Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 19
Found at i:2506336 original size:20 final size:20
Alignment explanation
Indices: 2506311--2506352 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2506301 TTGTGTTCTC
2506311 AGTAATAAAAGCTATCGGTT
1 AGTAATAAAAGCTATCGGTT
2506331 AGTAATAAAAGCTATCGGTT
1 AGTAATAAAAGCTATCGGTT
2506351 AG
1 AG
2506353 GTTTAGCCCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTAATAAAAGCTATCGGTT
Found at i:2508735 original size:18 final size:18
Alignment explanation
Indices: 2508712--2508802 Score: 75
Period size: 18 Copynumber: 5.2 Consensus size: 18
2508702 ACCGGTCACA
2508712 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2508730 ACCCGACCCGACCTGTT-
1 ACCCGACCCGACCCGTTG
*
2508747 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
2508761 ACCAGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
*
2508779 ACTCGACCCGGTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
2508800 ACC
1 ACC
2508803 TTTGACCCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
13 11 0.20
18 35 0.62
21 10 0.18
ACGTcount: A:0.18, C:0.44, G:0.22, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2508753 original size:31 final size:31
Alignment explanation
Indices: 2508716--2508796 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
2508706 GTCACAACCC
2508716 GACCCGACCCGTTGACCCGACCCGACCTGTT
1 GACCCGACCCGTTGACCCGACCCGACCTGTT
* *
2508747 TACCCGACCCGTTGACCAGACCCGACCTGTT
1 GACCCGACCCGTTGACCCGACCCGACCTGTT
* *
2508778 GACTCGACCCGGTGACCCG
1 GACCCGACCCGTTGACCCG
2508797 TTGACCTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCTGTT
Found at i:2513904 original size:13 final size:13
Alignment explanation
Indices: 2513904--2513951 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
2513894 CGTTTACCCG
2513904 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
2513917 ACCCGACCCATTT
1 ACCCGACCCGTTT
* *
2513930 ACTCGACCCGTTG
1 ACCCGACCCGTTT
2513943 ACCCGACCC
1 ACCCGACCC
2513952 AACCCGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.19, C:0.48, G:0.15, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:2513908 original size:18 final size:18
Alignment explanation
Indices: 2513885--2513925 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
2513875 GTCACAACCG
2513885 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCC
2513903 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTTACCC
2513921 GACCC
1 GACCC
2513926 ATTTACTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.17, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTTACCC
Found at i:2513983 original size:15 final size:15
Alignment explanation
Indices: 2513953--2513993 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2513943 ACCCGACCCA
2513953 ACCCGTTGA-C-TTG
1 ACCCGTTGACCGTTG
2513966 ACCCGTTGACCGTTG
1 ACCCGTTGACCGTTG
*
2513981 ACCCATTGACCGT
1 ACCCGTTGACCGT
2513994 CGTTGACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 9 0.36
14 1 0.04
15 15 0.60
ACGTcount: A:0.17, C:0.34, G:0.22, T:0.27
Consensus pattern (15 bp):
ACCCGTTGACCGTTG
Found at i:2518992 original size:25 final size:25
Alignment explanation
Indices: 2518963--2519012 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2518953 ATCGCTTTAG
2518963 TAAAATTGATCATATTGATGTAGAA
1 TAAAATTGATCATATTGATGTAGAA
2518988 TAAAATTGATCATATTGATGTAGAA
1 TAAAATTGATCATATTGATGTAGAA
2519013 CTAGTGACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (25 bp):
TAAAATTGATCATATTGATGTAGAA
Found at i:2519682 original size:14 final size:14
Alignment explanation
Indices: 2519637--2519674 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
