Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 120 of 343
Found at i:40328389 original size:27 final size:27
Alignment explanation
Indices: 40328348--40328473 Score: 155
Period size: 27 Copynumber: 4.7 Consensus size: 27
40328338 TAGTTTATCA
*
40328348 AATTACTGAAGTACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTATAAGGTAG
* * *
40328375 AATTACCGAAATACCCCCATAAGGTTG
1 AATTACTGAAATACCCCTATAAGGTAG
* **
40328402 AATTA-TCGAAATACCCCTGTAAGGTTT
1 AATTACT-GAAATACCCCTATAAGGTAG
* *
40328429 AATTACTAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTATAAGGTAG
40328456 AATTACTGAAATACCCCT
1 AATTACTGAAATACCCCT
40328474 TACTGAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 84 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTATAAGGTAG
Found at i:40328418 original size:54 final size:54
Alignment explanation
Indices: 40328359--40328675 Score: 302
Period size: 54 Copynumber: 6.1 Consensus size: 54
40328349 ATTACTGAAG
* * * *
40328359 TACCCCTATAAGGTAGAATTACCGAAATACCCCCATAAGGTTGAATTATCGAAA
1 TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
** * *
40328413 TACCCCTGTAAGGTTTAATTACTAAAATACCCCTGTAAGGTAGAATTA-CTGAAA
1 TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATC-GAAA
* *
40328467 TACCCC------------TTACTGAAATACCCCTGTAAGGTAGAATTATTGAAA
1 TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
* *
40328509 TACCCCTGT-AGTGTAGAATTACTAAAATACCCCCGTAAGGTAGAATTACCGAAA
1 TACCCCTGTAAG-GTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
* * * * *
40328563 TACCCTTGTAGGGTAGAATTACTGATATACCCCCGTAGGGTAGAATTATCAAAA
1 TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
* * * * * * *
40328617 TACCCTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGA
1 TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
40328671 TACCC
1 TACCC
40328676 TTGTGGGGTA
Statistics
Matches: 221, Mismatches: 27, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
42 39 0.18
53 1 0.00
54 180 0.81
55 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
TACCCCTGTAAGGTAGAATTACTGAAATACCCCCGTAAGGTAGAATTATCGAAA
Found at i:40328478 original size:15 final size:15
Alignment explanation
Indices: 40328458--40328488 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40328448 TAAGGTAGAA
40328458 TTACTGAAATACCCC
1 TTACTGAAATACCCC
40328473 TTACTGAAATACCCC
1 TTACTGAAATACCCC
40328488 T
1 T
40328489 GTAAGGTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (15 bp):
TTACTGAAATACCCC
Found at i:40328490 original size:42 final size:42
Alignment explanation
Indices: 40328431--40328515 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
40328421 TAAGGTTTAA
40328431 TTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
1 TTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
* *
40328473 TTACTGAAATACCCCTGTAAGGTAGAATTATTGAAATACCCC
1 TTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
40328515 T
1 T
40328516 GTAGTGTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (42 bp):
TTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
Found at i:40328515 original size:27 final size:27
Alignment explanation
Indices: 40328473--40328692 Score: 262
Period size: 27 Copynumber: 8.1 Consensus size: 27
40328463 GAAATACCCC
*
40328473 TTACTGAAATACCCCTGTAAGGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* *
40328500 TTATTGAAATACCCCTGTAGTGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* * *
40328527 TTACTAAAATACCCCCGTAAGGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* *
40328554 TTACCGAAATACCCTTGTAGGGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* *
40328581 TTACTGATATACCCCCGTAGGGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* *
40328608 TTA-TCAAAATACCCTTGTAGGGTAGAA
1 TTACT-GAAATACCCCTGTAGGGTAGAA
*
40328635 ATACTGAAATACCCCTGTAGGGTAGAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
* * * * *
40328662 TTACCGAGATACCCTTGTGGGGTAAAA
1 TTACTGAAATACCCCTGTAGGGTAGAA
40328689 TTAC
1 TTAC
40328693 CATTTTGCCC
Statistics
Matches: 161, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 159 0.99
28 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (27 bp):
TTACTGAAATACCCCTGTAGGGTAGAA
Found at i:40328525 original size:69 final size:69
Alignment explanation
Indices: 40328409--40328541 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 69
40328399 TTGAATTATC
** *
40328409 GAAATACCCCTGTAAGGTTTAATTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCCT
1 GAAATACCCCTGTAAGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACTAAAATACCCCT
40328474 TACT
66 TACT
* *
40328478 GAAATACCCCTGTAAGGTAGAATTATTGAAATACCCCTGT-AGTGTAGAATTACTAAAATACCCC
1 GAAATACCCCTGTAAGGTAGAATTACTAAAATACCCCTGTAAG-GTAGAATTACTAAAATACCCC
40328542 CGTAAGGTAG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 2 0.03
69 56 0.97
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (69 bp):
GAAATACCCCTGTAAGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACTAAAATACCCCT
TACT
Found at i:40328547 original size:96 final size:96
Alignment explanation
Indices: 40328377--40328567 Score: 285
Period size: 96 Copynumber: 2.0 Consensus size: 96
40328367 TAAGGTAGAA
* **
40328377 TTACCGAAATACCCCCATAAGGTTGAATTATCGAAATACCCCTGTAAGGTTTAATTACTAAAATA
1 TTACCGAAATACCCCCATAAGGTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACTAAAATA
* *
40328442 CCCCTGTAAGGTAGAATTACTGAAATACCCC
66 CCCCCGTAAGGTAGAATTACCGAAATACCCC
* ** *
40328473 TTACTGAAATACCCCTGTAAGGTAGAATTATTGAAATACCCCTGT-AGTGTAGAATTACTAAAAT
1 TTACCGAAATACCCCCATAAGGTAGAATTATCGAAATACCCCTGTAAG-GTAGAATTACTAAAAT
40328537 ACCCCCGTAAGGTAGAATTACCGAAATACCC
65 ACCCCCGTAAGGTAGAATTACCGAAATACCC
40328568 TTGTAGGGTA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 2 0.02
96 83 0.98
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (96 bp):
TTACCGAAATACCCCCATAAGGTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACTAAAATA
CCCCCGTAAGGTAGAATTACCGAAATACCCC
Found at i:40328578 original size:123 final size:123
Alignment explanation
Indices: 40328350--40328595 Score: 316
Period size: 123 Copynumber: 2.0 Consensus size: 123
40328340 GTTTATCAAA
* * *
40328350 TTACTGAAGTACCCCTATAAGGTAGAATTACCGAAATACCCCCATAAGGTTGAATTATCGAAATA
1 TTACTGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCCATAAGGTAGAATTATCAAAATA
* ** *
40328415 CCCCTGTAAGGTTTAATTACTAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
66 CCCCCGTAAGGTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
* ** **
40328473 TTACTGAAATACCCCTGTAAGGTAGAATTATTGAAATACCCCTGT-AGTGTAGAATTA-CTAAAA
1 TTACTGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCCATAAG-GTAGAATTATC-AAAA
* * * *
40328536 TACCCCCGTAAGGTAGAATTACCGAAATACCCTTGTAGGGTAGAATTACTGATATACCCC
64 TACCCCCGTAAGGTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
40328596 CGTAGGGTAG
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 3 0.03
123 102 0.97
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (123 bp):
TTACTGAAATACCCCTATAAGGTAGAATTACCGAAATACCCCCATAAGGTAGAATTATCAAAATA
CCCCCGTAAGGTAGAATTACCAAAATACCCCTGTAAGGTAGAATTACTGAAATACCCC
Found at i:40329139 original size:19 final size:19
Alignment explanation
Indices: 40329115--40329162 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
40329105 TTTTGGGCTT
40329115 AATGGGCCAAAAACGGGCC
1 AATGGGCCAAAAACGGGCC
* *
40329134 AATGGGCCGAAAATGGGCC
1 AATGGGCCAAAAACGGGCC
40329153 AATGGGCCAA
1 AATGGGCCAA
40329163 CGAGCATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.33, T:0.08
Consensus pattern (19 bp):
AATGGGCCAAAAACGGGCC
Found at i:40329464 original size:27 final size:26
Alignment explanation
Indices: 40329420--40329471 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
40329410 CTCGCTGCAA
40329420 TCTGGTGACCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
40329447 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
40329472 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:40333429 original size:20 final size:21
Alignment explanation
Indices: 40333388--40333434 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
40333378 AGCATAACAT
40333388 AATAGAACAAAACCAAAATAG
1 AATAGAACAAAACCAAAATAG
*
40333409 AATAGAACAAAA-CATAATAG
1 AATAGAACAAAACCAAAATAG
40333429 AATAGA
1 AATAGA
40333435 GCAGAACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (21 bp):
AATAGAACAAAACCAAAATAG
Found at i:40333442 original size:20 final size:20
Alignment explanation
Indices: 40333388--40333447 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
40333378 AGCATAACAT
*
40333388 AATAGAACAAAACCAAAATAG
1 AATAGAACAAAA-CAGAATAG
*
40333409 AATAGAACAAAACATAATAG
1 AATAGAACAAAACAGAATAG
* *
40333429 AATAGAGCAGAACAGAATA
1 AATAGAACAAAACAGAATA
40333448 ACAAATGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.63, C:0.12, G:0.13, T:0.12
Consensus pattern (20 bp):
AATAGAACAAAACAGAATAG
Found at i:40334468 original size:6 final size:6
Alignment explanation
Indices: 40334450--40334546 Score: 83
Period size: 6 Copynumber: 15.8 Consensus size: 6
40334440 AAGAAACATT
* *
40334450 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
40334499 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAG
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
40334547 GTAACAGAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.05
6 62 0.84
7 6 0.08
8 2 0.03
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:40334495 original size:31 final size:31
Alignment explanation
Indices: 40334434--40334558 Score: 164
Period size: 31 Copynumber: 4.1 Consensus size: 31
40334424 TAACCCATTA
* * *
40334434 CAGAATAAGAAACATTATCA-G-AACTAGAAT
1 CAGAATCAGAATCAGTATCAGGTAAC-AGAAT
* * *
40334464 CAGAATCAGAATCAGAATTAGGTGACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
40334495 CAGAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
*
40334526 CAAAATCAGAATCAGTATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAAT
40334557 CA
1 CA
40334559 AAAATCAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.18
31 66 0.80
32 2 0.02
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:40334525 original size:19 final size:19
Alignment explanation
