAGGTTTAGAGGTTTAAGA
Found at i:3826987 original size:46 final size:45
Alignment explanation
Indices: 3826898--3827084 Score: 119
Period size: 44 Copynumber: 4.2 Consensus size: 45
3826888 CTAAGGTTTT
* ** * *
3826898 GATTTTAGGGTTTAGAGGTTTAG-GCTGAAGGTTTAAAGGTTTA-G
1 GATTTAAGGGTTTAG-GGTTTAGATTTTAAGGTTTAGAGGTTTAGG
* * * * *
3826942 GATTTCATGTTTTGGGGTTTAAGATTTTAAGGTTTTGAGGGTTTAGG
1 GATTTAAGGGTTTAGGGTTT-AGATTTTAAGGTTTAGA-GGTTTAGG
* * *
3826989 GTTTTAAGGGTTTAGGGTTTTGATTTTAAGGTTTAGAGGTTTAAG
1 GATTTAAGGGTTTAGGGTTTAGATTTTAAGGTTTAGAGGTTTAGG
** ** * * * * *
3827034 G-TTTCTGATTTTAGAGTTTCGATTTTAGGGTTTAAAAGTTTAGG
1 GATTTAAGGGTTTAGGGTTTAGATTTTAAGGTTTAGAGGTTTAGG
*
3827078 GTTTTAA
1 GATTTAA
3827085 TTTCAATATT
Statistics
Matches: 109, Mismatches: 29, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
43 5 0.05
44 47 0.43
45 20 0.18
46 21 0.19
47 16 0.15
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.45
Consensus pattern (45 bp):
GATTTAAGGGTTTAGGGTTTAGATTTTAAGGTTTAGAGGTTTAGG
Found at i:3826991 original size:16 final size:16
Alignment explanation
Indices: 3826967--3827011 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
3826957 GGTTTAAGAT
*
3826967 TTTAAGGTTTTGAGGG
1 TTTAGGGTTTTGAGGG
*
3826983 TTTAGGGTTTTAAGGG
1 TTTAGGGTTTTGAGGG
3826999 TTTAGGGTTTTGA
1 TTTAGGGTTTTGA
3827012 TTTTAAGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.47
Consensus pattern (16 bp):
TTTAGGGTTTTGAGGG
Found at i:3826996 original size:32 final size:32
Alignment explanation
Indices: 3826950--3827011 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
3826940 AGGATTTCAT
* *
3826950 GTTTTGGGGTTTAAGATTTTAAGGTTTTGAGG
1 GTTTAGGGGTTTAAGAGTTTAAGGTTTTGAGG
* * *
3826982 GTTTAGGGTTTTAAGGGTTTAGGGTTTTGA
1 GTTTAGGGGTTTAAGAGTTTAAGGTTTTGA
3827012 TTTTAAGGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (32 bp):
GTTTAGGGGTTTAAGAGTTTAAGGTTTTGAGG
Found at i:3827046 original size:15 final size:14
Alignment explanation
Indices: 3826999--3827066 Score: 57
Period size: 14 Copynumber: 4.7 Consensus size: 14
3826989 GTTTTAAGGG
*
3826999 TTTAGGGTTTTGAT
1 TTTAAGGTTTTGAT
* *
3827013 TTTAAGGTTTAGAGG
1 TTTAAGGTTTTGA-T
3827028 TTTAAGGTTTCTGAT
1 TTTAAGGTTT-TGAT
*
3827043 TTT-AGAGTTTCGAT
1 TTTAAG-GTTTTGAT
*
3827057 TTTAGGGTTT
1 TTTAAGGTTT
3827067 AAAAGTTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 23 0.53
15 18 0.42
16 2 0.05
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.51
Consensus pattern (14 bp):
TTTAAGGTTTTGAT
Found at i:3827209 original size:24 final size:22
Alignment explanation
Indices: 3827180--3827274 Score: 77
Period size: 23 Copynumber: 4.2 Consensus size: 22
3827170 CTAGGTTTTG
3827180 GGTTTTGAAATTTAGATTTTAA
1 GGTTTTGAAATTTAGATTTTAA
* * **
3827202 GCTTTTTTAGTTTTTAGATTTTAA
1 G-GTTTTGA-AATTTAGATTTTAA
*
3827226 GGTTTTGAAATTTATGATTTAAA
1 GGTTTTGAAATTTA-GATTTTAA
**
3827249 GGTTTATG-GTTTTA-ATTTTAA
1 GGTTT-TGAAATTTAGATTTTAA
3827270 GGTTT
1 GGTTT
3827275 AAAGGGTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
21 11 0.19
22 5 0.09
23 26 0.46
24 15 0.26
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.55
Consensus pattern (22 bp):
GGTTTTGAAATTTAGATTTTAA
Found at i:3827233 original size:46 final size:44
Alignment explanation
Indices: 3827180--3827274 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 44
3827170 CTAGGTTTTG
* * * *
3827180 GGTTTTGAAATTTA-GATTTTAAGCTTTTTTAGTTTTTAGATTTTAA
1 GGTTTTGAAATTTATGATTTAAAG-GTTTAT-GGTTTTA-ATTTTAA
3827226 GGTTTTGAAATTTATGATTTAAAGGTTTATGGTTTTAATTTTAA
1 GGTTTTGAAATTTATGATTTAAAGGTTTATGGTTTTAATTTTAA
3827270 GGTTT
1 GGTTT
3827275 AAAGGGTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 12 0.27
45 6 0.14
46 18 0.41
47 8 0.18
ACGTcount: A:0.26, C:0.01, G:0.18, T:0.55
Consensus pattern (44 bp):
GGTTTTGAAATTTATGATTTAAAGGTTTATGGTTTTAATTTTAA
Found at i:3827268 original size:29 final size:30
Alignment explanation
Indices: 3827221--3827279 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3827211 GTTTTTAGAT
