Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_pilon, 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: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 15
Found at i:2477111 original size:20 final size:17
Alignment explanation
Indices: 2477095--2477126 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2477085 CATATTAGGT
2477095 ATAACTTTTATATATTA
1 ATAACTTTTATATATTA
2477112 ATAACTTTTAT-TATT
1 ATAACTTTTATATATT
2477127 TTTTTCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAACTTTTATATATTA
Found at i:2479790 original size:44 final size:45
Alignment explanation
Indices: 2479636--2479838 Score: 293
Period size: 45 Copynumber: 4.5 Consensus size: 45
2479626 CTTATCAATT
*
2479636 TTCCTATAAGCTCGTAAGCTTATTCTACCAATATACTTACCATTTA
1 TTCC-ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
* * * *
2479682 TTCTATAAGCTCGTAAGCTTATTTTATCAATACACTTACCATTTG
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
* *
2479727 TTCCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCCA-TTA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
* * *
2479771 TTCCATAAGTTCGTAAGCTTATTTTACCCATATACTTTCCA-TTA
1 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
2479815 TTCCATAAGCTCGTAAGCTTATTT
1 TTCCATAAGCTCGTAAGCTTATTT
2479839 GCATGGTTAC
Statistics
Matches: 143, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 67 0.47
45 73 0.51
46 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (45 bp):
TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTA
Found at i:2479998 original size:40 final size:40
Alignment explanation
Indices: 2479943--2480064 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
2479933 ACCGTAGTGC
* *
2479943 TACACATAAGGTCGTGCCCACCATAAACATCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2479983 TACACATAAGGTCGTGCTCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2480023 TACACATAATGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2480063 TA
1 TA
2480065 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2483919 original size:5 final size:5
Alignment explanation
Indices: 2483909--2483995 Score: 60
Period size: 5 Copynumber: 17.8 Consensus size: 5
2483899 TTTTTTGTCT
* * *
2483909 TTTTC TTTTC TTATC -TTTC TCTATA TTTT- TTTTC ATTTTC ATTTTC
1 TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC -TTTTC -TTTTC
*
2483955 TTTT- TGTTC -TTTC TTTT- TTGTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTT
2483996 ATATAATGTT
Statistics
Matches: 67, Mismatches: 7, Indels: 17
0.74 0.08 0.19
Matches are distributed among these distances:
4 19 0.28
5 32 0.48
6 16 0.24
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:2483972 original size:14 final size:15
Alignment explanation
Indices: 2483950--2483986 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
2483940 TTCATTTTCA
2483950 TTTTC-TTTTTGTTC
1 TTTTCTTTTTTGTTC
2483964 -TTTCTTTTTTGTTC
1 TTTTCTTTTTTGTTC
2483978 TTTTCTTTT
1 TTTTCTTTT
2483987 CTTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 9 0.43
15 8 0.38
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTGTTC
Found at i:2483994 original size:23 final size:23
Alignment explanation
Indices: 2483952--2483995 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2483942 CATTTTCATT
2483952 TTCTTTTTGTTCTTTCTTTTTTG
1 TTCTTTTTGTTCTTTCTTTTTTG
*
2483975 TTCTTTTCTTTTCTTT-TTTTT
1 TTCTTTT-TGTTCTTTCTTTTT
2483996 ATATAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (23 bp):
TTCTTTTTGTTCTTTCTTTTTTG
Found at i:2490462 original size:11 final size:11
Alignment explanation
Indices: 2490446--2490484 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
2490436 ATGTCAAGTA
2490446 AAAATGGTAAG
1 AAAATGGTAAG
2490457 AAAATGGTAAG
1 AAAATGGTAAG
2490468 AAAATGGTAAG
1 AAAATGGTAAG
2490479 AAAATG
1 AAAATG
2490485 TCAAGTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (11 bp):
AAAATGGTAAG
Found at i:2491056 original size:36 final size:36
Alignment explanation
Indices: 2491016--2491103 Score: 88
Period size: 44 Copynumber: 2.2 Consensus size: 36
2491006 TCCATAAGCT
2491016 CATAAGCTTATTTTACCCATATACTTGTC-ATTATTC
1 CATAAGCTTATTTTACCCATATACTTG-CAATTATTC
2491052 CATAAGCTCGTAAGCTTATTTTACCCATATACTTGCAATTATTC
1 C---A-----TAAGCTTATTTTACCCATATACTTGCAATTATTC
2491096 CATAAGCT
1 CATAAGCT
2491104 CGTAAACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
36 7 0.16
39 1 0.02
41 1 0.02
43 1 0.02
44 33 0.77
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (36 bp):
CATAAGCTTATTTTACCCATATACTTGCAATTATTC
Found at i:2491066 original size:44 final size:44
Alignment explanation
Indices: 2490908--2491108 Score: 226
Period size: 45 Copynumber: 4.5 Consensus size: 44
2490898 AAATTTCTTA
* *
2490908 TCATTTTTCCTATAAGCTCGTAAGCTTATTCTACCAATATACTT-
1 TCATTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATACTTG
* * ** * *
2490952 ACTACTTATTCCATAAGCTCGTAAGCTTAGTTTATTAATACACTTA
1 TC-A-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTG
* * * *
2490998 CCATTTGTTCCATAAGCTCATAAGCTTATTTTACCCATATACTTG
1 TCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTG
*
2491043 TCATTATTCCATAAGCTCGTAAGCTTATTTTACCCATATACTTG
1 TCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTG
2491087 -CAATTATTCCATAAGCTCGTAA
1 TC-ATTATTCCATAAGCTCGTAA
2491109 ACTTTTTGCA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.01
44 60 0.45
45 65 0.49
46 7 0.05
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (44 bp):
TCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTG
Found at i:2491269 original size:40 final size:40
Alignment explanation
Indices: 2491219--2491341 Score: 219
Period size: 40 Copynumber: 3.1 Consensus size: 40
2491209 CAACGTAGTG
*
2491219 TTACATATAAGGTCGTGCCCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
*
2491259 TTACACATAAGGTCGTGCTCACCATATACACCGAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
*
2491299 TTACACATAAGGTCGTGCCCACCATATACACCAAAGTGTA
1 TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
2491339 TTA
1 TTA
2491342 TAAACCTGCA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
Found at i:2494973 original size:40 final size:39
Alignment explanation
Indices: 2494918--2495001 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
2494908 ACGATCGACG
* * *
2494918 ATGAAAAATGTTGGTTAAAGGGTCACATTATACTTATATT
1 ATGAAAAATGTTGGTTAAAAGGCCACATTAAACTT-TATT
*
2494958 ATGAAACATGTTGGTTAAAAGGCCACATTAAACTTTATT
1 ATGAAAAATGTTGGTTAAAAGGCCACATTAAACTTTATT
*
2494997 CTGAA
1 ATGAA
2495002 TTAGAGGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 8 0.21
40 31 0.79
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (39 bp):
ATGAAAAATGTTGGTTAAAAGGCCACATTAAACTTTATT
Found at i:2501707 original size:3 final size:3
Alignment explanation
Indices: 2501699--2501751 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2501689 CCATCTCTTC
2501699 TAT 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 TAT
2501747 TAT TA
1 TAT TA
2501752 GTTTAGGGTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2502473 original size:27 final size:29
Alignment explanation
Indices: 2502443--2502498 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
2502433 AATATACTTT
2502443 TAATA-AATTCTAATTT-TTATTTAATAG
1 TAATACAATTCTAATTTATTATTTAATAG
* *
2502470 TAATACAATTTTTATTTCATTATTTAATA
1 TAATACAATTCTAATTT-ATTATTTAATA
2502499 TAGAGTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
30 10 0.42
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (29 bp):
TAATACAATTCTAATTTATTATTTAATAG
Found at i:2507504 original size:15 final size:15
Alignment explanation
Indices: 2507468--2507524 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
2507458 TCTTGTGTGA
*
2507468 GAGAAGAAGAAGAA-
1 GAGAAGAAGGAGAAT
2507482 GA-AAGAAGGAGAAT
1 GAGAAGAAGGAGAAT
2507496 GAGAAGAAGGAGAAT
1 GAGAAGAAGGAGAAT
2507511 GAGAAGAAGGAGAA
1 GAGAAGAAGGAGAA
2507525 GGGGATCACT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 10 0.25
14 4 0.10
15 26 0.65
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.04
Consensus pattern (15 bp):
GAGAAGAAGGAGAAT
Found at i:2508513 original size:7 final size:7
Alignment explanation
Indices: 2508498--2508540 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2508488 GGACTTTGGA
*
2508498 TTTATAT
1 TTTAAAT
2508505 TTTAAAT
1 TTTAAAT
2508512 TTTAAATT
1 TTTAAA-T
2508520 TTTAAAT
1 TTTAAAT
* *
2508527 TTTAGAG
1 TTTAAAT
2508534 TTTAAAT
1 TTTAAAT
2508541 AAATAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:2508520 original size:14 final size:14
Alignment explanation
Indices: 2508498--2508540 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2508488 GGACTTTGGA
*
2508498 TTTATATTTTAAAT
1 TTTAAATTTTAAAT
2508512 TTTAAATTTTTAAAT
1 TTTAAA-TTTTAAAT
* *
2508527 TTTAGAGTTTAAAT
1 TTTAAATTTTAAAT
2508541 AAATAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TTTAAATTTTAAAT
Found at i:2508528 original size:22 final size:22
Alignment explanation