2519627 GAGTAAAAAC
2519637 AATTATATTATTAT
1 AATTATATTATTAT
2519651 AATTATATTATTAT
1 AATTATATTATTAT
2519665 AATTATATTA
1 AATTATATTA
2519675 GAGTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATATTATTAT
Found at i:2521577 original size:20 final size:20
Alignment explanation
Indices: 2521508--2521583 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
2521498 TGTATACTCA
* * *
2521508 TCTTCGGTGTGGATACTAGT
1 TCTTCGGTATGGAGACCAGT
* * **
2521528 CCATCGGTATGGAGAATAGT
1 TCTTCGGTATGGAGACCAGT
*
2521548 TCTTCTGTATGGAGACCA-T
1 TCTTCGGTATGGAGACCAGT
*
2521567 TCTTTCGGTATAGAGAC
1 TC-TTCGGTATGGAGAC
2521584 TAGCCAATCT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
19 3 0.07
20 40 0.93
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (20 bp):
TCTTCGGTATGGAGACCAGT
Found at i:2525276 original size:41 final size:41
Alignment explanation
Indices: 2525212--2525491 Score: 249
Period size: 41 Copynumber: 6.8 Consensus size: 41
2525202 AGGTTCATCC
* * *
2525212 AGACTCGTACTTTAGTGGTGTTTTTATATAAACGCCACTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * *** *
2525253 AGACTAGTACTTTAATGGCGTTTTTATACAAACAATGCAAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * * *
2525294 AGACTCTTACTTTAGCGGCATTTTTAAATAAACGCCGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * * * ** *
2525335 AAACTTGTACTTTATTGGCGTTTTT-TCAATAAATACTGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTAT--ACAAACGCCGCTAA
* *
2525377 AGACTCGTACTTTAGTGGCTTTTTTATACAAACGTCGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
* * *
2525418 AGACCCGTATTTTAGTGGCATTTTT-TAACAAACGCCGCTAA
1 AGACTCGTACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTAA
* * **
2525459 ATAATTATACTTTAGTGGCGTTTTTATACAAAC
1 AGACTCGTACTTTAGTGGCGTTTTTATACAAAC
2525492 ACCACCGTTT
Statistics
Matches: 184, Mismatches: 50, Indels: 10
0.75 0.20 0.04
Matches are distributed among these distances:
40 1 0.01
41 149 0.81
42 33 0.18
43 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (41 bp):
AGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA
Found at i:2525438 original size:124 final size:124
Alignment explanation
Indices: 2525249--2525483 Score: 321
Period size: 124 Copynumber: 1.9 Consensus size: 124
2525239 ATAAACGCCA
* *
2525249 CTAAAGACTAGTACTTTAATGGCGTTTTTATACAAACAATGCAAAAGACTCTTACTTTAGCGGCA
1 CTAAAGACTAGTACTTTAATGGCGTTTTTATACAAACAATGCAAAAGACCCGTACTTTAGCGGCA
* * *
2525314 TTTTTAAATAAACGCCGCTAAA-AACTTGTACTTTATTGGCGTTTTTTCAATAAATACTG
66 TTTTTAAACAAACGCCGCTAAATAA-TTATACTTTAGTGGCGTTTTTTCAATAAATACTG
* * * * * * *
2525373 CTAAAGACTCGTACTTTAGTGGCTTTTTTATACAAAC-GTCGCTAAAGACCCGTATTTTAGTGGC
1 CTAAAGACTAGTACTTTAATGGCGTTTTTATACAAACAAT-GCAAAAGACCCGTACTTTAGCGGC
*
2525437 ATTTTTTAACAAACGCCGCTAAATAATTATACTTTAGTGGCGTTTTT
65 ATTTTTAAACAAACGCCGCTAAATAATTATACTTTAGTGGCGTTTTT
2525484 ATACAAACAC
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
123 1 0.01
124 93 0.97
125 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (124 bp):
CTAAAGACTAGTACTTTAATGGCGTTTTTATACAAACAATGCAAAAGACCCGTACTTTAGCGGCA
TTTTTAAACAAACGCCGCTAAATAATTATACTTTAGTGGCGTTTTTTCAATAAATACTG
Found at i:2528584 original size:43 final size:42
Alignment explanation
Indices: 2528519--2528612 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 42
2528509 AAAACGTTGT
* * *
2528519 TATAGATCTGACCTTTTGCGGTGTTT-TTAGATACAAACACCGC
1 TATAGATCTAACCTTTTACGGTGTTTGTTA-A-AAAAACACCGC
*
2528562 TATAGATCTAACCTTTTACGGTGTTTGTTAAAAAAACGCCGC
1 TATAGATCTAACCTTTTACGGTGTTTGTTAAAAAAACACCGC
*
2528604 TATATATCT
1 TATAGATCT
2528613 CGAGATTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 17 0.38
43 25 0.56