Indices: 40334501--40334558 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
40334491 GAATCAGAAT
40334501 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
40334520 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
40334532 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
40334551 CAGAATCA
1 CAGAATCA
40334559 AAAATCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:40335002 original size:27 final size:27
Alignment explanation
Indices: 40334972--40335161 Score: 168
Period size: 27 Copynumber: 7.0 Consensus size: 27
40334962 CCCTAGGGGC
* *
40334972 AAAATGGTAATTTTATAAATTAAGGGT
1 AAAATGGTAATTTTGTAAATCAAGGGT
* * **
40334999 AAAACGGTAATTCTGTAAATTGAGGGT
1 AAAATGGTAATTTTGTAAATCAAGGGT
*
40335026 AAAATAGTAATTTT-TCAAATCAAGGGT
1 AAAATGGTAATTTTGT-AAATCAAGGGT
* *
40335053 AAAATAGTAATTTTGTAAATCGAGGGT
1 AAAATGGTAATTTTGTAAATCAAGGGT
* * *
40335080 AAAA-GAGTAATTTTGTCAATCGAGGGA
1 AAAATG-GTAATTTTGTAAATCAAGGGT
** *
40335107 AAAACAGTAATTTTGTAAATCGAGGGT
1 AAAATGGTAATTTTGTAAATCAAGGGT
*** * *
40335134 AAAACAATAATTTTGTAATTCGAGGGT
1 AAAATGGTAATTTTGTAAATCAAGGGT
40335161 A
1 A
40335162 CTTTGATAAT
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.01
27 139 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (27 bp):
AAAATGGTAATTTTGTAAATCAAGGGT
Found at i:40335037 original size:54 final size:53
Alignment explanation
Indices: 40334972--40335161 Score: 218
Period size: 54 Copynumber: 3.5 Consensus size: 53
40334962 CCCTAGGGGC
* * * * *
40334972 AAAATGGTAATTTTATAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGT
1 AAAATAGTAATTTT-TAAATCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
*
40335026 AAAATAGTAATTTTTCAAATCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGT
1 AAAATAGTAATTTTT-AAATCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
* * * *
40335080 AAAAGAGTAATTTTGTCAATCGAGGGAAAAACAGTAATTTTGTAAATCGAGGGT
1 AAAATAGTAATTTT-TAAATCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
* * * *
40335134 AAAACAATAATTTTGTAATTCGAGGGTA
1 AAAATAGTAATTTT-TAAATCAAGGGTA
40335162 CTTTGATAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 116 0.98
55 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (53 bp):
AAAATAGTAATTTTTAAATCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
Found at i:40335116 original size:81 final size:81
Alignment explanation
Indices: 40334972--40335161 Score: 231
Period size: 81 Copynumber: 2.3 Consensus size: 81
40334962 CCCTAGGGGC
* * ** * * *
40334972 AAAATGGTAATTTTATAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATAGTAAT
1 AAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGAAAAACAGTAAT
40335037 TTT-TCAAATCAAGGGT
66 TTTGT-AAATCAAGGGT
* *
40335053 AAAATAGTAATTTTGTAAATCGAGGGTAAAA-GAGTAATTTTGTCAATCGAGGGAAAAACAGTAA
1 AAAATAGTAATTTTGTAAATCGAGGGTAAAACG-GTAATTCTGTAAATCGAGGGAAAAACAGTAA
*
40335117 TTTTGTAAATCGAGGGT
65 TTTTGTAAATCAAGGGT
* * *
40335134 AAAACAATAATTTTGTAATTCGAGGGTA
1 AAAATAGTAATTTTGTAAATCGAGGGTA
40335162 CTTTGATAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
80 1 0.01
81 92 0.98
82 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.32
Consensus pattern (81 bp):
AAAATAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGAAAAACAGTAAT
TTTGTAAATCAAGGGT
Found at i:40335183 original size:27 final size:27
Alignment explanation
Indices: 40335153--40335204 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
40335143 ATTTTGTAAT
*
40335153 TCGAGGGTACTTT-GATAATTTTACATG
1 TCGAGGGTA-TTTCAATAATTTTACATG
40335180 TCGAGGGTATTTCAATAATTTTACA
1 TCGAGGGTATTTCAATAATTTTACA
40335205 AACTGAGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (27 bp):
TCGAGGGTATTTCAATAATTTTACATG
Found at i:40335212 original size:27 final size:27
Alignment explanation
Indices: 40335182--40335307 Score: 116
Period size: 27 Copynumber: 4.7 Consensus size: 27
40335172 TTTACATGTC
**
40335182 GAGGGTATTTCAATAATTTTACAAACT
1 GAGGGTATTTCGGTAATTTTACAAACT
* *
40335209 GAGGGCATTTTGGTAATTTTACAAA-T
1 GAGGGTATTTCGGTAATTTTACAAACT
* * * *
40335235 CGAGGATATTTGGGTAATTTTATAAACC
1 -GAGGGTATTTCGGTAATTTTACAAACT
40335263 G-GGCGTACTTT-GGTAATTTTAC-AACT
1 GAGG-GTA-TTTCGGTAATTTTACAAACT
*
40335289 GAGGGTATTTCAGTAATTT
1 GAGGGTATTTCGGTAATTT
40335308 GGTAAACTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
25 3 0.04
26 17 0.21
27 57 0.71
28 3 0.04
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (27 bp):
GAGGGTATTTCGGTAATTTTACAAACT
Found at i:40335314 original size:53 final size:54
Alignment explanation
Indices: 40335113--40335307 Score: 178
Period size: 54 Copynumber: 3.6 Consensus size: 54
40335103 GGGAAAAACA
** *** * * **
40335113 GTAATTTTGTAAATCGAGGGTAAAACAATAATTTTGTAATTCGAGGGTACTTTG
1 GTAATTTTACAAATCGAGGGTATTTCAGTAATTTTATAAACCGAGGGTACTTTG
* ** * * * * *
40335167 ATAATTTTACATGTCGAGGGTATTTCAATAATTTTACAAACTGAGGGCATTTTG
1 GTAATTTTACAAATCGAGGGTATTTCAGTAATTTTATAAACCGAGGGTACTTTG
* **
40335221 GTAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAACCG-GGCGTACTTTG
1 GTAATTTTACAAATCGAGGGTATTTCAGTAATTTTATAAACCGAGG-GTACTTTG
*
40335275 GTAATTTTACAACT-GAGGGTATTTCAGTAATTT
1 GTAATTTTACAAATCGAGGGTATTTCAGTAATTT
40335308 GGTAAACTAA
Statistics
Matches: 110, Mismatches: 30, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 18 0.16
54 92 0.84
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
GTAATTTTACAAATCGAGGGTATTTCAGTAATTTTATAAACCGAGGGTACTTTG
Found at i:40336781 original size:40 final size:39
Alignment explanation
Indices: 40336707--40336808 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 39
40336697 AACCCAAGTA
* * *
40336707 CCTTCGGGAATTAGCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAAGG
*
40336746 CCTTCGGGACTTAGCCTGGGTATAGTC-ACTAGCACAAAGG
1 CCTTCGGGACTTAGCC-GGATATAG-CAACTAGCACAAAGG
*
40336786 CCTTCAGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAG-CCGGATAT
40336809 CATCCGAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
39 15 0.28
40 36 0.67
41 3 0.06
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTAGCACAAAGG
Found at i:40344637 original size:40 final size:40
Alignment explanation
Indices: 40344588--40344755 Score: 214
Period size: 40 Copynumber: 4.2 Consensus size: 40
40344578 CCGGAATTAG
* *
40344588 CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTATC
1 CCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTATC
* * *
40344628 CCGGGTATAGTCACTAGCACAAATGCCTTCAGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTATC
*
40344668 CCGAATATAGTCACTAGCACAAATGCCTTCGGGACTTAGT-
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTA-TC
* * *
40344708 CCGGATATAGTCACTAGCACAAAGGCCTTCAGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTATC
*
40344748 CCAGATAT
1 CCGGATAT
40344756 CATCCGAATA
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
40 110 0.99
41 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTATC
Found at i:40344717 original size:80 final size:80
Alignment explanation
Indices: 40344574--40344749 Score: 250
Period size: 80 Copynumber: 2.2 Consensus size: 80
40344564 AACCCAAGTA
* * * * * *
40344574 CCTTCCGGAATTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTATCCCGGGTATAG
1 CCTTCAGGACTTAGCCCGAATATAGCAACTAGCACAAATGCCTTCGGGACTTATCCCGGATATAG
*
40344638 TCACTAGCACAAATG
66 TCACTAGCACAAAGG
40344653 CCTTCAGGACTTAGCCCGAATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGT-CCGGATAT
1 CCTTCAGGACTTAGCCCGAATATAG-CAACTAGCACAAATGCCTTCGGGACTTA-TCCCGGATAT
40344716 AGTCACTAGCACAAAGG
64 AGTCACTAGCACAAAGG
40344733 CCTTCAGGACTTAGCCC
1 CCTTCAGGACTTAGCCC
40344750 AGATATCATC
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
79 12 0.14
80 73 0.84
81 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (80 bp):
CCTTCAGGACTTAGCCCGAATATAGCAACTAGCACAAATGCCTTCGGGACTTATCCCGGATATAG
TCACTAGCACAAAGG
Found at i:40348216 original size:6 final size:6
Alignment explanation
Indices: 40348198--40348354 Score: 117
Period size: 6 Copynumber: 25.3 Consensus size: 6
40348188 AAGAAACATT
* *
40348198 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGGCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
40348247 ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA
* * *
40348296 ATCAGGTA A-CAGA ATCAAA ATCAGA ATTAGT ATCAGGTA A-CAGA ATCAGAA
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAG-A
40348347 ATCAGA AT
1 ATCAGA AT
40348355 GTGAATGCAA
Statistics
Matches: 120, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
5 8 0.07
6 90 0.75
7 18 0.15
8 4 0.03
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:40348243 original size:31 final size:31
Alignment explanation
Indices: 40348207--40348354 Score: 170
Period size: 31 Copynumber: 4.5 Consensus size: 31
40348197 TATCAGAACT
*
40348207 AGAATCAGAATCAGAATCAGAATTAGGTGGCAGAATC
1 AGAATCAGAATCAGAATCAGAATCAGGT-----AA-C
*
40348244 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
40348275 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* * *
40348306 AGAATCAAAATCAGAATTAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
40348337 AGAATCAGAAATCAGAAT
1 AGAATCAG-AATCAGAAT
40348355 GTGAATGCAA
Statistics
Matches: 105, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
31 68 0.65
32 11 0.10
37 26 0.25
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:40348787 original size:27 final size:27
Alignment explanation
Indices: 40348757--40348863 Score: 124
Period size: 27 Copynumber: 4.0 Consensus size: 27
40348747 CCCTAGAGGC
* *
40348757 AAAATGGTAATTTTATAAATCGAGGTT
1 AAAATGGTAATTTTGTAAATCGAGGGT
*
40348784 AAAACGGTAATTTTGTAAATCGAGGGT
1 AAAATGGTAATTTTGTAAATCGAGGGT
* *
40348811 AAAATAGTAATTCTGTAAATCGAGGGT
1 AAAATGGTAATTTTGTAAATCGAGGGT
*** * *
40348838 AAAGCAGTAATTTTTTAATTCGAGGG
1 AAAATGGTAATTTTGTAAATCGAGGG
40348864 AACTTTGATA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (27 bp):
AAAATGGTAATTTTGTAAATCGAGGGT
Found at i:40348876 original size:54 final size:54
Alignment explanation
Indices: 40348757--40348863 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 54
40348747 CCCTAGAGGC
* * * * *
40348757 AAAATGGTAATTTTATAAATCGAGGTTAAAACGGTAATTTTGTAAATCGAGGGT
1 AAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