*
3827221 TTTAAGGTTTTGAAATTTATGATTTAAAGG
1 TTTAAGGTTTTGAAATTTAAGATTTAAAGG
* * *
3827251 TTTATGGTTTT-AATTTTAAGGTTTAAAGG
1 TTTAAGGTTTTGAAATTTAAGATTTAAAGG
3827280 GTTTTGAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (30 bp):
TTTAAGGTTTTGAAATTTAAGATTTAAAGG
Found at i:3827293 original size:25 final size:25
Alignment explanation
Indices: 3827256--3827312 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
3827246 AAAGGTTTAT
3827256 GGTTTT-A-ATTTTAAGGTTT-AAA
1 GGTTTTGAGATTTTAAGGTTTCAAA
*
3827278 GGGTTTTGAGATTTTAAGGTTTCGAA
1 -GGTTTTGAGATTTTAAGGTTTCAAA
3827304 GGTTTTGAG
1 GGTTTTGAG
3827313 GGTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 6 0.20
24 1 0.03
25 21 0.70
26 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.28, T:0.46
Consensus pattern (25 bp):
GGTTTTGAGATTTTAAGGTTTCAAA
Found at i:3827451 original size:3 final size:3
Alignment explanation
Indices: 3827443--3827495 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
3827433 TTATAAAAAT
* *
3827443 TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTCA TTT TTA TT- TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA
3827488 TTA TTA TT
1 TTA TTA TT
3827496 TAATAATTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
2 4 0.09
3 34 0.79
4 5 0.12
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3827504 original size:27 final size:29
Alignment explanation
Indices: 3827449--3827504 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
3827439 AAATTTATTA
* *
3827449 TTATTATTATTATTATTATTTACTCATTT
1 TTATTATTATTATTATTATTTAATAATTT
3827478 TTATT-TT-TTATTATTATTTAATAATTT
1 TTATTATTATTATTATTATTTAATAATTT
3827505 GTCAATATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (29 bp):
TTATTATTATTATTATTATTTAATAATTT
Found at i:3827655 original size:31 final size:29
Alignment explanation
Indices: 3827613--3827670 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
3827603 TATTATTTAG
*
3827613 TTATTTTTTAATT-ATTATTTTATAAGGTT
1 TTATTTTTTAATTAATTA-TATATAAGGTT
3827642 TTATTTTAATTAATTAATTATATATAAGG
1 TTATTTT--TTAATTAATTATATATAAGG
3827671 AATTTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
31 14 0.56
32 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (29 bp):
TTATTTTTTAATTAATTATATATAAGGTT
Found at i:3837137 original size:361 final size:361
Alignment explanation
Indices: 3836467--3837294 Score: 1165
Period size: 361 Copynumber: 2.3 Consensus size: 361
3836457 TTTGAATATA
* * * * *
3836467 ATATAGGCGTTTACTGAAAGTGGTTACAGATAATAACGCCTTCAATAATTTTCTTGTTAAAATTT
1 ATATAGGCATTTACTGAAAGCGATTACAGATAACAACGCCTTCAATAATTTTCTTGTTAAATTTT
* *
3836532 TTTCGCATTATTAAAGGTGTCTTTTATTATGACACGCTTTCAATATACGATGAGAGTAATGGAAG
66 TTTCGGATTATTAAAGGTGTCTTTTATTATGACACGCCTTCAATATACGATGAGAGTAATGGAAG
3836597 GCATTTATTAGAAACGATGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCGTTT
131 GCATTTATTAGAAACGATGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCGTTT
* * *
3836662 GTTAATAACATATGCCTTCAAAATTTTTTGACTAAAAATTTTAGAAATTATTAAAGGCGGCTTCT
196 GTTAATAACAGACGCCTTCAAAATTTTCTGACTAAAAATTTTAGAAATTATTAAAGGCGGCTTCT
* * *
3836727 ACTGTAAAATGCCTTTTATATACCACTACACAAATTCTAACAATATTATTAAAGGTGTATATCCA
261 ACTGTAAAATACCTTATATATACCACTACACAAATTCTAACAATATTATTAAAGGCGTATATCCA
*
3836792 AGAAAGACACCTTTAATAATTTTTATCACAGTTTGT
326 AGAAAGACACCTTTAATAATTTCTATCACAGTTTGT
*
3836828 ATATAGGCATTTACTGAAAGCGATTGCAGATAACAACGCCTTCAATAATTTTCTTGTTAAATTTT
1 ATATAGGCATTTACTGAAAGCGATTACAGATAACAACGCCTTCAATAATTTTCTTGTTAAATTTT
* *
3836893 TTTCGGATTATTAAAGGTATCTTTTATTATGACATGCCTTCAATATACGATGATG-GTAATGGAA
66 TTTCGGATTATTAAAGGTGTCTTTTATTATGACACGCCTTCAATATACGATGA-GAGTAATGGAA
* *
3836957 GGCGTTTATTAG-AA-GATGCACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCG
130 GGCATTTATTAGAAACGATG--CCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCG
*
3837020 TTTGTTAATAACAGACGCCTTCAAAATTTTCCT-ACTAAAAATTTTAGAAATTATTAAAGGCGTC
193 TTTGTTAATAACAGACGCCTTCAAAATTTT-CTGACTAAAAATTTTAGAAATTATTAAAGGCGGC