44 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (42 bp):
TATAGATCTAACCTTTTACGGTGTTTGTTAAAAAAACACCGC
Found at i:2528640 original size:43 final size:43
Alignment explanation
Indices: 2528553--2528747 Score: 178
Period size: 43 Copynumber: 4.6 Consensus size: 43
2528543 TTTTAGATAC
* * * * * *
2528553 AAACACCGCTATAGATCT-AACCTTTTACGGTGTTTGTTAAAA
1 AAACGCCGCTATATATCTCGACATTTTACGGCGTTTGTTCAAA
* * *
2528595 AAACGCCGCTATATATCTCGAGATTTTGCGGCGTTTGTTCCAA
1 AAACGCCGCTATATATCTCGACATTTTACGGCGTTTGTTCAAA
* * * * **
2528638 AAACGCCACTATAGT-TCTTGACCTATGGCGGCGTTTGTTCAAA
1 AAACGCCGCTATA-TATCTCGACATTTTACGGCGTTTGTTCAAA
* * *
2528681 AAACGCCGCTATATATCTCGACATTTTATGGCATTTGTTCCAA
1 AAACGCCGCTATATATCTCGACATTTTACGGCGTTTGTTCAAA
* * *
2528724 AAATGCCGCTATAGATCTTGACAT
1 AAACGCCGCTATATATCTCGACAT
2528748 ATGGCGGCAT
Statistics
Matches: 122, Mismatches: 28, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
42 17 0.14
43 104 0.85
44 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTATATATCTCGACATTTTACGGCGTTTGTTCAAA
Found at i:2528682 original size:86 final size:87
Alignment explanation
Indices: 2528584--2528779 Score: 270
Period size: 86 Copynumber: 2.3 Consensus size: 87
2528574 CTTTTACGGT
* * * *
2528584 GTTTGTTAAAAAAACGCCGCTATATATCTCGAGATTTTGCGGCGTTTGTTCCAAAAACGCCACTA
1 GTTTGTTCAAAAAACGCCGCTATATATCTCGACATTTTACGGCATTTGTTCCAAAAACGCCACTA
* *
2528649 TAGTTCTTGACCTATGGCGGC-
66 TAGATCTTGACATATGGCGGCA
* * *
2528670 GTTTGTTCAAAAAACGCCGCTATATATCTCGACATTTTATGGCATTTGTTCCAAAAATGCCGCTA
1 GTTTGTTCAAAAAACGCCGCTATATATCTCGACATTTTACGGCATTTGTTCCAAAAACGCCACTA
2528735 TAGATCTTGACATATGGCGGCA
66 TAGATCTTGACATATGGCGGCA
*
2528757 TTTTTGGTTC-AAAAACGCCGCTA
1 -GTTT-GTTCAAAAAACGCCGCTA
2528780 ACTTTAGCGA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
86 77 0.79
88 16 0.16
89 4 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (87 bp):
GTTTGTTCAAAAAACGCCGCTATATATCTCGACATTTTACGGCATTTGTTCCAAAAACGCCACTA
TAGATCTTGACATATGGCGGCA
Found at i:2528757 original size:43 final size:43
Alignment explanation
Indices: 2528593--2528779 Score: 178
Period size: 43 Copynumber: 4.3 Consensus size: 43
2528583 TGTTTGTTAA
* * * * *
2528593 AAAAACGCCGCTATATATCTCGAGATTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACATATGGCGGCATTTGTTCC
* * * * * *
2528636 AAAAACGCCACTATAGTTCTTGACCTATGGCGGCGTTTGTTCA
1 AAAAACGCCGCTATAGATCTCGACATATGGCGGCATTTGTTCC
* * ***
2528679 AAAAACGCCGCTATATATCTCGACATTTTATGGCATTTGTTCC
1 AAAAACGCCGCTATAGATCTCGACATATGGCGGCATTTGTTCC
* *
2528722 AAAAATGCCGCTATAGATCTTGACATATGGCGGCATTTTTGGTT-C
1 AAAAACGCCGCTATAGATCTCGACATATGGCGGCA--TTT-GTTCC
2528767 AAAAACGCCGCTA
1 AAAAACGCCGCTA
2528780 ACTTTAGCGA
Statistics
Matches: 113, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
43 94 0.83
45 16 0.14
46 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
AAAAACGCCGCTATAGATCTCGACATATGGCGGCATTTGTTCC
Found at i:2531028 original size:20 final size:21
Alignment explanation
Indices: 2531005--2531060 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
2530995 CTGGTCCTTC
*
2531005 GGTATGGAGACCAACTC-TTT
1 GGTATGGAGACCAACTCATGT
* *
2531025 GGTATAGAGACC-AGTCATGT
1 GGTATGGAGACCAACTCATGT
2531045 GGTATGGAGACCAACT
1 GGTATGGAGACCAACT
2531061 GGTCTCGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (21 bp):
GGTATGGAGACCAACTCATGT
Found at i:2538257 original size:23 final size:24
Alignment explanation
Indices: 2538225--2538274 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2538215 AAAACATGCC
2538225 AAAAGACAAAAGAAAACATGTCAT
1 AAAAGACAAAAGAAAACATGTCAT
* **
2538249 AAAAG-CAAATGAAAATGTGTCAT
1 AAAAGACAAAAGAAAACATGTCAT
2538272 AAA
1 AAA