* * *
40348811 AAAATAGTAATTCTGTAAATCGAGGGTAAAGCAGTAATTTTTTAATTCGAGGG
1 AAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTTTGTAAATCGAGGG
40348864 AACTTTGATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (54 bp):
AAAATAGTAATTCTGTAAATCGAGGGTAAAACAGTAATTTTGTAAATCGAGGGT
Found at i:40348900 original size:54 final size:53
Alignment explanation
Indices: 40348842--40349011 Score: 173
Period size: 54 Copynumber: 3.2 Consensus size: 53
40348832 GAGGGTAAAG
* * * *
40348842 CAGTAATTTT-TTAATTCGAGGGAACTTTGATAATTTTACATGTCGAGGGTATTT
1 CAGTAATTTTATAAACT-GAGGGTACTTTGGTAATTTTACA-GTCGAGGGTATTT
** * * * *
40348896 CAGTAATTTTGCAAACTGAGGGTATTTTGGTAACTTTACAAATCGAGGATATTT
1 CAGTAATTTTATAAACTGAGGGTACTTTGGTAATTTTAC-AGTCGAGGGTATTT
* * *
40348950 GAGTAATTTTATAAACTGGGGGTACTTTGGTAATTTTACAG-CTAGGGGTATTT
1 CAGTAATTTTATAAACTGAGGGTACTTTGGTAATTTTACAGTCGA-GGGTATTT
40349003 CAGTAATTT
1 CAGTAATTT
40349012 GGTAAACTAA
Statistics
Matches: 94, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
52 2 0.02
53 16 0.17
54 72 0.77
55 4 0.04
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (53 bp):
CAGTAATTTTATAAACTGAGGGTACTTTGGTAATTTTACAGTCGAGGGTATTT
Found at i:40348902 original size:27 final size:26
Alignment explanation
Indices: 40348828--40349011 Score: 86
Period size: 27 Copynumber: 6.9 Consensus size: 26
40348818 TAATTCTGTA
*** **
40348828 AATCGAGGGTAAAGCAGTAATTTTTT
1 AATCGAGGGTATTTCAGTAATTTTAC
* *
40348854 AATTCGAGGGAACTTTGA-TAATTTTAC
1 AA-TCGAGGGTA-TTTCAGTAATTTTAC
* *
40348881 ATGTCGAGGGTATTTCAGTAATTTTGC
1 A-ATCGAGGGTATTTCAGTAATTTTAC
* ** *
40348908 AAACTGAGGGTATTTTGGTAACTTTAC
1 AATC-GAGGGTATTTCAGTAATTTTAC
* * *
40348935 AAATCGAGGATATTTGAGTAATTTTAT
1 -AATCGAGGGTATTTCAGTAATTTTAC
* * *
40348962 AAACTGGGGGTACTTT-GGTAATTTTAC
1 AATC-GAGGGTA-TTTCAGTAATTTTAC
* *
40348989 -AGCTAGGGGTATTTCAGTAATTT
1 AATCGA-GGGTATTTCAGTAATTT
40349012 GGTAAACTAA
Statistics
Matches: 116, Mismatches: 32, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
25 3 0.03
26 24 0.21
27 82 0.71
28 7 0.06
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (26 bp):
AATCGAGGGTATTTCAGTAATTTTAC
Found at i:40350352 original size:12 final size:12
Alignment explanation
Indices: 40350335--40350367 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40350325 CTTGGGACAC
40350335 GCCCATGTGGTA
1 GCCCATGTGGTA
40350347 GCCCATGTGGTA
1 GCCCATGTGGTA
*
40350359 GCCCGTGTG
1 GCCCATGTG
40350368 ATTTTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.27, G:0.36, T:0.24
Consensus pattern (12 bp):
GCCCATGTGGTA
Found at i:40353134 original size:56 final size:56
Alignment explanation
Indices: 40353048--40353157 Score: 193
Period size: 56 Copynumber: 2.0 Consensus size: 56
40353038 ACATGTTACG
* *
40353048 TTATACATTAGCAATCATCTTTACTTATATTAAATCAAAACAGGCATATGTACACA
1 TTATACATTAGCAATCATCTTTACTTATATTAAATCAAAACAGACATACGTACACA
*
40353104 TTATACATTAGCAATCATCTTTACTTATATTAAATTAAAACAGACATACGTACA
1 TTATACATTAGCAATCATCTTTACTTATATTAAATCAAAACAGACATACGTACA
40353158 GATAGTGAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (56 bp):
TTATACATTAGCAATCATCTTTACTTATATTAAATCAAAACAGACATACGTACACA
Found at i:40365469 original size:16 final size:16
Alignment explanation
Indices: 40365448--40365479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40365438 ATAACACATA
40365448 AGTAAACTATGTTATG
1 AGTAAACTATGTTATG
40365464 AGTAAACTATGTTATG
1 AGTAAACTATGTTATG
40365480 TCATTGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
AGTAAACTATGTTATG
Found at i:40372527 original size:30 final size:30
Alignment explanation
Indices: 40372491--40372551 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40372481 TCCTGAACTC
40372491 AAACTTTGGAATAATTACAATTTTGCCCCT
1 AAACTTTGGAATAATTACAATTTTGCCCCT
* * * *
40372521 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAATAATTACAATTTTGCCCCT
40372551 A
1 A
40372552 TGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAATAATTACAATTTTGCCCCT
Found at i:40376969 original size:30 final size:30
Alignment explanation
Indices: 40376935--40376995 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40376925 TCCTTAACTC
40376935 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40376965 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40376995 A
1 A
40376996 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40389344 original size:40 final size:40
Alignment explanation
Indices: 40389296--40389471 Score: 289
Period size: 40 Copynumber: 4.4 Consensus size: 40
40389286 GGACTAAGAT
*
40389296 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
40389336 CCGAAGGCATTTTTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
40389376 CCGAAGGCATTTATGCTAGTGACTATATGCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
40389416 CCGAAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
40389456 CCGAAGGCATTCGTGC
1 CCGAAGGCATTTGTGC
40389472 GAGTTGCTAT
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 128 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:40394179 original size:47 final size:47
Alignment explanation
Indices: 40394125--40394618 Score: 834
Period size: 47 Copynumber: 10.5 Consensus size: 47
40394115 TATTTGAATA
*
40394125 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394172 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40394221 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATC
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394268 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394315 AATGTGAAAGTG--TATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394360 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394407 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394454 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394501 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* ** * *
40394548 AATGTGAAAGTGTATATATGTGA-CAGGGTTGAGTGGCC-AGCGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGA-TGTGATG
* *
40394595 GATGTGAAAGTGTATAAATGTGAT
1 AATGTGAAAGTGTATATATGTGAT
40394619 GAGTCCCGAA
Statistics
Matches: 428, Mismatches: 12, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
45 45 0.11
46 5 0.01
47 332 0.78
49 46 0.11
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40394313 original size:22 final size:22
Alignment explanation
Indices: 40394285--40394358 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
40394275 AAGTGTATAT
40394285 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* * ***
40394307 ATGTGATGAATG--TGAAAGTGTAT
1 ATGTGAT-AAGGCCT-AATG-GCCG
40394330 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
40394352 ATGTGAT
1 ATGTGAT
40394359 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:40394460 original size:186 final size:187
Alignment explanation
Indices: 40394125--40394618 Score: 823
Period size: 186 Copynumber: 2.6 Consensus size: 187
40394115 TATTTGAATA
*
40394125 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40394190 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
63 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
40394255 AGCCGATGTGATCAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
128 AGCCGATGTGATCAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394315 AATGTGAAAGTG-TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 AATGTGAAAGTGATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
*
40394379 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGC
66 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGC
*
40394444 CGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
131 CGATGTGATCAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40394501 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTG-ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* ** * * * *
40394566 TGTGA-CAGGGTTGAGTGGCC-AGCGTGATGGATGTGAAAGTGTATAAATGTGAT
65 TGTGATAAGGCCT-AATGGCCGA-TGTGATGAATGTGAAAGTGTATATATGTGAT
40394619 GAGTCCCGAA
Statistics
Matches: 290, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
186 139 0.48
187 5 0.02
188 134 0.46
190 12 0.04
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (187 bp):
AATGTGAAAGTGATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGC
CGATGTGATCAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40397107 original size:38 final size:38
Alignment explanation
Indices: 40397043--40397117 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
40397033 AATCCGAGTT
*
40397043 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
40397081 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
40397118 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:40397235 original size:40 final size:40
Alignment explanation
Indices: 40397171--40397411 Score: 331
Period size: 40 Copynumber: 6.0 Consensus size: 40
40397161 AGGTCTTGAC
* *
40397171 GATG-ATCCAGGCTAAGTCTCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40397210 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * *
40397250 GATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
*
40397290 GATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * ** *
40397330 GATGTATCCGGGCTAAGTTCTGAAGAGCATTTGTGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
* * * * *
40397370 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
40397410 GA
1 GA
40397412 CGTGTATTCG
Statistics
Matches: 177, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
39 4 0.02
40 173 0.98
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
Found at i:40397313 original size:80 final size:80
Alignment explanation
Indices: 40397171--40397411 Score: 378
Period size: 80 Copynumber: 3.0 Consensus size: 80
40397161 AGGTCTTGAC
* * *
40397171 GATG-ATCCAGGCTAAG-TCTCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAA
1 GATGTATCCGGGCTAAGTTCT-GAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAA
40397234 GAGCATTCATGCTAGT
65 GAGCATTCATGCTAGT
40397250 GATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAG
1 GATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAG
40397315 AGCATTCATGCTAGT
66 AGCATTCATGCTAGT
* * * *