Indices: 2508498--2508540 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2508488 GGACTTTGGA
* *
2508498 TTTATATTTTAAATTTTAAATT
1 TTTAAATTTTAAAGTTTAAATT
*
2508520 TTTAAATTTTAGAGTTTAAAT
1 TTTAAATTTTAAAGTTTAAAT
2508541 AAATAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTAAATTTTAAAGTTTAAATT
Found at i:2508586 original size:24 final size:26
Alignment explanation
Indices: 2508539--2508586 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
2508529 TAGAGTTTAA
*
2508539 ATAAATAAAATTATATGTATTTATAT
1 ATAAATAAAATTATATGTAATTATAT
*
2508565 ATAAA-AAAA-TATATTTAATTAT
1 ATAAATAAAATTATATGTAATTAT
2508587 TGAATTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 4 0.20
26 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAAATAAAATTATATGTAATTATAT
Found at i:2511940 original size:16 final size:16
Alignment explanation
Indices: 2511919--2511949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2511909 TAATCGGTTT
2511919 CGGTTTGTAAAAAAAC
1 CGGTTTGTAAAAAAAC
*
2511935 CGGTTTTTAAAAAAA
1 CGGTTTGTAAAAAAA
2511950 AAAATCGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (16 bp):
CGGTTTGTAAAAAAAC
Found at i:2511973 original size:21 final size:21
Alignment explanation
Indices: 2511949--2512025 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 21
2511939 TTTTAAAAAA
2511949 AAAAATCG-GATTTTTTCGGAT
1 AAAAATCGAG-TTTTTTCGGAT
* *
2511970 AAAAATCTAGTTTTTT--TA-
1 AAAAATCGAGTTTTTTCGGAT
* *
2511988 AAAAACTGGATTTTTTTCGGAT
1 AAAAA-TCGAGTTTTTTCGGAT
2512010 AAAAAATCGA-TTTTTT
1 -AAAAATCGAGTTTTTT
2512026 ATCCGGTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
18 5 0.12
19 9 0.21
21 20 0.47
22 4 0.09
23 5 0.12
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (21 bp):
AAAAATCGAGTTTTTTCGGAT
Found at i:2512487 original size:68 final size:68
Alignment explanation
Indices: 2512400--2512727 Score: 434
Period size: 68 Copynumber: 4.8 Consensus size: 68
2512390 TAGGGATTTT
* * *
2512400 TTTAGGGTAAACTACCTATTTGGTCACTCATATATTATCTAATTTATGTTTTGATCATTTGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGATCACTCGATTA
2512465 TTA
66 TTA
* * *
2512468 TTTAGGGTAAACTATCTATTTGGTTACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGATCACTCGATTA
2512533 TTA
66 TTA
*
2512536 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGATCACTCGATTA
2512601 TTA
66 TTA
* **
2512604 TTTAGGGTAAACTACTAAACTACCTATTTGGTCACTTATATATTATCTAATATAAT-TCAT-AT-
1 TTTAGGG--------TAAACTACCTATTTGGTCACTTATATATTATCTAAT-TTATGTTTTGATC
*
2512666 A-T--ATTTTTA
57 ACTCGATTATTA
2512675 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTG
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTG
2512728 GTTACTCTAT
Statistics
Matches: 233, Mismatches: 16, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
62 3 0.01
63 38 0.16
68 135 0.58
71 13 0.06
73 1 0.00
74 1 0.00
75 1 0.00
76 38 0.16
77 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGATCACTCGATTA
TTA
Found at i:2512535 original size:31 final size:31
Alignment explanation
Indices: 2512500--2512604 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
2512490 GTTACTTATA
2512500 TATTATCTAATTTATGTTTTGGTCACTCGAT
1 TATTATCTAATTTATGTTTTGGTCACTCGAT
* ** ** *
2512531 TATTATTTAGGGTAAACTACCTATTTGGTCACT-TAT
1 TATTA--T---CTAATTTATGT-TTTGGTCACTCGAT
2512567 ATATTATCTAATTTATGTTTTGGTCACTCGAT
1 -TATTATCTAATTTATGTTTTGGTCACTCGAT
2512599 TATTAT
1 TATTAT
2512605 TTAGGGTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
31 21 0.39
32 8 0.15
33 1 0.02
35 1 0.02
36 8 0.15
37 15 0.28
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (31 bp):
TATTATCTAATTTATGTTTTGGTCACTCGAT
Found at i:2512572 original size:37 final size:37
Alignment explanation
Indices: 2512463--2512573 Score: 101
Period size: 37 Copynumber: 3.2 Consensus size: 37
2512453 ATCATTTGAT
*
2512463 TATTATTTAGGGTAAACTATCTATTTGGTTACTTATA
1 TATTATTTAGGGTAAACTATCTATTTGGTCACTTATA
* ** * *
2512500 TATTA--T---CTAATTTATGT-TTTGGTCACTCGAT-
1 TATTATTTAGGGTAAACTATCTATTTGGTCACT-TATA
*
2512531 TATTATTTAGGGTAAACTACCTATTTGGTCACTTATA
1 TATTATTTAGGGTAAACTATCTATTTGGTCACTTATA
2512568 TATTAT
1 TATTAT
2512574 CTAATTTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
31 14 0.26
32 9 0.17
33 1 0.02
35 1 0.02
36 8 0.15
37 21 0.39
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (37 bp):
TATTATTTAGGGTAAACTATCTATTTGGTCACTTATA
Found at i:2512865 original size:32 final size:32
Alignment explanation
Indices: 2512824--2512887 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2512814 TGCTAACATG
*
2512824 ACATTTTTTAATTATGTTTGGGTGTTGGACTA
1 ACATTTTTTAATTATGTTTGGATGTTGGACTA
2512856 ACATTTTTTAATTATGTTTGGATGTTGGACTA
1 ACATTTTTTAATTATGTTTGGATGTTGGACTA
2512888 CATAATTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.50
Consensus pattern (32 bp):
ACATTTTTTAATTATGTTTGGATGTTGGACTA
Found at i:2514493 original size:13 final size:13
Alignment explanation
Indices: 2514475--2514501 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2514465 AAATTATATG
2514475 AAAAATTGATTTT
1 AAAAATTGATTTT
2514488 AAAAATTGATTTT
1 AAAAATTGATTTT
2514501 A
1 A
2514502 TTAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
AAAAATTGATTTT
Found at i:2514572 original size:3 final size:3
Alignment explanation
Indices: 2514564--2514607 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2514554 GAAAGAAAAC
2514564 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2514608 GAATTAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2523156 original size:22 final size:21
Alignment explanation
Indices: 2523130--2523172 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2523120 AAAATGTTGA
2523130 AAAAAAATAGCAGTTCGAAAAAG
1 AAAAAAA-A-CAGTTCGAAAAAG
*
2523153 AAAAAAAACTGTTCGAAAAA
1 AAAAAAAACAGTTCGAAAAA
2523173 AAGACATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAAAAACAGTTCGAAAAAG
Found at i:2526252 original size:64 final size:65
Alignment explanation
Indices: 2526143--2526276 Score: 180
Period size: 64 Copynumber: 2.1 Consensus size: 65
2526133 AGATGAAAAA
* * * * * **
2526143 TTATTGTTATACTGATTTGAGTGATTGGAAAAATGAATCCTAAGTTTAAGATGGTAAGAATAAAT
1 TTATCGTTATACTAATTTGAGTGATTGGAAAAACGAATCCCAAGTTAAAGATAATAAGAATAAAT
* *
2526208 TTATCGTT-TACTAATTTGAGTGATTGGAAAAACGAGTCCCAAGTTAAAGATAATAAGAATAGAT
1 TTATCGTTATACTAATTTGAGTGATTGGAAAAACGAATCCCAAGTTAAAGATAATAAGAATAAAT
2526272 TTATC
1 TTATC
2526277 ATTTTCCTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 53 0.88
65 7 0.12
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (65 bp):
TTATCGTTATACTAATTTGAGTGATTGGAAAAACGAATCCCAAGTTAAAGATAATAAGAATAAAT
Found at i:2527567 original size:21 final size:22
Alignment explanation
Indices: 2527530--2527584 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
2527520 AGTTTAAAAA
* *
2527530 AATATTTAT-TTATTTATGATT
1 AATATTTTTATTATTTATGAAT
* *
2527551 ATTATTTTTATTA-TTATTAAT
1 AATATTTTTATTATTTATGAAT
2527572 AATATTTTTATTA
1 AATATTTTTATTA
2527585 ATTTTTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
AATATTTTTATTATTTATGAAT
Found at i:2528775 original size:2 final size:2
Alignment explanation
Indices: 2528768--2528802 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2528758 CGTTATTTGG
2528768 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
2528803 GTTTAATCGT
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:2533392 original size:106 final size:106
Alignment explanation
Indices: 2533207--2533866 Score: 685
Period size: 106 Copynumber: 6.5 Consensus size: 106
2533197 GACGAAGGGG
* * *
2533207 CTTCCCAGTTTCAGAGCCAATTTTAACCTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
* *
2533272 TCAACTTTACAACGAAGGGGCGACTGGTTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
*
2533313 CTTCCCAGTTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
*
2533378 TCAACTTCACAACGAAGGGGCGACTGGTTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
* * ** * *
2533419 CTTCCCAATTTCAGAGCTAATTTCAACTTCTTAGCGAAGGATATTGGACTCAAGACAGCACAAAC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
* * *
2533484 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAAC--A-AA
66 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
* * * * *
2533522 --T---AATTTC----CCAATTTCAACTTCACAGTGAAGGATATTGGTCCCAAGATAACACAAGC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
* *
2533578 TCAACTTCACGACGAAGGGGCGGCTGATTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
* * *
2533619 -----C--TTTCAGAGTCAATTTCAAC-T-----C--AGGATATTAGACTCAAGACAGCACAAGC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
*** * *
2533669 TCAACTTCACGGTGAAGGGGCGGCTGACTGTCAACAAACAA
66 TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
* * * * * * *
2533710 -TTCCCCAATTTCATATCCAATTTCAACTTCACAGAGAAGGACATTGGACTCAAGACATCACAAA
1 CTT-CCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAG
** * * *
2533774 CTCAACTTCACGGCGAAGGGGCGGCCGACTGTCAACAAACAA
65 CTCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