2538275 CCTATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (24 bp):
AAAAGACAAAAGAAAACATGTCAT
Found at i:2553893 original size:2 final size:2
Alignment explanation
Indices: 2553886--2553911 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2553876 AACGATAAAC
2553886 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2553912 GCACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2559681 original size:2 final size:2
Alignment explanation
Indices: 2559674--2559733 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
2559664 TTCAATATCA
2559674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2559716 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
2559734 CCTGATAACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2566064 original size:22 final size:21
Alignment explanation
Indices: 2566036--2566097 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
2566026 TCGAGGGTTG
*
2566036 CATAGGTCCTTCAGGACATATA
1 CATAGGTCCTTCGGGACA-ATA
*
2566058 CATAGGTCATTCGGGAC-ATA
1 CATAGGTCCTTCGGGACAATA
2566078 CATGAGGTCCTTCGGGACAA
1 CAT-AGGTCCTTCGGGACAA
2566098 ATTTCACATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.17
21 13 0.37
22 16 0.46
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (21 bp):
CATAGGTCCTTCGGGACAATA
Found at i:2568250 original size:29 final size:30
Alignment explanation
Indices: 2568218--2568280 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
2568208 GACATATTAA
2568218 ATTTAATAAGTTAAGA-AAAAATAAAATAT
1 ATTTAATAAGTTAAGACAAAAATAAAATAT
2568247 ATTTAATAAGTTAAGACAAAAATAAAATAT
1 ATTTAATAAGTTAAGACAAAAATAAAATAT
2568277 ATTT
1 ATTT
2568281 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (30 bp):
ATTTAATAAGTTAAGACAAAAATAAAATAT
Found at i:2580671 original size:17 final size:17
Alignment explanation
Indices: 2580644--2580710 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
2580634 AGAGTTATTC
*
2580644 TAATAAATGAACTAGTT
1 TAATGAATGAACTAGTT
*
2580661 TGATGAATGAACTAGTT
1 TAATGAATGAACTAGTT
* *
2580678 TAATTAATGAACTAACTT
1 TAATGAATGAACT-AGTT
* *
2580696 TATTCAATGAACTAG
1 TAATGAATGAACTAG
2580711 ATGCATGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 27 0.66
18 14 0.34
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
TAATGAATGAACTAGTT
Found at i:2583990 original size:21 final size:17
Alignment explanation
Indices: 2583945--2583987 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
2583935 TATTCTAATA
2583945 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
2583962 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
2583979 AATGAACTA
1 AATGAACTA
2583988 ACTTTATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (17 bp):
AATGAACTAGTTTGATG
Found at i:2585367 original size:14 final size:13
Alignment explanation
Indices: 2585334--2585376 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
2585324 TATGGGCGTG
*
2585334 AATGGTGATGGAG
1 AATGGTGATGGAA
2585347 AATGGTGATGGAA
1 AATGGTGATGGAA
*
2585360 AGATGGTGATAGAA
1 A-ATGGTGATGGAA
2585374 AAT
1 AAT
2585377 AATATCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.37, T:0.23
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:2589907 original size:2 final size:2
Alignment explanation
Indices: 2589900--2589925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2589890 TTCATTACCA
2589900 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2589926 GATTTTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2590477 original size:25 final size:25
Alignment explanation
Indices: 2590449--2590501 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2590439 AATGTGCGAC
2590449 TATAATTATAAACTTAACACATAAT