40397330 GATGTATCCGGGCTAAGTTCTGAAGAGCATTTGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAG
1 GATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAG
* *
40397395 AGCAATCATGCTGGT
66 AGCATTCATGCTAGT
40397410 GA
1 GA
40397412 CGTGTATTCG
Statistics
Matches: 151, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
79 4 0.03
80 144 0.95
81 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (80 bp):
GATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAG
AGCATTCATGCTAGT
Found at i:40400655 original size:47 final size:47
Alignment explanation
Indices: 40400601--40400955 Score: 595
Period size: 47 Copynumber: 7.5 Consensus size: 47
40400591 TATTTGAATA
*
40400601 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40400648 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGACGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
40400697 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40400744 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40400791 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40400838 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
40400885 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCC-AGCGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGA-TGTGATG
* *
40400932 GATGTGAAAGTGTATAAATGTGAT
1 AATGTGAAAGTGTATATATGTGAT
40400956 GAGTCCCGAA
Statistics
Matches: 296, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 248 0.84
49 47 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40407449 original size:19 final size:19
Alignment explanation
Indices: 40407425--40407464 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40407415 TGTGTTATCA
*
40407425 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
40407444 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
40407463 TA
1 TA
40407465 CACAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:40408111 original size:27 final size:27
Alignment explanation
Indices: 40408081--40408238 Score: 185
Period size: 27 Copynumber: 5.9 Consensus size: 27
40408071 TTACCCTACA
* *
40408081 AGGGTATTTCAGTAATTTTACAAACCG
1 AGGGTATTTTAGTAATTTTACAAATCG
*
40408108 AGGGTATTTTAGTAATTTTA-AAAGTCA
1 AGGGTATTTTAGTAATTTTACAAA-TCG
* *
40408135 AGCGTATTTTAGTAATTTCACAAATCG
1 AGGGTATTTTAGTAATTTTACAAATCG
* *
40408162 AGGGTATTTTGGTAATTTCACAAATC-
1 AGGGTATTTTAGTAATTTTACAAATCG
** * *
40408188 AGGGATATTTCGGTAATTTTAGAACTCG
1 AGGG-TATTTTAGTAATTTTACAAATCG
40408216 AGGGTATTTTAGTAATTTTACAA
1 AGGGTATTTTAGTAATTTTACAA
40408239 GTCAGGGGGC
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.06
27 98 0.88
28 7 0.06
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (27 bp):
AGGGTATTTTAGTAATTTTACAAATCG
Found at i:40413911 original size:17 final size:20
Alignment explanation
Indices: 40413876--40413911 Score: 51
Period size: 17 Copynumber: 1.9 Consensus size: 20
40413866 GGAAAGTGAA
40413876 ATAATAAAAGATGATAAATG
1 ATAATAAAAGATGATAAATG
40413896 ATAA-AAAA-ATGA-AAAT
1 ATAATAAAAGATGATAAAT
40413912 ACCATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 4 0.25
20 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAATAAAAGATGATAAATG
Found at i:40415756 original size:43 final size:43
Alignment explanation
Indices: 40415619--40415758 Score: 112
Period size: 43 Copynumber: 3.3 Consensus size: 43
40415609 GCCAACGTAT
*
40415619 CAGACGTGGTCTGACA-TATAATCACATATCGATGCC-ACAGTCC
1 CAGACGTGGTCTTACAGT-TAATCACATATCGATGCCAACA-TCC
* * * ** *
40415662 CAAACAG-GGTCTTACACG--AATCAAATAT-GGTGCCAATGTCT
1 CAGAC-GTGGTCTTACA-GTTAATCACATATCGATGCCAACATCC
** *
40415703 CATTCATGGTCTTACAGTTAATCACATATCGATGCCAACATCC
1 CAGACGTGGTCTTACAGTTAATCACATATCGATGCCAACATCC
40415746 CAGACGTGGTCTT
1 CAGACGTGGTCTT
40415759 CAATGAGAAC
Statistics
Matches: 71, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
40 1 0.01
41 19 0.27
42 19 0.27
43 31 0.44
44 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
CAGACGTGGTCTTACAGTTAATCACATATCGATGCCAACATCC
Found at i:40422009 original size:19 final size:19
Alignment explanation
Indices: 40421971--40422009 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40421961 TGATTTTATT
* * *
40421971 TATCATATTATAATGTACA
1 TATCATATTAAAAAGAACA
40421990 TATCATATTAAAAAGAACA
1 TATCATATTAAAAAGAACA
40422009 T
1 T
40422010 TTTAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
TATCATATTAAAAAGAACA
Found at i:40424716 original size:40 final size:40
Alignment explanation
Indices: 40424670--40424813 Score: 182
Period size: 40 Copynumber: 3.6 Consensus size: 40
40424660 CTCACACAAG
* *
40424670 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAAT
* ** *
40424710 GCCTTCGGGACTTAGCCCGGATATAATTGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAAT
* * *
40424750 GCCTTC-GGATCTTAGTCCGGATATAGCCACTAGCATAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCACTAGCATAAAT
*
40424790 GCCTTCGGGACATAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
40424814 CATTCGAATA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.03
40 81 0.93
41 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAAT
Found at i:40428668 original size:40 final size:40
Alignment explanation
Indices: 40428613--40428834 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
40428603 TATTCGAATG
* *
40428613 ATATCTGGGCTAAGTCCCGAGGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
40428653 ATATCCGGGCTAAGTCCCGAA-GCATTTGTGCTAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* *
40428695 ATA-CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
40428734 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40428774 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
40428814 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
40428835 ATACTTGGGT
Statistics
Matches: 161, Mismatches: 16, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
39 31 0.19
40 94 0.58
41 17 0.11
42 19 0.12
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:40428754 original size:81 final size:79
Alignment explanation
Indices: 40428613--40428834 Score: 288
Period size: 81 Copynumber: 2.8 Consensus size: 79
40428603 TATTCGAATG
* * *
40428613 ATATCTGGGCTAAGTCCCGAGGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGCAT
** *
40428678 TTGTGCTAGTAGTTGCT
66 TCATGCTAGT-G--ACT
*
40428695 ATA-CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAA-GCA
40428759 TTCATGCTAGTGACT
65 TTCATGCTAGTGACT
* * *
40428774 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
40428835 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 18 0.14
80 37 0.29
81 56 0.44
82 15 0.12
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGCAT
TCATGCTAGTGACT
Found at i:40436808 original size:40 final size:40
Alignment explanation
Indices: 40436740--40436963 Score: 225
Period size: 40 Copynumber: 5.5 Consensus size: 40
40436730 TATTCGGATG
* *
40436740 ATATCCGGGCTAAGTCCTGAGGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40436780 ATATCCGGGCTAAGTGCCGAAGGAATTTGTGCAAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * **
40436823 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGAGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * *
40436863 ATATCTGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * ** *
40436903 ATATCCGGGCTAAGACCCGAAGGCATTTTTGCGGGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
40436943 ATATCC-GACTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
40436964 ATACTTGGGT
Statistics
Matches: 153, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
39 12 0.08
40 105 0.69
41 1 0.01
43 35 0.23
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:40436883 original size:83 final size:80
Alignment explanation
Indices: 40436744--40436930 Score: 223
Period size: 83 Copynumber: 2.3 Consensus size: 80
40436734 CGGATGATAT
* * ** * **
40436744 CCGGGCTAAGTCCTGAGGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTGCCGAAGGAATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGAGACTATATCCGGGCTAAGTCCCGAAGGAATTCA
40436809 TGCAAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
* * *
40436827 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGAGACTATATCTGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGAGACTATATCCGGGCTAAGTCCCGAAGGAATTCA
*
40436892 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
*
40436907 CCGGGCTAAGACCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTT
40436931 TTGCGGGTTG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
79 2 0.02
80 31 0.34
83 58 0.64
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGAGACTATATCCGGGCTAAGTCCCGAAGGAATTCA
TGCTAGTGACTATAC
Found at i:40438557 original size:43 final size:43
Alignment explanation
Indices: 40438502--40438636 Score: 156
Period size: 43 Copynumber: 3.2 Consensus size: 43
40438492 ATATCGAACA
*
40438502 ATGCCAACGTCCCAAAGGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAAAGGTGGTCTTACACGTAATCACATATCG
* *
40438545 ATGCCATA-GTCCCAAATAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCA-ACGTCCCAAA-GGTGGTCTTACACGTAATCACATATCG
*
40438586 ATGCCAATGTCCC--AGGCATGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAAAGG--TGGTCTTACACGTAATCACATATCG
40438629 ATGCCAAC
1 ATGCCAAC
40438637 ATCTTAGACG
Statistics
Matches: 78, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 1 0.01
41 24 0.31
42 16 0.21
43 33 0.42
44 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAAAGGTGGTCTTACACGTAATCACATATCG
Found at i:40438651 original size:43 final size:42
Alignment explanation
Indices: 40438502--40438656 Score: 145
Period size: 43 Copynumber: 3.6 Consensus size: 42
40438492 ATATCGAACA
* * *
40438502 ATGCCAACGTCCCAAAGGTGGTCTTACATGTAATCACATATCG
1 ATGCCAA-GTCCCAGACGTGGTCTTACACGTAATCACATATCG
* * *
40438545 ATGCCATAGTCCCAAATAG-GGTCTTACACG-AATCAAATA-CG
1 ATGCCA-AGTCCCAGA-CGTGGTCTTACACGTAATCACATATCG
* *
40438586 ATGCCAATGTCCCAGGCATGGTCTTACACGTAATCACATATCG
1 ATGCCAA-GTCCCAGACGTGGTCTTACACGTAATCACATATCG
* **
40438629 ATGCCAACATCTTAGACGTGGTCTTACA
1 ATGCCAA-GTCCCAGACGTGGTCTTACA
40438657 TGAGAACACA
Statistics
Matches: 92, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
40 1 0.01
41 25 0.27
42 16 0.17
43 48 0.52