* * *
2533816 TTTCCCAGTTCCAGAACCAATTTCAACTTCAC-GACGAAGGATATTGGACTC
1 CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2533867 GGAGCAATAC
Statistics
Matches: 475, Mismatches: 54, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
91 61 0.13
94 72 0.15
95 4 0.01
96 2 0.00
97 2 0.00
98 23 0.05
99 11 0.02
101 1 0.00
103 2 0.00
104 1 0.00
105 1 0.00
106 293 0.62
107 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CTTCCCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGC
TCAACTTCACAACGAAGGGGCGACTGATTGTCAACAAACAA
Found at i:2533673 original size:291 final size:296
Alignment explanation
Indices: 2533223--2533822 Score: 771
Period size: 291 Copynumber: 2.0 Consensus size: 296
2533213 AGTTTCAGAG
* * *
2533223 CCAATTTTAACCTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTTACAACGAA
1 CCAATTTCAACCTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAACGAA
* *
2533288 GGGGCGACTGGTTGTCAACAAACAACTTCCCAGTTTTAGAGCCAATTTCAACTTCACAGCGAAGG
66 GGGGCGACTGATTGTCAACAAACAA----CCA-TTTCAGAGCCAATTTCAACTT---A-C-AAGG
* **
2533353 ATATTGGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGGTTGTCAACAAACA
121 ATATTAGACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACA
* ** * *
2533418 ACTT-CCCAATTTCAGAGCTAATTTCAACTTCTTAGCGAAGGATATTGGACTCAAGACAGCACAA
186 A-TTCCCCAATTTCAGAGCCAATTTCAACTTCACAGAGAAGGACATTGGACTCAAGACAGCACAA
* *
2533482 ACTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTC
250 ACTCAACTTCACAGCGAAGGGGCGGCCGACTGTCAACAAACAATTTC
* ** * * *
2533529 CCAATTTCAACTTCACAGTGAAGGATATTGGTCCCAAGATAACACAAGCTCAACTTCACGACGAA
1 CCAATTTCAACCTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAACGAA
* *
2533594 GGGGCGGCTGATTGTCAACAAACAA-C-TTTCAGAGTCAATTTCAAC-T-C-AGGATATTAGACT
66 GGGGCGACTGATTGTCAACAAACAACCATTTCAGAGCCAATTTCAACTTACAAGGATATTAGACT
* *** *
2533654 CAAGACAGCACAAGCTCAACTTCACGGTGAAGGGGCGGCTGACTGTCAACAAACAATTCCCCAAT
131 CAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAATTCCCCAAT
* * *
2533719 TTCATATCCAATTTCAACTTCACAGAGAAGGACATTGGACTCAAGACATCACAAACTCAACTTCA
196 TTCAGAGCCAATTTCAACTTCACAGAGAAGGACATTGGACTCAAGACAGCACAAACTCAACTTCA
*
2533784 CGGCGAAGGGGCGGCCGACTGTCAACAAACAATTTC
261 CAGCGAAGGGGCGGCCGACTGTCAACAAACAATTTC
2533820 CCA
1 CCA
2533823 GTTCCAGAAC
Statistics
Matches: 261, Mismatches: 32, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
290 2 0.01
291 160 0.61
293 1 0.00
298 1 0.00
299 17 0.07
301 1 0.00
306 79 0.30
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (296 bp):
CCAATTTCAACCTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAACGAA
GGGGCGACTGATTGTCAACAAACAACCATTTCAGAGCCAATTTCAACTTACAAGGATATTAGACT
CAAGACAACACAAGCTCAACTTCACAACGAAGGGGCGACTGACTGTCAACAAACAATTCCCCAAT
TTCAGAGCCAATTTCAACTTCACAGAGAAGGACATTGGACTCAAGACAGCACAAACTCAACTTCA
CAGCGAAGGGGCGGCCGACTGTCAACAAACAATTTC
Found at i:2534147 original size:253 final size:252
Alignment explanation
Indices: 2533814--2534658 Score: 1302
Period size: 252 Copynumber: 3.3 Consensus size: 252
2533804 GTCAACAAAC
* * ** * * ***
2533814 AATTTCCCAGTTCCAGAACCAATTTCAACTTCAC-GACGAAGGATATTGGACTCGGAGCAATACA
1 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGA-GAAGGATATTGGCCTCGGAACAGCGCA
* *
2533878 ACGTACTCGGATTTCAACTTCACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACGACGAAG
65 ACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACGACGAAG
* * * *
2533943 GGGCCACCTGCAGTTTCAACTTCACGACAAAGAAAATCGTGCACACAAGCAGCAGCCATCTCCAT
130 GGGCCACCCGC-GTTTCAACTTCACGACGAAGGAAATCGTGCACACAAGCAGCATCCATCTCCAT
** *
2534008 ATTGGATTTCAACTTCATTACGAAGGATATCCAACTCAAAGAAGGAGTGCCTGTCAACA
194 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAACA
*
2534067 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGAGAAGGATATTGGCCTCGGAACAGTGCAA
1 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGAGAAGGATATTGGCCTCGGAACAGCGCAA
* *
2534132 TTTACTTGGATTTCAACTTCACGATGAAGGATATCCAATTC-CAGGCTCAACTTCACGACGAAGG
66 CTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACGACGAAGG
2534196 GGCCACCCGCGATTTCAACTTCACGACGAAGGAAATCGTGCACACAAGCAGCATCCATCTCCATA
131 GGCCACCCGCG-TTTCAACTTCACGACGAAGGAAATCGTGCACACAAGCAGCATCCATCTCCATA
2534261 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAACA
195 TTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAACA
* * * *
2534319 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCATGGTA-AAGAATATTAGCCTCGGAATAGCGCA
1 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGG-AGAAGGATATTGGCCTCGGAACAGCGCA
* *
2534383 ATTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATT-TCAGGCTCAATTTCACGACGAAG
65 ACTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACGACGAAG
* * * *
2534447 GGGCCACCCGCGGTTTCAACTTCACGATGAAGGAAATCGTACACACAAGCATCATCCATCTCTAT
130 GGGCCACCCGC-GTTTCAACTTCACGACGAAGGAAATCGTGCACACAAGCAGCATCCATCTCCAT
* *
2534512 ATTGGATTTCAACTTCACGACGAATGATATCCAACTCAAAGAATGAGTGTCTGTCAACA
194 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAACA
*
2534571 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGCGAAGGATATTGGCCTCGGAACAGCGCAA
1 AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGAGAAGGATATTGGCCTCGGAACAGCGCAA
2534636 CTTACATTGGATTTCAACTTCAC
66 CTTAC-TTGGATTTCAACTTCAC
2534659 AATGAAGGGG
Statistics
Matches: 547, Mismatches: 38, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
251 1 0.00
252 434 0.79
253 110 0.20
254 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (252 bp):
AATTTTCCAGTTTCAGAGTCAATTTCAACTTCACGGAGAAGGATATTGGCCTCGGAACAGCGCAA
CTTACTTGGATTTCAACTTCACGACGAAGGATATCCAATTCTCAGGCTCAACTTCACGACGAAGG
GGCCACCCGCGTTTCAACTTCACGACGAAGGAAATCGTGCACACAAGCAGCATCCATCTCCATAT
TGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAACA
Found at i:2534688 original size:32 final size:32
Alignment explanation
Indices: 2534647--2534765 Score: 114
Period size: 32 Copynumber: 3.7 Consensus size: 32
2534637 TTACATTGGA
*
2534647 TTTCAACTTCACAATGAAGGGGCCATCCACGG
1 TTTCAACTTCACAACGAAGGGGCCATCCACGG
* ** * *
2534679 TTTCAACTTCACGACGAAGGATATCCAATTCAAGG
1 TTTCAACTTCACAACGAAGG--GGCC-ATCCACGG
* * *
2534714 -CTCAACTTTACAACGAAGGGGCCATCCACGA
1 TTTCAACTTCACAACGAAGGGGCCATCCACGG
*
2534745 TTTCAACTTCACGACGAAGGG
1 TTTCAACTTCACAACGAAGGG
2534766 AATCGTACCT
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
31 5 0.08
32 37 0.56
34 18 0.27
35 6 0.09
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (32 bp):
TTTCAACTTCACAACGAAGGGGCCATCCACGG
Found at i:2535232 original size:21 final size:22
Alignment explanation
Indices: 2535195--2535249 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
2535185 AGTTTAAAAA
* *
2535195 AATATTTAT-TTATTTATGATT
1 AATATTTTTATTATTTATGAAT
* *
2535216 ATTATTTTTATTA-TTATTAAT
1 AATATTTTTATTATTTATGAAT
2535237 AATATTTTTATTA
1 AATATTTTTATTA
2535250 ATTGTTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
AATATTTTTATTATTTATGAAT
Found at i:2536438 original size:2 final size:2
Alignment explanation
Indices: 2536431--2536455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2536421 TGTTATTTGG
2536431 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2536456 GTTTAATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2538833 original size:24 final size:24
Alignment explanation
Indices: 2538806--2538860 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
2538796 CGTTCATTTA
*
2538806 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
2538830 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
2538854 CGTTCAT
1 CGTTCAT
2538861 TTATGTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.47
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:2538844 original size:14 final size:14
Alignment explanation
Indices: 2538827--2538867 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2538817 GTTCGGTTAT
2538827 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
2538841 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
*
2538855 GTTCATTTATGTT
1 GTTCGTTTATGTT
2538868 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:2539969 original size:16 final size:16
Alignment explanation
Indices: 2539948--2539978 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2539938 AAGGTTTACA
2539948 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
2539964 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
2539979 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:2540073 original size:16 final size:16
Alignment explanation
Indices: 2540049--2540081 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2540039 AAATTTTTTT
2540049 TGTTAGTTTATGTTCG
1 TGTTAGTTTATGTTCG
*
2540065 TGTTTGTTTATGTTCG
1 TGTTAGTTTATGTTCG
2540081 T
1 T
2540082 TTATTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTAGTTTATGTTCG
Found at i:2542596 original size:14 final size:14
Alignment explanation
Indices: 2542577--2542605 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2542567 ATGTTGTTGG
2542577 TAAATATTGATATT
1 TAAATATTGATATT