** * *
3837084 TTCTACTGTAAAATACCTTATATATACCGTTACACAAATTCTAACACTATTATTGAAGGCGTATA
257 TTCTACTGTAAAATACCTTATATATACCACTACACAAATTCTAACAATATTATTAAAGGCGTATA
* ** *
3837149 TCTAAGAAAGATGCCTTTAATAATTTCTATCATAGTTTGT
322 TCCAAGAAAGACACCTTTAATAATTTCTATCACAGTTTGT
* * * * *
3837189 ATATA---A-TTACTGAATGCGATTTTCAGATAACAATG-TTTTAATAATTTT-TCTGTTAAAAT
1 ATATAGGCATTTACTGAAAGCGA-TTACAGATAACAACGCCTTCAATAATTTTCT-TGTT-AAAT
* * * * * *
3837248 TTTCTT-AGATTATTAAAGGCGTCTTTTATTATAAAACACCTTCAATA
63 TTTTTTCGGATTATTAAAGGTGTCTTTTATTATGACACGCCTTCAATA
3837295 ATTTGTTATA
Statistics
Matches: 419, Mismatches: 41, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
356 1 0.00
357 61 0.15
358 23 0.05
359 4 0.01
360 2 0.00
361 326 0.78
362 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (361 bp):
ATATAGGCATTTACTGAAAGCGATTACAGATAACAACGCCTTCAATAATTTTCTTGTTAAATTTT
TTTCGGATTATTAAAGGTGTCTTTTATTATGACACGCCTTCAATATACGATGAGAGTAATGGAAG
GCATTTATTAGAAACGATGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTAAAGGCGTTT
GTTAATAACAGACGCCTTCAAAATTTTCTGACTAAAAATTTTAGAAATTATTAAAGGCGGCTTCT
ACTGTAAAATACCTTATATATACCACTACACAAATTCTAACAATATTATTAAAGGCGTATATCCA
AGAAAGACACCTTTAATAATTTCTATCACAGTTTGT
Found at i:3839610 original size:21 final size:21
Alignment explanation
Indices: 3839568--3839610 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3839558 GCAACAAATT
** * *
3839568 AATGACCAGGAGCAACGCCTC
1 AATGACCAACAGCAAAGACTC
3839589 AATGACCAACAGCAAAGACTC
1 AATGACCAACAGCAAAGACTC
3839610 A
1 A
3839611 CTGCTTTGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.19, T:0.09
Consensus pattern (21 bp):
AATGACCAACAGCAAAGACTC
Found at i:3842833 original size:24 final size:23
Alignment explanation
Indices: 3842806--3842854 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3842796 ATTTAATATT
* *
3842806 TAATTATAAAACTAAATAATTAAA
1 TAATAATAAAACTAAA-AATAAAA
*
3842830 TAATAATAAAATTAAAAATAAAA
1 TAATAATAAAACTAAAAATAAAA
3842853 TA
1 TA
3842855 GTATACCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATAATAAAACTAAAAATAAAA
Found at i:3843720 original size:151 final size:150
Alignment explanation
Indices: 3843557--3843848 Score: 399
Period size: 151 Copynumber: 1.9 Consensus size: 150
3843547 GGATTCAATT
* * * *
3843557 TATATATATATAATATTGGTTCCTTACAATATTTTGATGTGAGATTGAAATATTATAAATTCTTC
1 TATATATATATAATATTGGATCCTTACAATATTTTGATGTGAGATTAAAATATTACAAATTCCTC
* * * *
3843622 CCGTTAAAACTT-AAT-GTCCAGTTAAATCTAACACAGAACTAGGATGTCACCATGCATTAAGAA
66 CCGATAAAA-TTCAATAGTCC-GCTAAATCTAACACAGAACTAGGATGACACAATGCATTAAGAA
3843685 TCTAGAAGTGGTTCCTACCATA
129 TCTAGAAGTGGTTCCTACCATA
** * *
3843707 TATATATATTATAATATTGGATCCTTATGATATTTTGATGTGGGATTAAAATGTTACAAATTCCT
1 TATATATA-TATAATATTGGATCCTTACAATATTTTGATGTGAGATTAAAATATTACAAATTCCT
* * *
3843772 CTCGATAAAATTCAATATTCCGCTAAATCTAACACAGAACTAGGATGACACAATGCATTGAGAAT
65 CCCGATAAAATTCAATAGTCCGCTAAATCTAACACAGAACTAGGATGACACAATGCATTAAGAAT
*
3843837 CTAGATGTGGTT
130 CTAGAAGTGGTT
3843849 TTTACGATGT
Statistics
Matches: 123, Mismatches: 16, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
150 10 0.08
151 110 0.89
152 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (150 bp):
TATATATATATAATATTGGATCCTTACAATATTTTGATGTGAGATTAAAATATTACAAATTCCTC
CCGATAAAATTCAATAGTCCGCTAAATCTAACACAGAACTAGGATGACACAATGCATTAAGAATC
TAGAAGTGGTTCCTACCATA
Found at i:3844670 original size:14 final size:14
Alignment explanation
Indices: 3844648--3844680 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3844638 CAATATTCAA
3844648 ATAAT-AATAAAAT
1 ATAATAAATAAAAT
3844661 ATAATAAATAAAAT
1 ATAATAAATAAAAT
*
3844675 AAAATA
1 ATAATA
3844681 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAATAAATAAAAT
Found at i:3844685 original size:17 final size:17
Alignment explanation
Indices: 3844639--3844690 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 17
3844629 AAAAATTTTC
3844639 AATATTCAAATAATAATAA
1 AATATT-AAATAA-AATAA
3844658 AATATAATAAATAAAATAA
1 AATAT--TAAATAAAATAA
3844677 AATATTAAATAAAA
1 AATATTAAATAAAA