44 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAAGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:40448057 original size:26 final size:25
Alignment explanation
Indices: 40448009--40448060 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
40447999 TAACTGATAA
40448009 ATTTCACATTTCACAAATTAGTCCCT
1 ATTTCACATTTCACAAA-TAGTCCCT
40448035 ATTTCACATTTTCATCAAA-AGTCCCT
1 ATTTCACA-TTTCA-CAAATAGTCCCT
40448061 TAACTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.62
27 5 0.21
28 4 0.17
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTTCACATTTCACAAATAGTCCCT
Found at i:40455868 original size:86 final size:86
Alignment explanation
Indices: 40455726--40455894 Score: 302
Period size: 86 Copynumber: 2.0 Consensus size: 86
40455716 AATTTGACTG
* *
40455726 TGTTTGGCATCTACGAAAGAGCTTCAATAAATGGTAAGTTAATATGTAATTTTTTTAATAATTTA
1 TGTTTGGCATCTACGAAAGAGCTTCAATAAACGGTAAGTTAATAAGTAATTTTTTTAATAATTTA
40455791 AGGAATTTACCGAATTGTCTA
66 AGGAATTTACCGAATTGTCTA
**
40455812 TGTTTGGCATCTGTGAAAGAGCTTCAATAAACGGTAAGTTAATAAGTAATTTTTTTAATAATTTA
1 TGTTTGGCATCTACGAAAGAGCTTCAATAAACGGTAAGTTAATAAGTAATTTTTTTAATAATTTA
40455877 AGGAATTTACCGAATTGT
66 AGGAATTTACCGAATTGT
40455895 TATTCTCTGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (86 bp):
TGTTTGGCATCTACGAAAGAGCTTCAATAAACGGTAAGTTAATAAGTAATTTTTTTAATAATTTA
AGGAATTTACCGAATTGTCTA
Found at i:40461827 original size:27 final size:27
Alignment explanation
Indices: 40461786--40461840 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
40461776 TGTCATGTGA
* *
40461786 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
40461813 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
40461840 A
1 A
40461841 GTTGTACCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:40462145 original size:49 final size:50
Alignment explanation
Indices: 40462065--40462297 Score: 229
Period size: 49 Copynumber: 4.7 Consensus size: 50
40462055 ATCTATTGTG
* *
40462065 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGCACTGGAAAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGAAAATT
* * * * ** *
40462115 -GGTCGCATGTGTAGTACTAGGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGA-AAATT
* * * * * * ***
40462165 CGATTACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTA-TCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-GGAAAATT
* *
40462215 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGAAAATT
* *
40462265 -GGTCGCATGTGTAGTACTAACTGCAGGCTACTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA
40462298 TGCATACCAG
Statistics
Matches: 147, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
49 66 0.45
50 47 0.32
51 34 0.23
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGAAAATT
Found at i:40466967 original size:40 final size:40
Alignment explanation
Indices: 40466883--40467066 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
40466873 TTGAATGCTG
* * * *
40466883 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40466922 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40466963 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40467003 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40467043 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40467067 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40467020 original size:80 final size:81
Alignment explanation
Indices: 40466883--40467063 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
40466873 TTGAATGCTG
* * *
40466883 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40466947 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40466963 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
40467024 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
40467043 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40467064 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40467087 original size:39 final size:39
Alignment explanation
Indices: 40466951--40467113 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
40466941 GGTATTTGTG
* * * **
40466951 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
40466991 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
40467031 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
40467070 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
40467110 CGAG
1 CGAG
40467114 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:40474697 original size:40 final size:40
Alignment explanation
Indices: 40474613--40474796 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
40474603 TTGAATGCTG
* * * *
40474613 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
40474652 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
40474693 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40474733 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40474773 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40474797 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40474750 original size:80 final size:81
Alignment explanation
Indices: 40474613--40474793 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
40474603 TTGAATGCTG
* * *
40474613 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
40474677 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
40474693 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
40474754 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
40474773 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
40474794 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:40474817 original size:39 final size:38
Alignment explanation
Indices: 40474694--40474843 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
40474684 GTTATTAATT
* ** * *
40474694 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
40474734 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
40474773 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
40474813 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
40474844 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:40494310 original size:27 final size:27
Alignment explanation
Indices: 40494280--40494434 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
40494270 TGCTATTCAC
* *
40494280 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
40494307 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
40494334 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
40494362 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
* *
40494389 TC-TTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
40494415 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
40494435 TGTACAATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
26 22 0.21
27 61 0.59
28 21 0.20
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:40494351 original size:55 final size:54
Alignment explanation
Indices: 40494285--40494435 Score: 180
Period size: 55 Copynumber: 2.8 Consensus size: 54
40494275 TTCACTCAAC
* * *
40494285 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TT-CAT
* ** * *
40494340 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTCAT
* *
40494393 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
40494436 GTACAATTTA
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
53 37 0.46
54 3 0.04
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (54 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTCAT
Found at i:40502339 original size:27 final size:27
Alignment explanation
Indices: 40502309--40502464 Score: 145
Period size: 27 Copynumber: 5.7 Consensus size: 27
40502299 TGCTATTCAC
* *
40502309 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAATTCGCACACTTAGTGCCACATAA
* * * *
40502336 TCAAATCGCACCCTTAGTGCTACATAG
1 TCAATTCGCACACTTAGTGCCACATAA
* * **
40502363 TTAGATTCGCACACTTAGTGCCGCATGG
1 TCA-ATTCGCACACTTAGTGCCACATAA
*
40502391 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAATTCGCACACTTAGTGCCA-CATAA
** *
40502418 TCTTTTCGCACACTTAGTGCAACATAA
1 TCAATTCGCACACTTAGTGCCACATAA
40502445 TCGAA-TCGCACACTTAGTGC
1 TC-AATTCGCACACTTAGTGC
40502465 TGTACAATTT
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.01
27 81 0.78
28 22 0.21
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAATTCGCACACTTAGTGCCACATAA
Found at i:40502380 original size:55 final size:55
Alignment explanation
Indices: 40502314--40502465 Score: 182
Period size: 54 Copynumber: 2.8 Consensus size: 55
40502304 TTCACTCAAC
* *
40502314 TCGCACACTTAGTGCCACGTAATCAAATCGCACCCTTAGTGCTA-CATAGTTAGAT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATA-TTAGAT
* ** * ***
40502369 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCATATTCTTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
* *
40502423 TCGCACACTTAGTGCAACATAATCGAATCGCACACTTAGTGCT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCT
40502466 GTACAATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 40 0.50
55 40 0.50
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (55 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTATCATATTAGAT
Found at i:40506380 original size:50 final size:49
Alignment explanation
Indices: 40506249--40506429 Score: 211
Period size: 50 Copynumber: 3.6 Consensus size: 49
40506239 ATCTATTGTG
* *
40506249 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTGATAA-TT
* * * * * **
40506300 CGATTACGTGTGTAGTACTAAGTGCTGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CTGATAATT
40506350 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGAATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTG-ATAATT
* * *
40506400 -GGTCGCATGTGTAGTACTAACTGCAGGCTA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTA
40506430 TTATGCGTAC
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 29 0.27
50 42 0.39
51 38 0.35
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGATAATT
Found at i:40508626 original size:37 final size:37
Alignment explanation
Indices: 40508585--40508704 Score: 161
Period size: 37 Copynumber: 3.2 Consensus size: 37
40508575 TGTCCAAGTC
* *
40508585 ATGGTCTTACATGTGATAACAATGCCATAGCCCAGCT
1 ATGGTCTTACATGTGATTACGATGCCATAGCCCAGCT
* *
40508622 ATGGTCTTACATGTCATTACGATGCCATAGCCTAGCT