2542591 TAAATATTGATATT
1 TAAATATTGATATT
2542605 T
1 T
2542606 TTTTAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAAATATTGATATT
Found at i:2543898 original size:39 final size:39
Alignment explanation
Indices: 2543854--2543930 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
2543844 AAAAATAATT
2543854 TAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAGAATA
1 TAGAATGTT-ATGGTGGAAA-AATTTAAGAAATTAAGAATA
* *
2543893 TAGAATGTTATGGTGGTAAAATTTAAGAAATTAGGAAT
1 TAGAATGTTATGGTGGAAAAATTTAAGAAATTAAGAAT
2543931 TTTGAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 29 0.85
40 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (39 bp):
TAGAATGTTATGGTGGAAAAATTTAAGAAATTAAGAATA
Found at i:2544912 original size:21 final size:21
Alignment explanation
Indices: 2544886--2544959 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
2544876 GTGTTCCATT
2544886 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
2544907 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
2544927 TCGCATTACGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2544948 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2544960 TTTCCATTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2544924 original size:41 final size:41
Alignment explanation
Indices: 2544879--2544982 Score: 190
Period size: 41 Copynumber: 2.5 Consensus size: 41
2544869 CAAATTCGTG
2544879 TTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
1 TTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
* *
2544920 TTCCATTTCGCATTACGATAGTTGAAAATCGCGTTGCGATT
1 TTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
2544961 TTCCATTTCGCGTTGCGATAGT
1 TTCCATTTCGCGTTGCGATAGT
2544983 CTACAGTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
Found at i:2544999 original size:22 final size:21
Alignment explanation
Indices: 2544971--2545042 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
2544961 TTCCATTTCG
2544971 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
** * *
2544993 CGTTGCGATTTTCCAAATT-T
1 CGTTGCGATAGTCTAAGTTGT
2545013 -GTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTA-AGTTGT
2545034 CGTTGCGAT
1 CGTTGCGAT
2545043 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (21 bp):
CGTTGCGATAGTCTAAGTTGT
Found at i:2545017 original size:41 final size:41
Alignment explanation
Indices: 2544951--2545062 Score: 165
Period size: 41 Copynumber: 2.7 Consensus size: 41
2544941 TTGAAAATCG
2544951 CGTTGCGATTTTCC--ATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTT---GTTGCGATAGTCTACAGTTGT
*
2544993 CGTTGCGATTTTCCAAATTTGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATTTTCCAAATTTGTTGCGATAGTCTACAGTTGT
*
2545034 CGTTGCGATTTTCCAAATTCGTTGCGATA
1 CGTTGCGATTTTCCAAATTTGTTGCGATA
2545063 TTTAAAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
41 48 0.73
42 14 0.21
44 4 0.06
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTTGTTGCGATAGTCTACAGTTGT
Found at i:2545018 original size:19 final size:19
Alignment explanation
Indices: 2544994--2545061 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
2544984 TACAGTTGTC
2544994 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** * *
2545013 GTTGCGATAGTCTATAGTTGT
1 GTTGCGATTTTCCA-AATT-T
*
2545034 CGTTGCGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
2545054 GTTGCGAT
1 GTTGCGAT
2545062 ATTTAAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 19 0.51
20 3 0.08
21 4 0.11
22 11 0.30
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:2545155 original size:6 final size:6
Alignment explanation
Indices: 2545144--2545168 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2545134 GACACGCATT
2545144 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
2545169 GACGAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2545750 original size:6 final size:5
Alignment explanation
Indices: 2545704--2545748 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
2545694 CCGTCTCGTC
*
2545704 TCGGG TCAGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
2545749 TGATAATACG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 26 0.70
6 11 0.30
ACGTcount: A:0.02, C:0.20, G:0.53, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:2545898 original size:20 final size:20
Alignment explanation
Indices: 2545873--2545965 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
2545863 ACTGTAGACT
2545873 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2545893 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
2545914 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2545934 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2545954 ATCGCAACGCGA
1 ATCGCAACGCGA
2545966 TTTTCAACTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2545919 original size:21 final size:20
Alignment explanation
Indices: 2545873--2545993 Score: 125
Period size: 20 Copynumber: 6.0 Consensus size: 20
2545863 ACTGTAGACT
*
2545873 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
** * *
2545893 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
*
2545914 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
*
2545934 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
** * *
2545954 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
2545975 ATCGCAACGCGAAATGCAA
1 ATCGCAACGCGAAATGCAA
2545994 CGCGAATTTG
Statistics
Matches: 81, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
20 50 0.62
21 31 0.38
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGCAAA
Found at i:2546021 original size:61 final size:61
Alignment explanation
Indices: 2545873--2545990 Score: 236
Period size: 61 Copynumber: 1.9 Consensus size: 61
2545863 ACTGTAGACT
2545873 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
2545934 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
2545991 CAACGCGAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (61 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:2548019 original size:19 final size:18
Alignment explanation
Indices: 2547989--2548034 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
2547979 AATATGACAT
2547989 TTAAAT-AATAAAAAATGA
1 TTAAATAAAT-AAAAATGA
*
2548007 TTAAATAAATAAAAGTGA
1 TTAAATAAATAAAAATGA
2548025 TTAAAGTAAA
1 TTAAA-TAAA
2548035 AATAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
TTAAATAAATAAAAATGA
Found at i:2552207 original size:18 final size:17
Alignment explanation
Indices: 2552176--2552218 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2552166 AGATTTAAAT
2552176 AGTAAAAAAATGATTAA
1 AGTAAAAAAATGATTAA
2552193 A-TAAATAAAAGTGATTAA
1 AGTAAA-AAAA-TGATTAA
2552211 AGTAAAAA
1 AGTAAAAA
2552219 TAAAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 10 0.43
19 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (17 bp):
AGTAAAAAAATGATTAA
Found at i:2554295 original size:7 final size:7
Alignment explanation
Indices: 2554283--2554320 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
2554273 TGTTGGCTAG
2554283 TGGATTA
1 TGGATTA
2554290 TGGATTA
1 TGGATTA
2554297 TGGATTA
1 TGGATTA
2554304 TGGATTA
1 TGGATTA
2554311 TGGATTA
1 TGGATTA
2554318 TGG
1 TGG
2554321 CTAGTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (7 bp):
TGGATTA
Found at i:2554309 original size:21 final size:21
Alignment explanation
Indices: 2554276--2554337 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2554266 CCGATCGTGT
2554276 TGGCTAGTGGATTATGGATTA
1 TGGCTAGTGGATTATGGATTA
*
2554297 TGGATTA-TGGATTATGGATTA
1 TGG-CTAGTGGATTATGGATTA
*
2554318 TGGCTAGTGAATTATGGATT
1 TGGCTAGTGGATTATGGATT
2554338 TAAGAGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.40
Consensus pattern (21 bp):
TGGCTAGTGGATTATGGATTA
Found at i:2555485 original size:6 final size:6
Alignment explanation
Indices: 2555474--2555718 Score: 369
Period size: 6 Copynumber: 41.3 Consensus size: 6
2555464 CTCCGTCATG
2555474 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
2555522 GTATAT GTATAT GTATAT GTATAT GTATATAT GTAT-T GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT G--TATAT GTATAT GTATAT GTATAT
* * * *
2555571 ATGTAT ATATAT GTATAT GTATAT G--TAT GTATAT GTATATAT ATATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT G--TATAT GTATAT
2555619 GTATAT GTATAT GTATAT GTATAT G--TAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
2555665 G--TAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
2555711 GTATAT GT
1 GTATAT GT
2555719 TTACATATGA
Statistics
Matches: 222, Mismatches: 6, Indels: 22
0.89 0.02 0.09
Matches are distributed among these distances:
4 12 0.05
5 5 0.02
6 194 0.87
8 11 0.05
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:2559873 original size:7 final size:7
Alignment explanation
Indices: 2559779--2559871 Score: 168
Period size: 7 Copynumber: 13.3 Consensus size: 7
2559769 TTGAACCAAT
2559779 GGTAGAA
1 GGTAGAA
2559786 GGTAGAA
1 GGTAGAA
2559793 GGTAGAA
1 GGTAGAA
2559800 GGTAGAA