3844691 AACTATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.29
19 15 0.48
20 6 0.19
21 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATTAAATAAAATAA
Found at i:3846400 original size:44 final size:45
Alignment explanation
Indices: 3846335--3846420 Score: 122
Period size: 44 Copynumber: 1.9 Consensus size: 45
3846325 AATTTGATTC
* *
3846335 GTAATCACATTCTTTTAATCGTCGAAAA-GATAGAAAGATAGGTAA
1 GTAATCACATTCTTTTAATCGT-AAAAAGGATACAAAGATAGGTAA
*
3846380 GTAATTACATT-TTTTAATCGTAAAAAGGATACAAAGATAGG
1 GTAATCACATTCTTTTAATCGTAAAAAGGATACAAAGATAGG
3846421 CAACAAAGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 4 0.11
44 23 0.62
45 10 0.27
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (45 bp):
GTAATCACATTCTTTTAATCGTAAAAAGGATACAAAGATAGGTAA
Found at i:3852168 original size:3 final size:3
Alignment explanation
Indices: 3852147--3852189 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
3852137 CATTTTAGTG
* ** *
3852147 TAA TAT TAA TAA TTT TAA TAA TAA TAT TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3852190 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:3852170 original size:12 final size:12
Alignment explanation
Indices: 3852153--3852189 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
3852143 AGTGTAATAT
*
3852153 TAATAATTTTAA
1 TAATAATATTAA
3852165 TAATAATATTAA
1 TAATAATATTAA
*
3852177 TAATAATAATAA
1 TAATAATATTAA
3852189 T
1 T
3852190 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:3853231 original size:20 final size:19
Alignment explanation
Indices: 3853206--3853263 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
3853196 AGGTAAAAAA
*
3853206 TTTTTTTTTTAATTTTCTAT
1 TTTTTTTTTTAATTAT-TAT
* *
3853226 TTTTTTATATATATTATTAT
1 TTTTTTTTTTA-ATTATTAT
*
3853246 TTTTTTATTTTAAGTATT
1 TTTTTT-TTTTAATTATT
3853264 TTTATATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTAATTATTAT
Found at i:3853330 original size:3 final size:3
Alignment explanation
Indices: 3853322--3853346 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3853312 TTAATTGTTT
3853322 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3853347 GAAAACGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3853689 original size:17 final size:17
Alignment explanation
Indices: 3853667--3853704 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3853657 CTAGGTTTCT
*
3853667 AAAACCCCTTAAAATCC
1 AAAACCCCCTAAAATCC
3853684 AAAACCCCCTAAAATCC
1 AAAACCCCCTAAAATCC
3853701 AAAA
1 AAAA
3853705 TCCTAAAAAT
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:0.53, C:0.34, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAACCCCCTAAAATCC
Found at i:3857467 original size:21 final size:21
Alignment explanation
Indices: 3857424--3857468 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
3857414 TCTCATACTC
3857424 ATTTTATGAAATTTATCTAAAA
1 ATTTTATG-AATTTATCTAAAA
3857446 ATTTTATG-ATTTGATCTTAAAA
1 ATTTTATGAATTT-ATC-TAAAA
3857468 A
1 A
3857469 CACTTCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 3 0.14
22 14 0.67
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTTTATGAATTTATCTAAAA
Found at i:3859801 original size:259 final size:255
Alignment explanation
Indices: 3859336--3859822 Score: 749
Period size: 259 Copynumber: 1.9 Consensus size: 255
3859326 TAAAATTGAT
* * * * *
3859336 TTTTTTTCCTTTTCAAATGGTTTTGTGGTTTTGTTTCAATTAAATCAAAATGATTTTGAAATTGA
1 TTTTTGTCCCTTTCAAATGGTTGTGTGGTTTTGTTTCAATTAAATCAAAATGATTCTGAAATTAA
*
3859401 AAAAAAAAAAATAGTGTTAGCTGATGTCACCTTTTAACGATATTAATTGACTTGGGGTCAATGTT
66 AAAAAAAAAAATAGTGTTAGCTAATGTCACCTTTTAACGATATTAATTGACTTGGGGTCAATGTT
* * * *
3859466 GTTATCTTCCGTTTAGAAGACATGAATATATAGTAATTGAAATTAAGTCCGTGGAATTTGGAAAT
131 ATTATCTTCCATTGAAAAGACATGAATATATAGTAATTGAAATTAAGTCCGTGGAATTTGGAAAT
3859531 TGATGTGAACCATAAAAATGGTTTATTTATCTTATAACAGGTCTACCTACAACCTCATGA
196 TGATGTGAACCATAAAAATGGTTTATTTATCTTATAACAGGTCTACCTACAACCTCATGA
* * * *
3859591 TTTTTGTCCCTTTCAAATGGTTGTGTGGTTTTGTTTCAAATTAGATCGAGATGGTTCTGAAATTA