1 ATGGTCTTACATGTGATTACGATGCCATAGCCCAGCT
* * *
40508659 ATGGTCGTACACG-GTTTTACGATGCCATAGCCCAGCT
1 ATGGTCTTACATGTG-ATTACGATGCCATAGCCCAGCT
40508696 ATGGTCTTA
1 ATGGTCTTA
40508705 TACGTACTCA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (37 bp):
ATGGTCTTACATGTGATTACGATGCCATAGCCCAGCT
Found at i:40510845 original size:40 final size:40
Alignment explanation
Indices: 40510800--40510992 Score: 318
Period size: 40 Copynumber: 4.8 Consensus size: 40
40510790 CTAAGATCCA
*
40510800 AAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
*
40510840 AAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
40510880 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
*
40510920 AAGGCATTTGTGCTAGTGACTATGTCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
* *
40510960 AAGGCATTCGTGCGAGTTG-CTATATCC-GGCTAA
1 AAGGCATTTGTGCTAG-TGACTATATCCGGGCTAA
40510993 ATTTCGAAGG
Statistics
Matches: 147, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
39 6 0.04
40 139 0.95
41 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
Found at i:40515033 original size:40 final size:40
Alignment explanation
Indices: 40514796--40515019 Score: 260
Period size: 40 Copynumber: 5.6 Consensus size: 40
40514786 TGAATGATGT
* * * *
40514796 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTAACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * * *
40514836 CTGGACTAAGAT-CCGAAGACATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
40514876 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40514914 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
40514955 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
40514995 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40515020 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
39 34 0.21
40 115 0.72
41 10 0.06
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:40520825 original size:14 final size:14
Alignment explanation
Indices: 40520806--40520833 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40520796 AGACTTTGGG
40520806 TATAATGGTTGAAA
1 TATAATGGTTGAAA
40520820 TATAATGGTTGAAA
1 TATAATGGTTGAAA
40520834 ACACTGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
TATAATGGTTGAAA
Found at i:40525243 original size:40 final size:40
Alignment explanation
Indices: 40525188--40525383 Score: 225
Period size: 40 Copynumber: 4.9 Consensus size: 40
40525178 GGCATGACTT
*
40525188 CTAGCATAAATGCCTTTGGGACTTAGCCCGGATATAGTCA
1 CTAGCACAAATGCCTTTGGGACTTAGCCCGGATATAGTCA
** * *
40525228 CTAGCACAAATGCCTTTGGGTTTTAGCCCGGATATAATCG
1 CTAGCACAAATGCCTTTGGGACTTAGCCCGGATATAGTCA
* *
40525268 CTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG-CAA
1 CTAGCACAAATGCCTTTGGGACTTAGCCCGGATATAGTC-A
* * * * *
40525308 CTCGCACCAATGCC-TTCGGATCTTAGTCCGGTTATAGTCA
1 CTAGCACAAATGCCTTTGGGA-CTTAGCCCGGATATAGTCA
* *
40525348 CCTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 -CTAGCACAAATGCCTTTGGGACTTAGCCCGGATAT
40525384 CATTCGAATA
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 4 0.03
40 96 0.75
41 24 0.19
42 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CTAGCACAAATGCCTTTGGGACTTAGCCCGGATATAGTCA
Found at i:40525297 original size:80 final size:81
Alignment explanation
Indices: 40525188--40525383 Score: 252
Period size: 80 Copynumber: 2.4 Consensus size: 81
40525178 GGCATGACTT
* * * * *
40525188 CTAGCATAAATGCCTTTGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTTGGGTTTT
1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGATCTT
*
40525252 AGCCCGGATATAATC-G
65 AGCCCGGATATAATCAC
* * *
40525268 CTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACCAATGCCTTCGGATCTTA
1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGATCTTA
* * *
40525333 GTCCGGTTATAGTCAC
66 GCCCGGATATAATCAC
*
40525349 CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
40525384 CATTCGAATA
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 66 0.66
81 33 0.33
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGATCTTA
GCCCGGATATAATCAC
Found at i:40531754 original size:13 final size:13
Alignment explanation
Indices: 40531736--40531761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40531726 AATTTGCTTG
40531736 AGAAAAAAATTAT
1 AGAAAAAAATTAT
40531749 AGAAAAAAATTAT
1 AGAAAAAAATTAT
40531762 TAAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AGAAAAAAATTAT
Found at i:40532337 original size:21 final size:21
Alignment explanation
Indices: 40532313--40532354 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40532303 TCCCCCACCT
*
40532313 CCCCCGATTCCTCAACCTGTA
1 CCCCCGATGCCTCAACCTGTA
*
40532334 CCCCCGATGCCTCAAGCTGTA
1 CCCCCGATGCCTCAACCTGTA
40532355 GATATGATGA
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:0.19, C:0.45, G:0.14, T:0.21
Consensus pattern (21 bp):
CCCCCGATGCCTCAACCTGTA
Found at i:40541034 original size:34 final size:34
Alignment explanation
Indices: 40540958--40541034 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
40540948 TGATTGCATT
40540958 ACTGTTACTATTACTGAATTGGGCTAAGGCCCAC
1 ACTGTTACTATTACTGAATTGGGCTAAGGCCCAC
* *
40540992 ACTTTTACTGA-TACTGTATTGGGCTAAGGCCCTA-
1 ACTGTTACT-ATTACTGAATTGGGCTAAGGCCC-AC
40541026 ACTGTTACT
1 ACTGTTACT
40541035 CGACTGTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 36 0.95
35 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (34 bp):
ACTGTTACTATTACTGAATTGGGCTAAGGCCCAC
Found at i:40548444 original size:27 final size:27
Alignment explanation
Indices: 40548383--40548446 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
40548373 GGCATATTCA
40548383 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCATACAGGGGTATTACGG
* *
40548410 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAGGGG-TATTACGG
*
40548437 TCTTTTTACC
1 TCATTTTACC
40548447 TATTAGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAGGGGTATTACGG
Found at i:40548530 original size:27 final size:27
Alignment explanation
Indices: 40548477--40548604 Score: 84
Period size: 27 Copynumber: 4.7 Consensus size: 27
40548467 TTTCATCTTA
* * * **
40548477 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTCTGTAAAC
40548504 CAAGGGTATTTTAGTAATTCTGTAAAC
1 CAAGGGTATTTTAGTAATTCTGTAAAC
* * *
40548531 CAATGGTATTTCTA-TAATT-TTTAAAAGT
1 CAAGGGTATTT-TAGTAATTCTGT-AAA-C
* *
40548559 CAAGGGTATTTCTA-TAATTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTCTGTAAAC
*
40548586 C-AGAGGTATTTTGGTAATT
1 CAAG-GGTATTTTAGTAATT
40548605 TTACAAATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
26 5 0.06
27 54 0.64
28 23 0.27
29 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTCTGTAAAC
Found at i:40548604 original size:55 final size:54
Alignment explanation
Indices: 40548497--40548665 Score: 141
Period size: 54 Copynumber: 3.1 Consensus size: 54
40548487 TTGGTAAATC
* *
40548497 TACAAACCAAGGGTATTT-TAGTAATTCTGTAAACCAATGGTATTTCTATAATTTT
1 TACAAATCAAGGGTATTTCTA-TAATTTTGTAAACCAATGGTATTTCTATAA-TTT
* *
40548552 TA-AAAGTCAAGGGTATTTCTATAATTTTGTAAATCAGA-GGTATTT-TGGTAATTT
1 TACAAA-TCAAGGGTATTTCTATAATTTTGTAAACCA-ATGGTATTTCT-ATAATTT
*** *** * *
40548606 TACAAATTGTGGGTATTTCTATAATTTCAAAAACCAATGGCATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCTATAATTTTGTAAACCAATGGTATTTCT-ATAATTT
40548660 TACAAA
1 TACAAA
40548666 CTAGGGGTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
53 1 0.01
54 53 0.55
55 39 0.41
56 3 0.03
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCTATAATTTTGTAAACCAATGGTATTTCTATAATTT
Found at i:40548612 original size:27 final size:27
Alignment explanation
Indices: 40548573--40548685 Score: 72
Period size: 27 Copynumber: 4.2 Consensus size: 27
40548563 GGTATTTCTA
**
40548573 TAATTTTGTAAATCAGAGGTATTTTGG
1 TAATTTTACAAATCAGAGGTATTTTGG
* * *
40548600 TAATTTTACAAAT-TGTGGGTATTTCT-A
1 TAATTTTACAAATCAG-AGGTATTT-TGG
* * * *
40548627 TAATTTCAAAAACCA-ATGGCATTTTGG
1 TAATTTTACAAATCAGA-GGTATTTTGG
*
40548654 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTACAAATC-AGAGGTATTTTGG
40548681 TAATT
1 TAATT
40548686 CTACCCTATA
Statistics
Matches: 63, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
26 3 0.05
27 59 0.94
28 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
TAATTTTACAAATCAGAGGTATTTTGG
Found at i:40548631 original size:54 final size:54
Alignment explanation
Indices: 40548562--40548665 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
40548552 TAAAAGTCAA
*** * *
40548562 GGGTATTTCTATAATTTTGTAAATCAGA-GGTATTTTGGTAATTTTACAAATTGT
1 GGGTATTTCTATAATTTCAAAAACCA-ATGGCATTTTGGTAATTTTACAAATTGT
40548616 GGGTATTTCTATAATTTCAAAAACCAATGGCATTTTGGTAATTTTACAAA
1 GGGTATTTCTATAATTTCAAAAACCAATGGCATTTTGGTAATTTTACAAA
40548666 CTAGGGGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.02
54 43 0.98
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (54 bp):
GGGTATTTCTATAATTTCAAAAACCAATGGCATTTTGGTAATTTTACAAATTGT
Found at i:40548674 original size:54 final size:54
Alignment explanation
Indices: 40548562--40548677 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 54
40548552 TAAAAGTCAA
*** * * *
40548562 GGGTATTTCTATAATTTTGTAAATCAGAGGTATTTTGGTAATTTTACAAATTGT
1 GGGTATTTCTATAATTTCAAAAACCAGAGGCATTTTGGTAATTTTACAAATAGT
40548616 GGGTATTTCTATAATTTCAAAAACCA-ATGGCATTTTGGTAATTTTACAAACTAG-
1 GGGTATTTCTATAATTTCAAAAACCAGA-GGCATTTTGGTAATTTTACAAA-TAGT
40548670 GGGTATTT
1 GGGTATTT
40548678 TGGTAATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
53 1 0.02
54 51 0.94
55 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (54 bp):
GGGTATTTCTATAATTTCAAAAACCAGAGGCATTTTGGTAATTTTACAAATAGT
Found at i:40548747 original size:27 final size:27
Alignment explanation
Indices: 40548717--40548808 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
40548707 GTAATTTCAC
* *
40548717 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
*
40548744 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAATAGTAATTCTGTA
* * *
40548771 AATCAAGGGTAAAATAGTGATTCTATA
1 AATCGAGGGTAAAATAGTAATTCTGTA
40548798 AATCGAGGGTA
1 AATCGAGGGTA
40548809 CTTTGGTAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAATAGTAATTCTGTA
Found at i:40551190 original size:31 final size:31
Alignment explanation