1 GGTAGAA
2559807 GGTAGAA
1 GGTAGAA
2559814 GGTAGAA
1 GGTAGAA
2559821 GGTAGAA
1 GGTAGAA
2559828 GGTAGAA
1 GGTAGAA
2559835 GGTAGAA
1 GGTAGAA
2559842 GGTAGAA
1 GGTAGAA
2559849 GGTAGAA
1 GGTAGAA
*
2559856 GGGAGAA
1 GGTAGAA
*
2559863 GGGAGAA
1 GGTAGAA
2559870 GG
1 GG
2559872 GACTTGTGGA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 85 1.00
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (7 bp):
GGTAGAA
Found at i:2562240 original size:3 final size:3
Alignment explanation
Indices: 2562232--2562298 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
2562222 TACCCATATG
*
2562232 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2562280 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
2562299 AATATATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2575104 original size:10 final size:10
Alignment explanation
Indices: 2575089--2575173 Score: 67
Period size: 10 Copynumber: 8.9 Consensus size: 10
2575079 ATTATGCTTG
2575089 AAGAAAAAGA
1 AAGAAAAAGA
*
2575099 AAGAAAAAAA
1 AAGAAAAAGA
2575109 AAGAGAAAAG-
1 AAGA-AAAAGA
2575119 -AG-AAAAGA
1 AAGAAAAAGA
*
2575127 AAAAAAAAGGA
1 AAGAAAAA-GA
*
2575138 AA-AAAAGGA
1 AAGAAAAAGA
2575147 AA-AAAAAG-
1 AAGAAAAAGA
2575155 AAGAAGAAA-A
1 AAGAA-AAAGA
2575165 AAGAAAAAG
1 AAGAAAAAG
2575174 GGGGTCAAGG
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
7 5 0.08
8 2 0.03
9 17 0.28
10 29 0.48
11 8 0.13
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:2575124 original size:19 final size:17
Alignment explanation
Indices: 2575092--2575173 Score: 60
Period size: 17 Copynumber: 4.6 Consensus size: 17
2575082 ATGCTTGAAG
*
2575092 AAAAAGAAAGA-AAAAA
1 AAAAAAAAAGAGAAAAA
* *
2575108 AAAGAGAAAAGAGAAAAG
1 AAA-AAAAAAGAGAAAAA
2575126 AAAAAAAAAG-GAAAAAA
1 AAAAAAAAAGAG-AAAAA
2575143 AGGAAAAAAAAGAAGAAGAAA
1 A--AAAAAAAAG-AGAA-AAA
*
2575164 AAAGAAAAAG
1 AAAAAAAAAG
2575174 GGGGTCAAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
16 4 0.08
17 17 0.33
18 7 0.13
19 17 0.33
20 2 0.04
21 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGAAAAA
Found at i:2575130 original size:24 final size:23
Alignment explanation
Indices: 2575090--2575171 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 23
2575080 TTATGCTTGA
2575090 AGAAAAAG-AAAGAAAAAAAAAG
1 AGAAAAAGAAAAGAAAAAAAAAG
2575112 AGAAAAGAGAAAAGAAAAAAAAAGG
1 AGAAAA-AGAAAAGAAAAAAAAA-G
* *
2575137 AAAAAAAGGAAAA-AAAAGAAGAAG
1 AGAAAAA-GAAAAGAAAA-AAAAAG
2575161 A-AAAAAGAAAA
1 AGAAAAAGAAAA
2575172 AGGGGGTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.21
23 7 0.13
24 20 0.38
25 15 0.28
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AGAAAAAGAAAAGAAAAAAAAAG
Found at i:2575131 original size:7 final size:7
Alignment explanation
Indices: 2575092--2575172 Score: 62
Period size: 7 Copynumber: 11.6 Consensus size: 7
2575082 ATGCTTGAAG
2575092 AAAAAGA
1 AAAAAGA
2575099 AAGAAA-A
1 AA-AAAGA
2575106 AAAAAGA
1 AAAAAGA
*
2575113 GAAAAGA
1 AAAAAGA
*
2575120 GAAAAGA
1 AAAAAGA
2575127 AAAAA-A
1 AAAAAGA
*
2575133 AAGGAA-A
1 AA-AAAGA
*
2575140 AAAAGGA
1 AAAAAGA
2575147 AAAAA-A
1 AAAAAGA
2575153 AGAAGAAGA
1 A-AA-AAGA
2575162 AAAAAGA
1 AAAAAGA
2575169 AAAA
1 AAAA
2575173 GGGGGTCAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
6 9 0.15
7 43 0.70
8 7 0.11
9 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2575141 original size:34 final size:35
Alignment explanation
Indices: 2575088--2575166 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
2575078 TATTATGCTT
* * *
2575088 GAAGAAAAAGAAAGAAAAAAAAAGAGAAAAGAGAA
1 GAAGAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAA
* *
2575123 -AAGAAAAAAAAAGGAAAAAAAGGAAAAAAAAGAA
1 GAAGAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAA
2575157 GAAGAAAAAA
1 GAAGAAAAAA
2575167 GAAAAAGGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 29 0.76
35 9 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (35 bp):
GAAGAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAA
Found at i:2575511 original size:16 final size:16
Alignment explanation
Indices: 2575490--2575529 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2575480 ATACAATTCT
2575490 ATTTATTTCA-AGTTCA
1 ATTTATTTCAGAG-TCA
*
2575506 ATTTATTTGAGAGTCA
1 ATTTATTTCAGAGTCA
2575522 ATTTATTT
1 ATTTATTT
2575530 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (16 bp):
ATTTATTTCAGAGTCA
Found at i:2576847 original size:83 final size:83
Alignment explanation
Indices: 2576207--2576849 Score: 1117
Period size: 83 Copynumber: 7.7 Consensus size: 83
2576197 AACATTAAAT
* *
2576207 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
**
2576271 GAACCAATCATTGAATTTA
65 GAACCAATCATTGAATTGG
* *
2576290 GAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
2576355 AACCAATCATTGAATTGG
66 AACCAATCATTGAATTGG
* *
2576373 GAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
2576438 AACCAATCATTGAATTGG
66 AACCAATCATTGAATTGG
*
2576456 GAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
2576521 AACCAATCATTGAATTTG
66 AACCAATCATTGAATTGG
* *
2576539 GAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
2576604 AACCAATCATTGAATTGG
66 AACCAATCATTGAATTGG
* *
2576622 GAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
2576687 AACCAATCATTGAATTGG
66 AACCAATCATTGAATTGG
*
2576705 GAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
2576770 AACCAATCATTGAATTTG
66 AACCAATCATTGAATTGG
*
2576788 GAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
2576850 TAAGAACTAC
Statistics
Matches: 539, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
83 535 0.99
84 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
GAAGATGAATATGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACCAATCATTGAATTGG
Found at i:2577989 original size:116 final size:115
Alignment explanation
Indices: 2577612--2578228 Score: 912
Period size: 116 Copynumber: 5.4 Consensus size: 115
2577602 TTCCAGAGAA
*
2577612 AGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* ** * * *
2577675 TCAATCTTTTACCCGAATCCATCATTTGATGGATCAGTCTTTTCCAGAG-AA
66 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCA-TCTTTGCCAG-GTAG
*
2577726 AGTTCATAATGAGAAGAACT-T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
2577789 TCAACCTTTT-TTCTGAATTCATCAATTTGATGGATTATCTTTGCCAGGTAG
66 TCAATCTTTTGCT-TGAATTCATC-ATTTGATGGATCATCTTTGCCAGGTAG
2577840 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
*
2577905 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATTATCTTTGCCAGGTAG
65 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTGCCAGGTAG
2577956 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
2578021 TTCAAACTTTTGCTTGAATTCATCATTTGATGGATCAACTTTGCCAGGTAG
65 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTGCCAGGTAG
2578072 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* ** *
2578137 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGCAG-AA
65 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTGCCAG--GTAG
*
2578189 AGTTCATAATGAGAAGAA--CTCATCTGAAGAAAG-AGAAGAA
1 AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAA
2578229 TTTATTCAAT
Statistics
Matches: 471, Mismatches: 21, Indels: 23
0.91 0.04 0.04
Matches are distributed among these distances:
113 8 0.02
114 120 0.25
115 14 0.03
116 248 0.53
117 79 0.17
118 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (115 bp):
AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAATCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTGCCAGGTAG
Found at i:2578377 original size:3 final size:3
Alignment explanation
Indices: 2578371--2578449 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
2578361 CCATATGATG
2578371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2578419 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2578450 AATATATATT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2581712 original size:11 final size:12
Alignment explanation
Indices: 2581685--2581727 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
2581675 TGTGTAAAAA
*
2581685 TAAATATTTAAAT
1 TAAATATAT-AAT
2581698 TAAATATAT-AT
1 TAAATATATAAT
*
2581709 TAAATATTTAAT
1 TAAATATATAAT
2581721 TAAATAT
1 TAAATAT
2581728 GGGTCGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 9 0.33
13 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAATATATAAT
Found at i:2585966 original size:19 final size:20
Alignment explanation
Indices: 2585925--2585968 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2585915 TTTTTAAAAC
2585925 TTTTA-AATTTTTTACATGA
1 TTTTATAATTTTTTACATGA
*
2585944 -TTTATAATTTTTTATAT-A
1 TTTTATAATTTTTTACATGA
2585962 TTTTATA
1 TTTTATA
2585969 TTAATAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTACATGA
Found at i:2588894 original size:13 final size:13
Alignment explanation
Indices: 2588876--2588914 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2588866 GCAGCTCTTC
2588876 CTTAAATTGTTCT
1 CTTAAATTGTTCT
2588889 CTTAAATTGTTCT