1 TTTTTGTCCCTTTCAAATGGTTGTGTGGTTTTGTTTC-AATTAAATCAAAATGATTCTGAAATT-
** * **
3859656 AAAAAAAAAAAAAAATAGTGTTAGCTAATGTCACCTTTTAATTATTTTTGTTGACTTGGGGTCAA
64 --AAAAAAAAAAAAATAGTGTTAGCTAATGTCACCTTTTAACGATATTAATTGACTTGGGGTCAA
**
3859721 TGTTATTATCTTCCATTGAAAAGACATGAATATATAGTAATTGAAATTAAGTCTTTGGAATTTGG
127 TGTTATTATCTTCCATTGAAAAGACATGAATATATAGTAATTGAAATTAAGTCCGTGGAATTTGG
3859786 AAATTGATGTGAACCATAAAAATGGTTTATTTATCTT
192 AAATTGATGTGAACCATAAAAATGGTTTATTTATCTT
3859823 GTACTTTAAC
Statistics
Matches: 207, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
255 34 0.16
256 21 0.10
259 152 0.73
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (255 bp):
TTTTTGTCCCTTTCAAATGGTTGTGTGGTTTTGTTTCAATTAAATCAAAATGATTCTGAAATTAA
AAAAAAAAAAATAGTGTTAGCTAATGTCACCTTTTAACGATATTAATTGACTTGGGGTCAATGTT
ATTATCTTCCATTGAAAAGACATGAATATATAGTAATTGAAATTAAGTCCGTGGAATTTGGAAAT
TGATGTGAACCATAAAAATGGTTTATTTATCTTATAACAGGTCTACCTACAACCTCATGA
Found at i:3862870 original size:23 final size:23
Alignment explanation
Indices: 3862837--3862900 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
3862827 GTCGAAATTC
3862837 AATAAAAATAGAAAATAATG-AA
1 AATAAAAATAGAAAATAATGAAA
3862859 AATAATAAATAGAAAATAATGATAA
1 AATAA-AAATAGAAAATAATGA-AA
*
3862884 AATAAAAAATAAAAAAT
1 AAT-AAAAATAGAAAAT
3862901 TAATTATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 5 0.14
23 15 0.41
25 15 0.41
26 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (23 bp):
AATAAAAATAGAAAATAATGAAA
Found at i:3870238 original size:203 final size:200
Alignment explanation
Indices: 3869886--3870251 Score: 468
Period size: 203 Copynumber: 1.8 Consensus size: 200
3869876 TTTTAATTTT
* *
3869886 GAAAAAAAAATTATTGTATTGAAGTTTTTCTATAAATATTCCAATACACTGGTAATATTTTAAAA
1 GAAAAAAAAATTATTGTATTGAAGTTTTTCTATAAATACTCCAATACACTGGTAATATTTAAAAA
* * * *
3869951 AAATCTTCTCACTTAGGGATTTCGTAAAGCATCACTACTCAGAATACTTTTAGAATCCCATCATT
66 AAATATTCTCACTTAGGGATTTCATAAAGCATCACTACTCAGAATACCTTTAGAATCCCATCATC
* *
3870016 GGATAAAATTTCCTTTTTCTTTATTTATATTATTATTTTTTAATATATTAATTAATTTTTTGTTA
131 AGATAAAATATCCTTTTTC-TTATTT-T-TTATTATTTTTTAATATATTAATTAATTTTTTGTTA
3870081 TTTTATAA
193 TTTTATAA
** * * * *
3870089 GAAAAAAATTTTATTGTATTGAAATTTTTTTTTATAAATACTCCAATACATTGGTAGTA-TTAAA
1 GAAAAAAAAATTATTGTATTG-AA-GTTTTTCTATAAATACTCCAATACACTGGTAATATTTAAA
* * * * * *
3870153 AAAAATATTCTCACTTAGGGATTTCAT-AGGTATCACTACTCGGAGTACCTTTA-AATCTCATTA
64 AAAAATATTCTCACTTAGGGATTTCATAAAGCATCACTACTCAGAATACCTTTAGAATCCCATCA
*
3870216 TCAGATAAAAATATCTTTTTTCTTATTTTTTATTAT
129 TCAGAT-AAAATATCCTTTTTCTTATTTTTTATTAT
3870252 ATTAATTAAT
Statistics
Matches: 139, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
200 7 0.05
201 1 0.01
202 18 0.13
203 53 0.38
204 31 0.22
205 29 0.21
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (200 bp):
GAAAAAAAAATTATTGTATTGAAGTTTTTCTATAAATACTCCAATACACTGGTAATATTTAAAAA
AAATATTCTCACTTAGGGATTTCATAAAGCATCACTACTCAGAATACCTTTAGAATCCCATCATC
AGATAAAATATCCTTTTTCTTATTTTTTATTATTTTTTAATATATTAATTAATTTTTTGTTATTT
TATAA
Found at i:3871361 original size:23 final size:22
Alignment explanation
Indices: 3871332--3871377 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
3871322 AAGAAGTAGG
3871332 AAAAAGAAAAAAAAATAAAATTA
1 AAAAAGAAAAAAAAA-AAAATTA
*
3871355 AAAAAGAAAAATAAAAAAATTA
1 AAAAAGAAAAAAAAAAAAATTA
3871377 A
1 A
3871378 TATAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAAAATTA
Found at i:3871364 original size:22 final size:23
Alignment explanation
Indices: 3871332--3871377 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
3871322 AAGAAGTAGG
3871332 AAAAAGAAAAAA-AAATAAAATTA
1 AAAAAGAAAAAATAAA-AAAATTA
3871355 AAAAAG-AAAAATAAAAAAATTA
1 AAAAAGAAAAAATAAAAAAATTA
3871377 A
1 A
3871378 TATAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAAAGAAAAAATAAAAAAATTA
Found at i:3871627 original size:46 final size:50
Alignment explanation
Indices: 3871574--3871679 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 50
3871564 TCCTCTGAGT
*