Indices: 40551147--40551229 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
40551137 TCAGTCTCGA
40551147 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
40551177 CATATCACTGGGCCGAAGCTTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
40551208 CATATCACT-GGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40551230 ACAGTAAGCG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 17 0.34
31 33 0.66
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:40552466 original size:27 final size:26
Alignment explanation
Indices: 40552417--40552499 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 26
40552407 GTAAATCTAC
40552417 AAACCAAGGTA-TT-TAGTAATTTTGT
1 AAACCAAGGTATTTCTA-TAATTTTGT
40552442 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAA-GGTATTTCTATAATTTTGT
* *
40552468 GAAAGTCAAGGGTATTTCTGTAATTTTGT
1 -AAA-CCAA-GGTATTTCTATAATTTTGT
40552497 AAA
1 AAA
40552500 TCAGGGGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
25 7 0.14
26 5 0.10
27 12 0.24
28 24 0.49
29 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (26 bp):
AAACCAAGGTATTTCTATAATTTTGT
Found at i:40552481 original size:28 final size:27
Alignment explanation
Indices: 40552433--40552511 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
40552423 AGGTATTTAG
* *
40552433 TAATTTTGTAAACCAATGGTATTTCTA
1 TAATTTTGTAAATCAAGGGTATTTCTA
*
40552460 TAATTTT-TGAAAGTCAAGGGTATTTCTG
1 TAATTTTGT-AAA-TCAAGGGTATTTCTA
*
40552488 TAATTTTGTAAATCAGGGGTATTT
1 TAATTTTGTAAATCAAGGGTATTT
40552512 TGGTAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.02
27 21 0.47
28 22 0.49
29 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (27 bp):
TAATTTTGTAAATCAAGGGTATTTCTA
Found at i:40552507 original size:27 final size:26
Alignment explanation
Indices: 40552424--40552521 Score: 99
Period size: 27 Copynumber: 3.6 Consensus size: 26
40552414 TACAAACCAA
* * *
40552424 GGTATTTAGTAATTTTGTAAACCAAT
1 GGTATTTTGTAATTTTGTAAATCAAG
*
40552450 GGTATTTCTATAATTTT-TGAAAGTCAAG
1 GGTATTT-TGTAATTTTGT-AAA-TCAAG
*
40552478 GGTATTTCTGTAATTTTGTAAATCAGG
1 GGTATTT-TGTAATTTTGTAAATCAAG
40552505 GGTATTTTGGTAATTTT
1 GGTATTTT-GTAATTTT
40552522 ACAAATTGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
26 9 0.15
27 29 0.48
28 22 0.36
29 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (26 bp):
GGTATTTTGTAATTTTGTAAATCAAG
Found at i:40552527 original size:27 final size:27
Alignment explanation
Indices: 40552477--40552599 Score: 117
Period size: 27 Copynumber: 4.6 Consensus size: 27
40552467 TGAAAGTCAA
**
40552477 GGGTATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAATCAG
*
40552504 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * * *
40552530 AGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
* *
40552557 TGGTATTTTGGTAATTTTACAAA-CTAT
1 GGGTATTTTGGTAATTTTACAAATC-AG
*
40552584 GGGTATTTTCGTAATT
1 GGGTATTTTGGTAATT
40552600 CTACCTTATA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
26 23 0.29
27 56 0.71
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:40552562 original size:53 final size:53
Alignment explanation
Indices: 40552478--40552579 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
40552468 GAAAGTCAAG
* *** *
40552478 GGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGA
1 GGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAATTGA
*
40552531 GGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAA
1 GGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAA
40552580 CTATGGGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (53 bp):
GGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAATTGA
Found at i:40552653 original size:26 final size:26
Alignment explanation
Indices: 40552619--40552722 Score: 93
Period size: 27 Copynumber: 3.9 Consensus size: 26
40552609 AGGGATATTT
*
40552619 CAGTAATTT-CACAATTGAGGGTAAAA
1 CAGTAATTTGCA-AATCGAGGGTAAAA
* *
40552645 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAGGGTAAAA
* *
40552672 CAGTAATTCTGTAAATCAAGGGTAAAA
1 CAGTAATT-TGCAAATCGAGGGTAAAA
* **
40552699 CAGTGATTCTATAAATCGAGGGTA
1 CAGTAATT-TGCAAATCGAGGGTA
40552723 CTTTTGTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.10
27 59 0.88
28 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (26 bp):
CAGTAATTTGCAAATCGAGGGTAAAA
Found at i:40552665 original size:27 final size:27
Alignment explanation
Indices: 40552635--40552722 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
40552625 TTTCACAATT
* *
40552635 GAGGGTAAAACGGTAATTTTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
40552662 GAGGGTAAAACAGTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* * *
40552689 AAGGGTAAAACAGTGATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
40552716 GAGGGTA
1 GAGGGTA
40552723 CTTTTGTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTGTAAATC
Found at i:40554409 original size:27 final size:28
Alignment explanation
Indices: 40554346--40554414 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
40554336 ATCGTAGAGC
*
40554346 AAATCAGTCATTTTACCTTATAGGGGTA
1 AAATCAGTCATTTTACCCTATAGGGGTA
**
40554374 TTA-CAGTCATTTTACCCTATAGGGGTA
1 AAATCAGTCATTTTACCCTATAGGGGTA
40554401 AAATC-GTCATTTTA
1 AAATCAGTCATTTTA
40554415 TCACATGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (28 bp):
AAATCAGTCATTTTACCCTATAGGGGTA
Found at i:40555553 original size:27 final size:27
Alignment explanation
Indices: 40555492--40555556 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40555482 GGCATATTCG
* *
40555492 TCATTTTACCATACAGGGGTATTACGG
1 TCATTTTACCTTACAGGGGTATTACGA
*
40555519 TCACTTTACCTTACAGGGGCT-TTACGA
1 TCATTTTACCTTACAGGGG-TATTACGA
*
40555546 TCTTTTTACCT
1 TCATTTTACCT
40555557 ATTAGGGGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (27 bp):
TCATTTTACCTTACAGGGGTATTACGA
Found at i:40555639 original size:27 final size:28
Alignment explanation
Indices: 40555609--40555742 Score: 107
Period size: 27 Copynumber: 4.9 Consensus size: 28
40555599 GTAAATCTAC
*
40555609 AAACCAAAGGTATTT-TAGTAATTTTGT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
* *
40555636 AAACCAATGGTATTTCTA-TAATTTTTT
1 AAACCAAGGGTATTTCTAGTAATTTTGT
**
40555663 GAAGGTCAAGGGTATTTCT-GTAATTTTGT
1 -AA-ACCAAGGGTATTTCTAGTAATTTTGT
* * **
40555692 AAACCAGGGGTATTT-TGGTAATTTTAC
1 AAACCAAGGGTATTTCTAGTAATTTTGT
** *
40555719 AAATTAAGGGTATTTCGA-TAATTT
1 AAACCAAGGGTATTTCTAGTAATTT
40555743 CACAAACCAG
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
27 58 0.68
28 6 0.07
29 20 0.24
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (28 bp):
AAACCAAGGGTATTTCTAGTAATTTTGT
Found at i:40555752 original size:54 final size:54
Alignment explanation
Indices: 40555670--40555795 Score: 157
Period size: 54 Copynumber: 2.3 Consensus size: 54
40555660 TTTGAAGGTC
*** *
40555670 AAGGGTATTTCTGTAATTTTGTAAACCAGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTCTGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACT
* *
40555724 AAGGGTATTTC-GATAATTTCACAAACCAGTGGTGTTTTGGTAATTTTACAAACT
1 AAGGGTATTTCTG-TAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACT
*
40555778 AGGGGTATTT-TGGTAATT
1 AAGGGTATTTCT-GTAATT
40555796 CTACCCTATA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
53 1 0.02
54 60 0.97
55 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
AAGGGTATTTCTGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACT
Found at i:40555767 original size:27 final size:27
Alignment explanation
Indices: 40555672--40555795 Score: 133
Period size: 27 Copynumber: 4.6 Consensus size: 27
40555662 TGAAGGTCAA
**
40555672 GGGTATTTCT-GTAATTTTGTAAACCAG
1 GGGTATTT-TGGTAATTTTACAAACCAG
** *
40555699 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
40555726 GGGTATTTCGATAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
40555753 TGGTGTTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
40555780 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
40555796 CTACCCTATA
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
26 1 0.01
27 76 0.99
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:40555846 original size:26 final size:26
Alignment explanation
Indices: 40555815--40555894 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
40555805 AGGGGTATTT
40555815 CAGTAATTT-CACAATCGAGGGTAAAA
1 CAGTAATTTGCA-AATCGAGGGTAAAA
* *
40555841 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CAGTAA-TTTGCAAATCGAGGGTAAAA
* * *
40555868 CAGTAATTCTGTAAATCAAAGGTAAAA
1 CAGTAATT-TGCAAATCGAGGGTAAAA
40555895 ATAGTGATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.15
27 38 0.83
28 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.26
Consensus pattern (26 bp):
CAGTAATTTGCAAATCGAGGGTAAAA
Found at i:40555857 original size:27 final size:27
Alignment explanation
Indices: 40555827--40555919 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
40555817 GTAATTTCAC
* *
40555827 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
40555854 AATCGAGGGTAAAACAGTAATTCTGTA
1 AATCGAGGGTAAAACAGTAATTCTGTA
* * * * *
40555881 AATCAAAGGTAAAAATAGTGATTCTATA
1 AATCGAGGGT-AAAACAGTAATTCTGTA
40555909 AATCGAGGGTA
1 AATCGAGGGTA
40555920 GTTTGGTAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
27 34 0.61
28 22 0.39
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACAGTAATTCTGTA
Found at i:40557757 original size:18 final size:18
Alignment explanation
Indices: 40557733--40557774 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40557723 AAATTTTAAA
*
40557733 AAAAATTACCAAAGTCTC
1 AAAAATTACCAAAATCTC
* *
40557751 TAAAATTACGAAAATCTC
1 AAAAATTACCAAAATCTC
40557769 AAAAAT
1 AAAAAT
40557775 CAGGGTGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAAATTACCAAAATCTC
Found at i:40557859 original size:20 final size:20
Alignment explanation
Indices: 40557834--40557873 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40557824 TCAGCACATA
40557834 TTTCAGCT-AATCATATATAT
1 TTTCAGCTCAAT-ATATATAT
*
40557854 TTTCAGTTCAATATATATAT
1 TTTCAGCTCAATATATATAT
40557874 CAATTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTCAGCTCAATATATATAT
Found at i:40558281 original size:19 final size:20