1 CTTAAATTGTTCT
2588902 CTTAAATTGTTCT
1 CTTAAATTGTTCT
2588915 TGGTTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CTTAAATTGTTCT
Found at i:2590150 original size:2 final size:2
Alignment explanation
Indices: 2590139--2590167 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2590129 TGATTACAAA
2590139 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2590168 TTTAATTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2591016 original size:16 final size:16
Alignment explanation
Indices: 2590998--2591120 Score: 183
Period size: 16 Copynumber: 7.7 Consensus size: 16
2590988 TAGTTGGACT
* *
2590998 GAAAGTAACCCGAACT
1 GAAAGCAACCCGAACC
* *
2591014 GAAAGAAACTCGAACC
1 GAAAGCAACCCGAACC
2591030 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
*
2591046 GAAAGCAACTCGAACC
1 GAAAGCAACCCGAACC
*
2591062 GAAAGTAACCCGAACC
1 GAAAGCAACCCGAACC
2591078 GAAAGCAACCCGAACC
1 GAAAGCAACCCGAACC
*
2591094 GAAAGTAACCCGAACC
1 GAAAGCAACCCGAACC
2591110 GAAAGCAACCC
1 GAAAGCAACCC
2591121 AAATTTAGTT
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 96 1.00
ACGTcount: A:0.45, C:0.32, G:0.19, T:0.05
Consensus pattern (16 bp):
GAAAGCAACCCGAACC
Found at i:2591040 original size:32 final size:32
Alignment explanation
Indices: 2590998--2591118 Score: 206
Period size: 32 Copynumber: 3.8 Consensus size: 32
2590988 TAGTTGGACT
* *
2590998 GAAAGTAACCCGAACTGAAAGAAACTCGAACC
1 GAAAGTAACCCGAACCGAAAGCAACTCGAACC
*
2591030 GAAAGCAACCCGAACCGAAAGCAACTCGAACC
1 GAAAGTAACCCGAACCGAAAGCAACTCGAACC
*
2591062 GAAAGTAACCCGAACCGAAAGCAACCCGAACC
1 GAAAGTAACCCGAACCGAAAGCAACTCGAACC
2591094 GAAAGTAACCCGAACCGAAAGCAAC
1 GAAAGTAACCCGAACCGAAAGCAAC
2591119 CCAAATTTAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.45, C:0.31, G:0.19, T:0.05
Consensus pattern (32 bp):
GAAAGTAACCCGAACCGAAAGCAACTCGAACC
Found at i:2591612 original size:20 final size:20
Alignment explanation
Indices: 2591589--2591650 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
2591579 GATTGGCCTA
**
2591589 AAAATATAAAGATTTGCCCG
1 AAAATATAAAGATTAACCCG
* *
2591609 AAAATATTAAGGTTAACCCG
1 AAAATATAAAGATTAACCCG
* * *
2591629 AAAATCTAAAGACTGACCCG
1 AAAATATAAAGATTAACCCG
2591649 AA
1 AA
2591651 TTGAAATATA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (20 bp):
AAAATATAAAGATTAACCCG
Found at i:2592110 original size:18 final size:18
Alignment explanation
Indices: 2592087--2592136 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2592077 TTTTTGTTTG
2592087 GTTGTTCATATTCTTCTA
1 GTTGTTCATATTCTTCTA
2592105 GTTGTTCATATTCTTCTA
1 GTTGTTCATATTCTTCTA
*
2592123 GTTGTTCATTTTCT
1 GTTGTTCATATTCT
2592137 ATGGATTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.58
Consensus pattern (18 bp):
GTTGTTCATATTCTTCTA
Found at i:2593939 original size:12 final size:12
Alignment explanation
Indices: 2593922--2593947 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2593912 TACTGATGTA
2593922 TTATATCAAGTT
1 TTATATCAAGTT
2593934 TTATATCAAGTT
1 TTATATCAAGTT
2593946 TT
1 TT
2593948 GCAGTAAAAA
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:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATATCAAGTT
Found at i:2594089 original size:15 final size:15
Alignment explanation
Indices: 2594069--2594108 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2594059 GTGAAAAGAA
2594069 TGAATTAAATGTTCT
1 TGAATTAAATGTTCT
2594084 TGAATTAAATGTTCT
1 TGAATTAAATGTTCT
2594099 TGAATTAAAT
1 TGAATTAAAT
2594109 ATACAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (15 bp):
TGAATTAAATGTTCT
Found at i:2601111 original size:168 final size:164
Alignment explanation
Indices: 2600787--2601119 Score: 630
Period size: 168 Copynumber: 2.0 Consensus size: 164
2600777 GATTGTATGC
2600787 GAACATGTGTTGTATAATAATGATCTATGAGATATTGATAATAAGACATAAGATTACATGCATAT
1 GAACATGTGTTGTATAATAATGATCTATGAGATATTGATAATAAGACATAAGATTACATGCATAT
2600852 GTAATATATTAAAGATAAGAATAATATGTTATATGCATATGAGAAAATGGTATATGTGATATGAC
66 GTAATATATTAAAGATAAGAATAATATGTTATATGCATATGAGAAAATGGTATATGTGATATGAC
2600917 CATTTGTGAAAAGGATGAATAATGTGAATTTCAT
131 CATTTGTGAAAAGGATGAATAATGTGAATTTCAT
2600951 GAACATGTGTTGTATAATAATGATCTATGAGATATTGATAATAAGACATAAGATTACATGCATAT
1 GAACATGTGTTGTATAATAATGATCTATGAGATATTGATAATAAGACATAAGATTACATGCATAT
2601016 GTAATATAAGTTAAAAGATAAGAAATAATATGTTATATGCATATGAGAAAATGGTATATGTGATA
66 GTAATAT-A-TT-AAAGATAAG-AATAATATGTTATATGCATATGAGAAAATGGTATATGTGATA
2601081 TGACCATTTGTGAAAAGGATGAATAATGTGAATTTCAT
127 TGACCATTTGTGAAAAGGATGAATAATGTGAATTTCAT
2601119 G
1 G
2601120 GAAAATGCTA
Statistics
Matches: 165, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
164 72 0.44
165 1 0.01
166 2 0.01
167 9 0.05
168 81 0.49
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (164 bp):
GAACATGTGTTGTATAATAATGATCTATGAGATATTGATAATAAGACATAAGATTACATGCATAT
GTAATATATTAAAGATAAGAATAATATGTTATATGCATATGAGAAAATGGTATATGTGATATGAC
CATTTGTGAAAAGGATGAATAATGTGAATTTCAT
Found at i:2601321 original size:21 final size:21
Alignment explanation
Indices: 2601295--2601336 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2601285 GAGTCGAGGG
*
2601295 TCTACGCGGTTCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
*
2601316 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
2601337 AATTCTACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (21 bp):
TCTACGCGGTCCTTCGGGACA
Found at i:2602145 original size:59 final size:59
Alignment explanation
Indices: 2602051--2602579 Score: 740
Period size: 59 Copynumber: 9.1 Consensus size: 59
2602041 GGGGTGTTAC
* * * * *
2602051 AGTGCCCTATATAGAAATTCATACACTTAGTATGATTTTCTTATCTTTTTAGCACACTTA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACAC-GA
* * *
2602111 A-TGCCCTATCTAGAAATTCATGCACTTAGTATGATTTTCTTATCG--TT---ACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
*
2602164 AGTGCCCTATCTAGAAATTCATACACTTAGTATGA--T--TTATCGTTTTAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* *
2602219 AGTACCCTATATGGAAATTCATACA-TTAGTATGATTTCCTTATCG-TTTAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * *
2602276 AGTGCCCTTATCTTGAAATTCATACACTTAATATGATTTCCTTATCGTTTTAGAACACGA
1 AGTGCCC-TATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * *
2602336 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCTTTATCATTTTATCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
*
2602395 AGTGCCCTATATGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* * *
2602454 ATTGCCCTATCCGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTATCACACGA
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
* **
2602513 AGTGCCCTATCTGGAAATTCATACATTTAGTATGATTTCCTTATCGTTTTAGCACACTT
1 AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
2602572 AGTGCCCT
1 AGTGCCCT
2602580 TTTTGGTAAT
Statistics
Matches: 423, Mismatches: 33, Indels: 27
0.88 0.07 0.06
Matches are distributed among these distances:
50 6 0.01
52 3 0.01
53 2 0.00
54 45 0.11
55 28 0.07
56 1 0.00
57 20 0.05
58 22 0.05
59 277 0.65
60 19 0.04
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (59 bp):
AGTGCCCTATCTGGAAATTCATACACTTAGTATGATTTCCTTATCGTTTTAGCACACGA
Found at i:2603024 original size:20 final size:19
Alignment explanation
Indices: 2602999--2603049 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 19
2602989 GTTTCCTGGC
2602999 ATCGATACCCTTACCATGGT
1 ATCGATACCCTT-CCATGGT
*
2603019 ATCGATACTACCCTTCTATGGT
1 ATCG--A-TACCCTTCCATGGT
2603041 ATCGATACC
1 ATCGATACC
2603050 AAAATTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
22 11 0.41
23 7 0.26
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.31
Consensus pattern (19 bp):
ATCGATACCCTTCCATGGT
Found at i:2603042 original size:22 final size:23
Alignment explanation
Indices: 2603004--2603048 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2602994 CTGGCATCGA
2603004 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
*
2603027 TACCCTT-CTATGGTATCGATAC
1 TACCCTTACCATGGTATCGATAC
2603049 CAAAATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33
Consensus pattern (23 bp):
TACCCTTACCATGGTATCGATAC
Found at i:2603426 original size:17 final size:15
Alignment explanation
Indices: 2603406--2603441 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2603396 TTCAAAGATA
2603406 TATTTAATTTATAATT
1 TATTTAATTTA-AATT
2603422 CTATTTAATTTAAATT
1 -TATTTAATTTAAATT
2603438 TATT
1 TATT
2603442 ACTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTAATTTAAATT
Found at i:2604963 original size:3 final size:3
Alignment explanation
Indices: 2604955--2605033 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
2604945 CCGGTTTGTA
* *
2604955 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
2604997 AAT ATTT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2605034 TTAAGTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
2 7 0.11
3 49 0.80
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2605279 original size:76 final size:76
Alignment explanation
Indices: 2605187--2606128 Score: 1740