3871574 AGAGGCTCAAGAACTTT-AAAATTCTC-T-TGA-AAAAGCTTCTCTCAGC
1 AGAGGCTCAACAACTTTAAAAATTCTCATCTGAGAAAAGCTTCTCTCAGC
*
3871620 AGAGGCTCAACAACTTTAAAAATTCTCATCTTAGAAAAGCTTCTCTCAGC
1 AGAGGCTCAACAACTTTAAAAATTCTCATCTGAGAAAAGCTTCTCTCAGC
3871670 AGAGGCTCAA
1 AGAGGCTCAA
3871680 TAATTCTCAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
46 16 0.30
47 9 0.17
48 1 0.02
49 2 0.04
50 26 0.48
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (50 bp):
AGAGGCTCAACAACTTTAAAAATTCTCATCTGAGAAAAGCTTCTCTCAGC
Found at i:3871697 original size:41 final size:41
Alignment explanation
Indices: 3871640--3871723 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
3871630 CAACTTTAAA
*
3871640 AATTCTCATCTTAGAAAAGCTTCTCTCAGCAGAGGCTCAAT
1 AATTCTCATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAAT
*
3871681 AATTCTCATCTTAGAAAAGCTCCTCTCAGCAGAGGTTCAAT
1 AATTCTCATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAAT
3871722 AA
1 AA
3871724 CTTTAACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (41 bp):
AATTCTCATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAAT
Found at i:3880925 original size:22 final size:22
Alignment explanation
Indices: 3880880--3880925 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3880870 CAAATTTTCT
* * *
3880880 CTTTTTATTTCTTCTTTTTCAG
1 CTTTTAATTTCTTCTTTATAAG
*
3880902 CTTTTAATTTTTTCTTTATAAG
1 CTTTTAATTTCTTCTTTATAAG
3880924 CT
1 CT
3880926 CAACTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.65
Consensus pattern (22 bp):
CTTTTAATTTCTTCTTTATAAG
Found at i:3882569 original size:19 final size:17
Alignment explanation
Indices: 3882537--3882594 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
3882527 TTTTCTGTTC
3882537 TATTTTTTTATATTTTG
1 TATTTTTTTATATTTTG
* *
3882554 TATTATTTT-TATTAT-
1 TATTTTTTTATATTTTG
* *
3882569 T-TTTTTTTGTATTCTG
1 TATTTTTTTATATTTTG
3882585 TATTTTTTTA
1 TATTTTTTTA
3882595 ATGTTTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 6 0.18
15 6 0.18
16 6 0.18
17 15 0.45
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (17 bp):
TATTTTTTTATATTTTG
Found at i:3882609 original size:30 final size:31
Alignment explanation
Indices: 3882547--3882611 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
3882537 TATTTTTTTA
* * * *
3882547 TATTTTGTATTATTTTTATTATTTTTTTTTG
1 TATTCTGTATTATTTTTAATATTTATTATTG
*
3882578 TATTCTGTATT-TTTTTAATGTTTATTATTG
1 TATTCTGTATTATTTTTAATATTTATTATTG
3882608 TATT
1 TATT
3882612 TAATAATCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (31 bp):
TATTCTGTATTATTTTTAATATTTATTATTG
Found at i:3884786 original size:50 final size:50
Alignment explanation
Indices: 3884724--3884821 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
3884714 TACTAATATG
* *
3884724 TTGAATGGATGAATTTGAAACAAATTAAATATTAGGTCATGGATGAAATT
1 TTGAATGAATGAATTTGAAACAAATTAAATATTAAGTCATGGATGAAATT
*
3884774 TTGAATGAATGAATTTGAAACTAATTAAATATTAAGTCATGGATGAAA
1 TTGAATGAATGAATTTGAAACAAATTAAATATTAAGTCATGGATGAAA
3884822 AAAAAAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (50 bp):
TTGAATGAATGAATTTGAAACAAATTAAATATTAAGTCATGGATGAAATT
Found at i:3884834 original size:24 final size:24
Alignment explanation
Indices: 3884804--3884854 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3884794 CTAATTAAAT
*
3884804 ATTAAGTCATGGATGAAAAAAAAA
1 ATTAAGTCATGAATGAAAAAAAAA
* *
3884828 ATTAAGTTATGAATGAAAATAAAA
1 ATTAAGTCATGAATGAAAAAAAAA
3884852 ATT
1 ATT
3884855 TGCAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.14, T:0.27
Consensus pattern (24 bp):
ATTAAGTCATGAATGAAAAAAAAA
Found at i:3885093 original size:21 final size:20
Alignment explanation
Indices: 3885067--3885125 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 20
3885057 CACTATTTTA
3885067 TAATTAAATTAAATAATATTT
1 TAATT-AATTAAATAATATTT
*
3885088 TAATTAATT--TTAAT-TTT
1 TAATTAATTAAATAATATTT
*
3885105 AAATT-ATTAAATAATATTT
1 TAATTAATTAAATAATATTT
3885124 TA
1 TA
3885126 CATAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.10