Alignment explanation
Indices: 40558247--40558287 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
40558237 AATTCCAATT
*
40558247 TTTCTTTTTGCTTTCTTTCC
1 TTTCTTTTTGCCTTCTTTCC
40558267 TTTCTTTTT-CCTTCTTTCC
1 TTTCTTTTTGCCTTCTTTCC
40558286 TT
1 TT
40558288 CCCTTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTCTTTTTGCCTTCTTTCC
Found at i:40558390 original size:14 final size:16
Alignment explanation
Indices: 40558371--40558402 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40558361 CAATAAAGAT
40558371 ATCTA-TTAATAA-AA
1 ATCTATTTAATAACAA
40558385 ATCTATTTAATAACAA
1 ATCTATTTAATAACAA
40558401 AT
1 AT
40558403 ATTTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCTATTTAATAACAA
Found at i:40563344 original size:18 final size:18
Alignment explanation
Indices: 40563321--40563452 Score: 147
Period size: 18 Copynumber: 7.3 Consensus size: 18
40563311 CGATCAGTCA
* *
40563321 TCAGTATTAATCAATTAT
1 TCAGTAATAGTCAATTAT
* *
40563339 TCAGTAATAATCATTTAT
1 TCAGTAATAGTCAATTAT
* *
40563357 TCAGTAACAGTCATTTAT
1 TCAGTAATAGTCAATTAT
*
40563375 TCAGTCATAGTCAATTAT
1 TCAGTAATAGTCAATTAT
* *
40563393 TCAGTAATAATCAGTTAT
1 TCAGTAATAGTCAATTAT
* *
40563411 TTAGTAATAGTCATTTAT
1 TCAGTAATAGTCAATTAT
* *
40563429 TCAGTCACAGTCAATTAT
1 TCAGTAATAGTCAATTAT
40563447 TCAGTA
1 TCAGTA
40563453 GCAGACAGTT
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 96 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (18 bp):
TCAGTAATAGTCAATTAT
Found at i:40563375 original size:36 final size:36
Alignment explanation
Indices: 40563331--40563470 Score: 163
Period size: 36 Copynumber: 3.9 Consensus size: 36
40563321 TCAGTATTAA
*
40563331 TCAATTATTCAGTAATAATCATTTATTCAGTAACAG
1 TCAATTATTCAGTAATAGTCATTTATTCAGTAACAG
* * * * *
40563367 TCATTTATTCAGTCATAGTCAATTATTCAGTAATAA
1 TCAATTATTCAGTAATAGTCATTTATTCAGTAACAG
* * *
40563403 TCAGTTATTTAGTAATAGTCATTTATTCAGTCACAG
1 TCAATTATTCAGTAATAGTCATTTATTCAGTAACAG
** * *
40563439 TCAATTATTCAGTAGCAGACAGTTATTCAGTA
1 TCAATTATTCAGTAATAGTCATTTATTCAGTA
40563471 TCTTTATTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 84 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (36 bp):
TCAATTATTCAGTAATAGTCATTTATTCAGTAACAG
Found at i:40563389 original size:54 final size:54
Alignment explanation
Indices: 40563331--40563470 Score: 210
Period size: 54 Copynumber: 2.6 Consensus size: 54
40563321 TCAGTATTAA
* *
40563331 TCAATTATTCAGTAATAATCATTTATTCAGTAACAGTCATTTATTCAGTCATAG
1 TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
* *
40563385 TCAATTATTCAGTAATAATCAGTTATTTAGTAATAGTCATTTATTCAGTCACAG
1 TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
**
40563439 TCAATTATTCAGTAGCAGA-CAGTTATTCAGTA
1 TCAATTATTCAGTAATA-ATCAGTTATTCAGTA
40563471 TCTTTATTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 77 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (54 bp):
TCAATTATTCAGTAATAATCAGTTATTCAGTAACAGTCATTTATTCAGTCACAG
Found at i:40563464 original size:18 final size:17
Alignment explanation
Indices: 40563353--40563470 Score: 58
Period size: 18 Copynumber: 6.6 Consensus size: 17
40563343 TAATAATCAT
* *
40563353 TTATTCAGTAACAGTCAT
1 TTATTCAGT-ACAGACAA
* *
40563371 TTATTCAGTCATAGTCAA
1 TTATTCAGT-ACAGACAA
* *
40563389 TTATTCAGTA-ATAATCAG
1 TTATTCAGTACA-GA-CAA
* * * *
40563407 TTATTTAGTAATAGTCAT
1 TTATTCAGT-ACAGACAA
*
40563425 TTATTCAGTCACAGTCAA
1 TTATTCAGT-ACAGACAA
*
40563443 TTATTCAGTAGCAGACAG
1 TTATTCAGTA-CAGACAA
40563461 TTATTCAGTA
1 TTATTCAGTA
40563471 TCTTTATTTT
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
16 1 0.01
17 2 0.03
18 74 0.94
19 1 0.01
20 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (17 bp):
TTATTCAGTACAGACAA
Found at i:40563704 original size:51 final size:53
Alignment explanation
Indices: 40563596--40563710 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 53
40563586 AACAGTAACG
* *
40563596 GTAACAGTAACAGTAGAAGTACAGAGAGTACCTCATCAGAACAAATCCAGAATA
1 GTAACAGTAACAGTAGAAGTACA-ACAGTACCTCATCAGAACAAATCCAGAACA
* * * ** *
40563650 GTAACAGTAACAGTA-AGGTAC-ACAGTACCTCTTCGGAATGAATCCGGAACA
1 GTAACAGTAACAGTAGAAGTACAACAGTACCTCATCAGAACAAATCCAGAACA
*
40563701 GTAATAGTAA
1 GTAACAGTAA
40563711 GGCAACACTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
51 32 0.62
53 5 0.10
54 15 0.29
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (53 bp):
GTAACAGTAACAGTAGAAGTACAACAGTACCTCATCAGAACAAATCCAGAACA
Found at i:40563877 original size:20 final size:20
Alignment explanation
Indices: 40563852--40563889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40563842 TCAGTACATA
40563852 TTTCAGCT-AATCATATATAT
1 TTTCAGCTCAAT-ATATATAT
40563872 TTTCAGCTCAATATATAT
1 TTTCAGCTCAATATATAT
40563890 TTCAATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTCAGCTCAATATATATAT
Found at i:40564426 original size:15 final size:16
Alignment explanation
Indices: 40564401--40564442 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
40564391 CAATAAAGAT
40564401 ATCTA-TTAATAA-AA
1 ATCTATTTAATAACAA
40564415 ATCTATTTAATAACAA
1 ATCTATTTAATAACAA
40564431 ATACTTATTTAA
1 AT-C-TATTTAA
40564443 CACTTGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 4 0.17
17 1 0.04
18 7 0.29
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (16 bp):
ATCTATTTAATAACAA
Found at i:40567106 original size:23 final size:23
Alignment explanation
Indices: 40567062--40567106 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40567052 CGTAATGCTC
**
40567062 TGTAAAGCCTTCGTGGTGTATTT
1 TGTAAAGCCTTCGTGGCATATTT
* *
40567085 TGTAAAGCTTTTGTGGCATATT
1 TGTAAAGCCTTCGTGGCATATT
40567107 CTATGATACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (23 bp):
TGTAAAGCCTTCGTGGCATATTT
Found at i:40570642 original size:43 final size:43
Alignment explanation
Indices: 40570586--40570804 Score: 253
Period size: 44 Copynumber: 5.0 Consensus size: 43
40570576 ATATCTTACA
** *
40570586 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATATCCCAGACGTGGTCTTACACGTAATCACATATCG
*
40570629 ATGCCACTATCCCAGACAG-GGTCTTACACGTAAATCACATATCG
1 ATGCCAATATCCCAGAC-GTGGTCTTACACGT-AATCACATATCG
* * * *
40570673 ATGCCAATGTCCCAGACATGGTCTTACACGTACTCACATATTG
1 ATGCCAATATCCCAGACGTGGTCTTACACGTAATCACATATCG
* * * *
40570716 ATGCCAA-AGTCCCAAACATGGTCTTACACGTACCTCACATATGG
1 ATGCCAATA-TCCCAGACGTGGTCTTACACGTA-ATCACATATCG
* * *
40570760 ATGCCAATGTCCTAGACGTGGTCTTACACATAATCACATATCG
1 ATGCCAATATCCCAGACGTGGTCTTACACGTAATCACATATCG
40570803 AT
1 AT
40570805 ATCACATATC
Statistics
Matches: 151, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
43 75 0.50
44 76 0.50
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATATCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:40570685 original size:87 final size:87
Alignment explanation
Indices: 40570586--40570804 Score: 305
Period size: 87 Copynumber: 2.5 Consensus size: 87
40570576 ATATCTTACA
* * * *
40570586 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTA-TCCCAGACAGGG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCA-AAGTCCCAAACAGGG
40570650 TCTTACACGTAAATCACATATCG
65 TCTTACACGTAAATCACATATCG
* * * *
40570673 ATGCCAATGTCCCAGACATGGTCTTACACGTACTCACATATTGATGCCAAAGTCCCAAACATGGT
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAAAGTCCCAAACAGGGT
** *
40570738 CTTACACGTACCTCACATATGG
66 CTTACACGTAAATCACATATCG
* *
40570760 ATGCCAATGTCCTAGACGTGGTCTTACACATAATCACATATCGAT
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCGAT
40570805 ATCACATATC
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
86 1 0.01
87 114 0.99
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (87 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCACATATCGATGCCAAAGTCCCAAACAGGGT
CTTACACGTAAATCACATATCG
Found at i:40571931 original size:14 final size:15
Alignment explanation
Indices: 40571912--40571940 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40571902 AAATGAAATT
40571912 TTCACACAT-ATAAA
1 TTCACACATAATAAA
40571926 TTCACACATAATAAA
1 TTCACACATAATAAA
40571941 CACAGTAAAT
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:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:40573370 original size:22 final size:22
Alignment explanation
Indices: 40573342--40573385 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40573332 CCATACAATA
40573342 CTTAGTTGTTTCTCTATTCATT
1 CTTAGTTGTTTCTCTATTCATT
40573364 CTTAGTTGTTTCTCTATTCATT
1 CTTAGTTGTTTCTCTATTCATT
40573386 TACTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.09, T:0.59
Consensus pattern (22 bp):
CTTAGTTGTTTCTCTATTCATT
Found at i:40590484 original size:13 final size:14
Alignment explanation
Indices: 40590464--40590493 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
40590454 TGTAACCATT
40590464 AACTTTTTCCATAG
1 AACTTTTTCCATAG
40590478 AACTTTTTCCATAG
1 AACTTTTTCCATAG
40590492 AA
1 AA
40590494 TTTACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (14 bp):
AACTTTTTCCATAG
Found at i:40592963 original size:27 final size:28
Alignment explanation
Indices: 40592853--40593002 Score: 214
Period size: 27 Copynumber: 5.4 Consensus size: 28
40592843 GAGATTGGCG
* * * *
40592853 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
40592882 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40592910 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40592938 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40592965 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40592992 CTGAGTGTGCG
1 CTAAGTGTGCG
40593003 GACTTAATAT
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 50 0.44
28 49 0.43
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:40592970 original size:55 final size:55
Alignment explanation
Indices: 40592878--40593002 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 55
40592868 TAAATTGTAC
* *
40592878 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATAT
40592934 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
*
40592988 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40593003 GACTTAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 23 0.35
55 26 0.39
56 17 0.26
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATAT
Done.