Period size: 76 Copynumber: 12.4 Consensus size: 76
2605177 GAGGTCTTAA
*
2605187 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACACCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605252 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2605263 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605328 AGGCTTTTTGG
66 AGGCTTTTTGG
2605339 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605404 AGGCTTTTTGG
66 AGGCTTTTTGG
2605415 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
2605480 AGGCTTGTTGG
66 AGGCTTTTTGG
* *
2605491 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
2605556 AGACTTTTTGG
66 AGGCTTTTTGG
* *
2605567 AAACATCATGCACTGCAAGACTTACATATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605632 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2605643 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605708 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2605719 AAACATCATGCACTGCAGGACTTACAGATGACTCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605784 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2605795 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605860 AGGCTTTTTGG
66 AGGCTTTTTGG
2605871 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2605936 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2605947 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2606012 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2606023 AAACATCATGCACTGTAGGACTTACATATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2606088 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2606099 AAACATCATGCACTACAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
2606129 TGGGAAATAG
Statistics
Matches: 836, Mismatches: 30, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 836 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2607017 original size:22 final size:22
Alignment explanation
Indices: 2606983--2607033 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2606973 CATAAAGCTT
**
2606983 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTCAAAAAGAGAATCTA
*
2607005 TTATCTTCAAAAAGAGAATCTA
1 TCATCTTCAAAAAGAGAATCTA
2607027 TCATCTT
1 TCATCTT
2607034 TGAAGAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTCAAAAAGAGAATCTA
Found at i:2607491 original size:54 final size:54
Alignment explanation
Indices: 2607404--2607667 Score: 368
Period size: 54 Copynumber: 4.9 Consensus size: 54
2607394 AGAATAGTAG
* * * * * * *
2607404 GTTCTTAAAACATTTGACAGCGCATTCATCCTTTCCTATGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* *
2607458 GTTCGTAAAACATTTGAAAACACATTCATCCTTTCTTGTGGTTTCTGTTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* *
2607512 GTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGAA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* *
2607566 GTTCGTAAAGCATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
* * *
2607620 GTTCGTAAAGCGTTTGACAACACATTCATCCTTT-TCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCT-TGTGGTTTCTGC
2607668 CAATATTTTT
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
53 1 0.01
54 190 0.99
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTGCTCAGAC
Found at i:2612042 original size:12 final size:10
Alignment explanation
Indices: 2612027--2612092 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 10
2612017 CCCATTTTTA
*
2612027 TTTTTCCTTT
1 TTTTTTCTTT
2612037 TCTTTTTCTTT
1 T-TTTTTCTTT
*
2612048 TTTTTATTTTT
1 TTTTT-TCTTT
2612059 TATTTTTCATCTT
1 T-TTTTTC-T-TT
2612072 TTTTTTCTTTT
1 TTTTTTC-TTT
2612083 TTTTTTCTTT
1 TTTTTTCTTT
2612093 CTTTGCTGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
10 8 0.17
11 24 0.51
12 12 0.26
13 3 0.06
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:2612062 original size:34 final size:34
Alignment explanation
Indices: 2612021--2612086 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
2612011 ATTTCTCCCA
*
2612021 TTTTTATTTTTCCT-TTTCTTTTTCTTTTTTTTAT
1 TTTTTATTTTTCATCTTT-TTTTTCTTTTTTTTAT
2612055 TTTTTATTTTTCATCTTTTTTTTCTTTTTTTT
1 TTTTTATTTTTCATCTTTTTTTTCTTTTTTTT
2612087 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (34 bp):
TTTTTATTTTTCATCTTTTTTTTCTTTTTTTTAT
Found at i:2612120 original size:26 final size:24
Alignment explanation
Indices: 2612079--2612129 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 24
2612069 CTTTTTTTTC
2612079 TTTTTTTTTTCTTTCTTTGCTGGA
1 TTTTTTTTTTCTTTCTTTGCTGGA
2612103 TTTTTCTTATTTCTTTCTTTGCTGGA
1 TTTTT-TT-TTTCTTTCTTTGCTGGA
2612129 T
1 T
2612130 GAGTATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 5 0.20
25 2 0.08
26 18 0.72
ACGTcount: A:0.06, C:0.14, G:0.12, T:0.69
Consensus pattern (24 bp):
TTTTTTTTTTCTTTCTTTGCTGGA
Found at i:2614977 original size:27 final size:27
Alignment explanation
Indices: 2614947--2615002 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2614937 GTAATTATGT
2614947 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
2614974 AAAAATGCAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
2615001 AA
1 AA
2615003 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:2614991 original size:12 final size:12
Alignment explanation
Indices: 2614976--2615003 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2614966 CAAACGTAAA
2614976 AAATGCAAATGT
1 AAATGCAAATGT
2614988 AAATGCAAATGT
1 AAATGCAAATGT
2615000 AAAT
1 AAAT
2615004 ATGTGAATGT
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:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:2617092 original size:17 final size:15
Alignment explanation
Indices: 2617072--2617107 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2617062 TTCAAAGATA
2617072 TATTTAATTTATAATT
1 TATTTAATTTA-AATT
2617088 CTATTTAATTTAAATT
1 -TATTTAATTTAAATT
2617104 TATT
1 TATT
2617108 ACTATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTAATTTAAATT
Found at i:2617360 original size:14 final size:15
Alignment explanation
Indices: 2617330--2617362 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2617320 AATAGAATAA
2617330 ATAAATAAATATTAT
1 ATAAATAAATATTAT
*
2617345 ATAAATATAT-TTAT
1 ATAAATAAATATTAT
2617359 ATAA
1 ATAA
2617363 CTTAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAATAAATATTAT
Found at i:2617440 original size:16 final size:16
Alignment explanation
Indices: 2617419--2617474 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
2617409 ATATCAAACG
2617419 TAATAATAAAATAAAA
1 TAATAATAAAATAAAA
*
2617435 TAATAAT-AATTAAAA
1 TAATAATAAAATAAAA
* *
2617450 TGA-AAGAAAATTAAAA
1 TAATAATAAAA-TAAAA
2617466 GTAATAATA
1 -TAATAATA
2617475 TTAAACACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 12 0.40
17 2 0.07
18 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TAATAATAAAATAAAA
Found at i:2618738 original size:3 final size:3
Alignment explanation
Indices: 2618730--2618808 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
2618720 CCAGTTTGTA
* *
2618730 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
2618772 AAT ATTT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2618809 TTAAGTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
2 7 0.11
3 49 0.80
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2626286 original size:18 final size:18
Alignment explanation
Indices: 2626265--2626303 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2626255 TCTGCACAGG
2626265 ATGATTCTTTAACCTGAA
1 ATGATTCTTTAACCTGAA
2626283 ATGATTCTTTAACCTGAA
1 ATGATTCTTTAACCTGAA
2626301 ATG
1 ATG
2626304 GTGAGTAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
ATGATTCTTTAACCTGAA
Found at i:2626795 original size:33 final size:32
Alignment explanation
Indices: 2626756--2626844 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 32
2626746 AAGGAATTCA
* * *
2626756 TTGGGGCCTTAGAGCCTACCTAAGGGAGTATGT
1 TTGGGGCCTAAGAGCCTACCTAAGGGAGCAT-C
*
2626789 TTGGGGCCTAAGAGTCTA-CTCAA--GAGCATC
1 TTGGGGCCTAAGAGCCTACCT-AAGGGAGCATC
*
2626819 TCGGGGCCTAAGAGCCTACCTAAGGG
1 TTGGGGCCTAAGAGCCTACCTAAGGG
2626845 TCACCTTAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
30 18 0.39
31 7 0.15
32 3 0.07
33 18 0.39
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (32 bp):
TTGGGGCCTAAGAGCCTACCTAAGGGAGCATC
Found at i:2633520 original size:20 final size:22
Alignment explanation
Indices: 2633467--2633524 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
2633457 GCATGGGTAG
2633467 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
* *
2633491 TACATTGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
2633511 TGCATCGATGCACT
1 TGCATCGATGCACT
2633525 TCAAGGGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 16 0.53
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2634469 original size:18 final size:18
Alignment explanation
Indices: 2634346--2634461 Score: 178
Period size: 18 Copynumber: 6.4 Consensus size: 18
2634336 GAGGGTCTAC
*