17 7 0.23
18 8 0.26
19 4 0.13
20 4 0.13
21 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTAATTAAATAATATTT
Found at i:3887388 original size:214 final size:213
Alignment explanation
Indices: 3887036--3887438 Score: 680
Period size: 214 Copynumber: 1.9 Consensus size: 213
3887026 AGTAAATGAT
** * *
3887036 CAAAATACGTTTAGTAAATCAAAAGTGATTATAAAATAACTTTTTGTTATTAAATTTTTATTGAG
1 CAAAATACCCTTAGTAAATCAAAAGTGATAATAAAATAACTTTTTATTATTAAATTTTTATTGAG
* *
3887101 ATAAATTATAATTTGAACTCTTTTATTATTAGACTTCTTAAAAATTGTAATTTAAACTCTTTTTT
66 ATAAATTATAATTTGAACTCTTTTACTATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTT
* * *
3887166 TATATTATTAGACTTCTATACCAAAAAAAATTAAAATGACTTTTTATTGTTAAATTTTTATTAAA
131 TATATTATTAGACTTCTATACC-AAAAAAATTAAAATGACCTTTTATTATCAAATTTTTATTAAA
3887231 AATGATAATAATAAACAAC
195 AATGATAATAATAAACAAC
**
3887250 CAAAATACCCTTAGTAAATCAAAAGTGATAATAAAATGGCTTTTTATTATTAAATTTTTATTGAG
1 CAAAATACCCTTAGTAAATCAAAAGTGATAATAAAATAACTTTTTATTATTAAATTTTTATTGAG
*
3887315 ATAAATTATAATTTGAACTCTTTTACTATTAGACTTCTTAAAAATTATACTTTAAACTCTTTTTT
66 ATAAATTATAATTTGAACTCTTTTACTATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTT
*
3887380 TATATTATTAGACTTCTATGCCAAAAAAATTAAAATGACCTTTTATTATCAAATTTTTA
131 TATATTATTAGACTTCTATACCAAAAAAATTAAAATGACCTTTTATTATCAAATTTTTA
3887439 ATGAGATAAA
Statistics
Matches: 176, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
213 34 0.19
214 142 0.81
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.43
Consensus pattern (213 bp):
CAAAATACCCTTAGTAAATCAAAAGTGATAATAAAATAACTTTTTATTATTAAATTTTTATTGAG
ATAAATTATAATTTGAACTCTTTTACTATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTT
TATATTATTAGACTTCTATACCAAAAAAATTAAAATGACCTTTTATTATCAAATTTTTATTAAAA
ATGATAATAATAAACAAC
Found at i:3887414 original size:129 final size:130
Alignment explanation
Indices: 3887277--3887543 Score: 412
Period size: 129 Copynumber: 2.1 Consensus size: 130
3887267 ATCAAAAGTG
* * * *
3887277 ATAA-TAAAATGGCTTTTTATTATTAAATTTTTATTGAGATAAATTATAATTTGAACTCTTTTAC
1 ATAATTAAAATGACCTTTTATTATCAAATTTTTAATGAGATAAATTATAATTTGAACTCTTTTAC
* * **
3887341 TATTAGACTTCTTAAAAATTATACTTTAAACTCTTTTTTTATATTATTAGACTTCTATGCCAAAA
66 TATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTTCATATTATTAGACTTCTATAACAAAA
*
3887406 A-AATTAAAATGACCTTTTATTATCAAATTTTTAATGAGATAAATTATAATTTGAACTCTTTTAT
1 ATAATTAAAATGACCTTTTATTATCAAATTTTTAATGAGATAAATTATAATTTGAACTCTTTTAC
* * *
3887470 TATTAGACTTCTTAAAATTTGTAATTTAAACTCTTTTTTCATATTATTAGATTTCTATAACAAAA
66 TATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTTCATATTATTAGACTTCTATAACAAAA
3887535 ATAATTAAA
1 ATAATTAAA
3887544 TATTCAAGCT
Statistics
Matches: 124, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
128 2 0.02
129 115 0.93
130 7 0.06
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (130 bp):
ATAATTAAAATGACCTTTTATTATCAAATTTTTAATGAGATAAATTATAATTTGAACTCTTTTAC
TATTAGACTTCTTAAAAATTATAATTTAAACTCTTTTTTCATATTATTAGACTTCTATAACAAAA
Found at i:3890653 original size:16 final size:15
Alignment explanation
Indices: 3890632--3890682 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
3890622 TTAGGGTTTT
3890632 GATTTTAGAGTTTGG
1 GATTTTAGAGTTTGG
3890647 AGATTTTAG-GATTTGG
1 -GATTTTAGAG-TTTGG
3890663 G-TTTT-GAGGTTTGG
1 GATTTTAGA-GTTTGG
3890677 GATTTT
1 GATTTT
3890683 GAATTTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 1 0.03
14 10 0.32
15 7 0.23
16 13 0.42
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (15 bp):
GATTTTAGAGTTTGG
Found at i:3890655 original size:30 final size:29
Alignment explanation
Indices: 3890621--3890682 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
3890611 ATATGTAAGG
* *
3890621 TTTAGGGTTTTGATTTT-AGAGTTTGGAGAT
1 TTTAGGATTTGGATTTTGAG-GTTTGG-GAT
*
3890651 TTTAGGATTTGGGTTTTGAGGTTTGGGAT
1 TTTAGGATTTGGATTTTGAGGTTTGGGAT
3890680 TTT
1 TTT
3890683 GAATTTTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 20 0.71
31 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (29 bp):