2634346 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACACA
* *
2634364 ATGGTCCTTCGGAACACA
1 GTGGTCCTTCGGGACACA
2634382 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACACA
* *
2634400 ATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACACA
2634418 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACACA
*
2634436 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACACA
2634454 GTGGTCCT
1 GTGGTCCT
2634462 ACAGGACAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACACA
Found at i:2654528 original size:34 final size:35
Alignment explanation
Indices: 2654471--2654555 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 35
2654461 CCTCCCCAGG
*
2654471 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCT
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
2654506 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
2654540 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
2654556 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 30 0.62
35 18 0.38
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:2654621 original size:20 final size:20
Alignment explanation
Indices: 2654592--2654629 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2654582 AGATTACTCG
2654592 GAGGGAACCGATTCCCTCTT
1 GAGGGAACCGATTCCCTCTT
*
2654612 GAGGGTACCGATTCCCTC
1 GAGGGAACCGATTCCCTC
2654630 ACTGTTCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (20 bp):
GAGGGAACCGATTCCCTCTT
Found at i:2654693 original size:21 final size:21
Alignment explanation
Indices: 2654667--2654708 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2654657 ATTTGAATAT
*
2654667 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2654688 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2654709 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2654770 original size:21 final size:21
Alignment explanation
Indices: 2654737--2654776 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2654727 TTTTTGCAGA
*
2654737 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2654759 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2654777 AGATATGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2656061 original size:3 final size:3
Alignment explanation
Indices: 2656040--2656077 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2656030 TAAAGAAAGG
* *
2656040 GAA G-A GAA GAA AAA TAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2656078 TGAGGACGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2657825 original size:20 final size:20
Alignment explanation
Indices: 2657800--2657839 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2657790 ATCAGATTGT
2657800 CCAGGGAGTA-CAGATTCCCC
1 CCAGGGAGTATC-GATTCCCC
*
2657820 CCAGGGGGTATCGATTCCCC
1 CCAGGGAGTATCGATTCCCC
2657840 GGGAACAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (20 bp):
CCAGGGAGTATCGATTCCCC
Found at i:2658043 original size:21 final size:21
Alignment explanation
Indices: 2658010--2658049 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2658000 TGTTTGCAGA
*
2658010 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2658032 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2658050 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2661388 original size:16 final size:16
Alignment explanation
Indices: 2661367--2661400 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2661357 TTACTATTCA
*
2661367 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2661383 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2661399 CG
1 CG
2661401 GTTGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:2667546 original size:15 final size:15
Alignment explanation
Indices: 2667517--2667559 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2667507 ACGACCACAA
*
2667517 CCGAGCCGAGCCGAG
1 CCGAGCCGAGACGAG
*
2667532 CCGAGCCGTGACGAG
1 CCGAGCCGAGACGAG
* *
2667547 ACGAGACGAGACG
1 CCGAGCCGAGACG
2667560 GACAGCGGCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.33, G:0.40, T:0.02
Consensus pattern (15 bp):
CCGAGCCGAGACGAG
Found at i:2670559 original size:44 final size:44
Alignment explanation
Indices: 2670497--2670611 Score: 178
Period size: 44 Copynumber: 2.6 Consensus size: 44
2670487 TTTGTGAGCA
*
2670497 CAATAACCTTCG-TCGTGAAGTTGAAATCGTGGATGTTTCGAGTC
1 CAATATCCTTCGCT-GTGAAGTTGAAATCGTGGATGTTTCGAGTC
*
2670541 CAATATCCTTCGCTGTGAAGTTGAAATCGTGGATGTTTCGGGTC
1 CAATATCCTTCGCTGTGAAGTTGAAATCGTGGATGTTTCGAGTC
* *
2670585 CAATATCTTTCGCCGTGAAGTTGAAAT
1 CAATATCCTTCGCTGTGAAGTTGAAAT
2670612 TGGCTCTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
44 65 0.98
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (44 bp):
CAATATCCTTCGCTGTGAAGTTGAAATCGTGGATGTTTCGAGTC
Found at i:2680186 original size:21 final size:21
Alignment explanation
Indices: 2680160--2680199 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2680150 CCCCCTTTGA
*
2680160 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2680181 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2680200 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2688457 original size:15 final size:17
Alignment explanation
Indices: 2688425--2688461 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
2688415 AATACGAATG
2688425 TAAAAACATGGAAAATA
1 TAAAAACATGGAAAATA
2688442 TAAAAACAT-G-AAATA
1 TAAAAACATGGAAAATA
2688457 TAAAA
1 TAAAA
2688462 TGCAAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (17 bp):
TAAAAACATGGAAAATA
Found at i:2693162 original size:28 final size:29
Alignment explanation
Indices: 2693126--2693183 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
2693116 ATTTATCATA
*
2693126 AAACTTAATGTTA-TTATTTTTAAAATATT
1 AAACTTAAT-TTATTTATTATTAAAATATT
2693155 AAAC-TAATTTATTTATTATTAAAATATT
1 AAACTTAATTTATTTATTATTAAAATATT
2693183 A
1 A
2693184 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.11
28 20 0.74
29 4 0.15
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (29 bp):
AAACTTAATTTATTTATTATTAAAATATT
Found at i:2693315 original size:23 final size:23
Alignment explanation
Indices: 2693286--2693330 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2693276 AGTGTTATAT
2693286 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
2693309 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
2693331 AAATATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:2693334 original size:14 final size:15
Alignment explanation
Indices: 2693317--2693345 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2693307 AGTATATTTT
2693317 AAATATATT-TATTA
1 AAATATATTATATTA
2693331 AAATATATTATATTA
1 AAATATATTATATTA
2693346 TTATTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATATTATATTA
Found at i:2693336 original size:23 final size:23
Alignment explanation
Indices: 2693287--2693352 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
2693277 GTGTTATATT
* * **
2693287 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
2693310 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
* *
2693333 ATATATTATAT-TA-TTATTAA
1 ATATTTTAAATATATTTATTAA
2693353 TATTAAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 7 0.19
22 2 0.05
23 28 0.76
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:2693465 original size:47 final size:46
Alignment explanation
Indices: 2693377--2693466 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
2693367 ACATTATTCA
*
2693377 TTATTAATAATTTAATATTATTTCTATGAAATAAATAATAATAAATT
1 TTATTAATAATTTAATATTATTTCTA-GAAATAAAAAATAATAAATT
*
2693424 TTATTAATAATTTATTATATATTAT-TA-AAATAAAAATATAATA
1 TTATTAATAATTTAATAT-TATT-TCTAGAAATAAAAA-ATAATA
2693467 TCTTATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
46 8 0.21
47 23 0.61
48 6 0.16
49 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (46 bp):
TTATTAATAATTTAATATTATTTCTAGAAATAAAAAATAATAAATT
Found at i:2693531 original size:22 final size:24
Alignment explanation
Indices: 2693506--2693568 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
2693496 TTTATTGTAA
*
2693506 TATTAAAAATA-TAAT-ATTATAT
1 TATTAAAAATATTAATAAATATAT
*
2693528 TATTAGAAATATTAATAAATATAT
1 TATTAAAAATATTAATAAATATAT
* *
2693552 T-TTAAATATTTTAATAA
1 TATTAAAAATATTAATAA
2693569 TTAATATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 10 0.29
23 17 0.50
24 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTAAAAATATTAATAAATATAT
Found at i:2693531 original size:30 final size:34
Alignment explanation
Indices: 2693471--2693550 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 34
2693461 ATAATATCTT
* * *
2693471 ATATTATTATAATATAATTGATTATTTTATT-GTA
1 ATATTAATA-AATATAATTGATTATATTATTAGAA
2693505 ATATTAA-AAATATAA-T-ATTATATTATTAGAA
1 ATATTAATAAATATAATTGATTATATTATTAGAA
2693536 ATATTAATAAATATA
1 ATATTAATAAATATA
2693551 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.24
31 10 0.24
32 14 0.34
33 1 0.02
34 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (34 bp):
ATATTAATAAATATAATTGATTATATTATTAGAA
Done.