TTTAGGATTTGGATTTTGAGGTTTGGGAT
Found at i:3890722 original size:16 final size:15
Alignment explanation
Indices: 3890694--3890812 Score: 112
Period size: 16 Copynumber: 7.5 Consensus size: 15
3890684 AATTTTGAGG
3890694 GGGTTTTGGATTTTA
1 GGGTTTTGGATTTTA
3890709 GGGTTTTCGGATTTTA
1 GGGTTTT-GGATTTTA
* *
3890725 GGGCTTTGGATTTAAA
1 GGGTTTTGGATTT-TA
* *
3890741 GGATTTTGAATTTTTA
1 GGGTTTTGGA-TTTTA
*
3890757 GGGGTTTTAGATTTTA
1 -GGGTTTTGGATTTTA
*
3890773 GGATTTTGGATTTTA
1 GGGTTTTGGATTTTA
*
3890788 GAAGATTTTGGATTTTA
1 G--GGTTTTGGATTTTA
3890805 GGAGTTTT
1 GG-GTTTT
3890813 AGAAACCTAG
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
15 28 0.33
16 32 0.38
17 25 0.29
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.50
Consensus pattern (15 bp):
GGGTTTTGGATTTTA
Found at i:3890756 original size:48 final size:47
Alignment explanation
Indices: 3890697--3890815 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 47
3890687 TTTGAGGGGG
* * *
3890697 TTTTGGATTTTAGGGTTTTCGGATTTTAGGGCTTTGGA-TTTA-AAGGA
1 TTTTGAATTTTAGGGTTTT-AGATTTTAGGACTTTGGATTTTAGAA-GA
*
3890744 TTTTGAATTTTTAGGGGTTTTAGATTTTAGGATTTTGGATTTTAGAAGA
1 TTTTGAA-TTTTA-GGGTTTTAGATTTTAGGACTTTGGATTTTAGAAGA
*
3890793 TTTTGGATTTTAGGAGTTTTAGA
1 TTTTGAATTTTAGG-GTTTTAGA
3890816 AACCTAGGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
47 8 0.13
48 33 0.53
49 19 0.31
50 2 0.03
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.50
Consensus pattern (47 bp):
TTTTGAATTTTAGGGTTTTAGATTTTAGGACTTTGGATTTTAGAAGA
Found at i:3890776 original size:32 final size:31
Alignment explanation
Indices: 3890676--3890812 Score: 132
Period size: 32 Copynumber: 4.2 Consensus size: 31
3890666 TTGAGGTTTG
3890676 GGATTTTGAATTTTGAGGGGGTTTTGGATTTTA
1 GGATTTTGAATTTT-A-GGGGTTTTGGATTTTA
* * * *
3890709 GGGTTTTCGGATTTTA-GGGCTTTGGATTTAAA
1 GGATTTT-GAATTTTAGGGGTTTTGGATTT-TA
*
3890741 GGATTTTGAATTTTTAGGGGTTTTAGATTTTA
1 GGATTTTGAA-TTTTAGGGGTTTTGGATTTTA
* * *
3890773 GGATTTTGGATTTTAGAAGATTTTGGATTTTA
1 GGATTTTGAATTTTAG-GGGTTTTGGATTTTA
3890805 GGAGTTTT
1 GGA-TTTT
3890813 AGAAACCTAG
Statistics
Matches: 85, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
31 20 0.24
32 37 0.44
33 22 0.26
34 6 0.07
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.49
Consensus pattern (31 bp):
GGATTTTGAATTTTAGGGGTTTTGGATTTTA
Found at i:3891245 original size:21 final size:22
Alignment explanation
Indices: 3891220--3891261 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3891210 TCAAAATAAC
*
3891220 AAAAATAAAAAAAAAAATTTAG
1 AAAATTAAAAAAAAAAATTTAG
*
3891242 AAAATTCAAAAAAAAAATTT
1 AAAATTAAAAAAAAAAATTT
3891262 TTTTTACCTG
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:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATTAAAAAAAAAAATTTAG
Found at i:3892248 original size:16 final size:16
Alignment explanation
Indices: 3892214--3892259 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3892204 GCCACCCTAC
3892214 TTTCTATTTTTCTCT-TT
1 TTTCTATTTTT-T-TGTT
*
3892231 TTTTTATTTTTTTGTT
1 TTTCTATTTTTTTGTT
3892247 TTTCTATTTTTTT
1 TTTCTATTTTTTT
3892260 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.04
16 15 0.58
17 10 0.38
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTCTATTTTTTTGTT
Found at i:3892256 original size:24 final size:26
Alignment explanation
Indices: 3892220--3892268 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
3892210 CTACTTTCTA
*
3892220 TTTTTCTCTTTTTTTTATTT-TTTTG
1 TTTTTCTCATTTTTTTATTTATTTTG
3892245 TTTTTCT-ATTTTTTTATTTATTTT
1 TTTTTCTCATTTTTTTATTTATTTT
3892269 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.08, C:0.06, G:0.02, T:0.84
Consensus pattern (26 bp):
TTTTTCTCATTTTTTTATTTATTTTG
Found at i:3892282 original size:3 final size:3
Alignment explanation
Indices: 3892274--3892298 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3892264 ATTTTTTAAA
3892274 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
3892299 AAATTATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.