1 TATAATTATAAACTTAACACATAAT
2590474 TATAATTATAAACTTAACACATAAT
1 TATAATTATAAACTTAACACATAAT
2590499 TAT
1 TAT
2590502 GATATTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (25 bp):
TATAATTATAAACTTAACACATAAT
Found at i:2598590 original size:23 final size:23
Alignment explanation
Indices: 2598526--2598632 Score: 132
Period size: 22 Copynumber: 4.8 Consensus size: 23
2598516 CAAAAATACA
* *
2598526 AATGGGTACCGATACCCC-TATG
1 AATGGGTATCAATACCCCTTATG
*
2598548 AAT-GGTATCAAT-CCCCTTATC
1 AATGGGTATCAATACCCCTTATG
2598569 AATGGGTATCAATACCCCTTATG
1 AATGGGTATCAATACCCCTTATG
*
2598592 AATCGGTATCAATA-CCCTTATG
1 AATGGGTATCAATACCCCTTATG
* *
2598614 AATGGGTACCGATACCCCT
1 AATGGGTATCAATACCCCT
2598633 ATGGGTATCA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
20 4 0.05
21 13 0.18
22 31 0.42
23 25 0.34
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (23 bp):
AATGGGTATCAATACCCCTTATG
Found at i:2598612 original size:45 final size:44
Alignment explanation
Indices: 2598526--2598649 Score: 168
Period size: 45 Copynumber: 2.9 Consensus size: 44
2598516 CAAAAATACA
*
2598526 AATGGGTACCGATACCCC-TATGAATGGTATCAATCCCCTTATC
1 AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCTTATC
* * *
2598569 AATGGGTATCAATACCCCTTATGAATCGGTATCAATACCCTTATG
1 AATGGGTACCGATACCCCTTATGAAT-GGTATCAATACCCTTATC
2598614 AATGGGTACCGATACCCC-TATG---GGTATCAATACCCT
1 AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCT
2598650 AGGTACTGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
40 14 0.19
43 16 0.22
44 11 0.15
45 32 0.44
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (44 bp):
AATGGGTACCGATACCCCTTATGAATGGTATCAATACCCTTATC
Found at i:2598638 original size:18 final size:18
Alignment explanation
Indices: 2598615--2598668 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
2598605 ACCCTTATGA
2598615 ATGGGTACCGATACCCCT
1 ATGGGTACCGATACCCCT
* *
2598633 ATGGGTATCAATA-CCCT
1 ATGGGTACCGATACCCCT
* *
2598650 A--GGTACTGATACCACT
1 ATGGGTACCGATACCCCT
2598666 ATG
1 ATG
2598669 ATTGGGTATC
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 5 0.19
18 11 0.41
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (18 bp):
ATGGGTACCGATACCCCT
Found at i:2599858 original size:23 final size:22
Alignment explanation
Indices: 2599820--2599862 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2599810 CAATTCATTT
2599820 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
2599842 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
2599863 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:2606394 original size:22 final size:22
Alignment explanation
Indices: 2606369--2606410 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2606359 CAATTCATTT
2606369 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
2606391 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
2606411 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:2607733 original size:11 final size:11
Alignment explanation
Indices: 2607714--2607759 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
2607704 TTTGGTGCTG
2607714 AAAACAAGATA
1 AAAACAAGATA
*
2607725 AAAATAAGA-A
1 AAAACAAGATA
2607735 TAAAACAAGATA
1 -AAAACAAGATA
2607747 AAGAA-AAGATA
1 AA-AACAAGATA
2607758 AA
1 AA
2607760 TGAATTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 26 0.87
12 3 0.10
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (11 bp):
AAAACAAGATA
Found at i:2607755 original size:22 final size:21
Alignment explanation
Indices: 2607714--2607759 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
2607704 TTTGGTGCTG
2607714 AAAACAAGATAAAAATAAGAAT
1 AAAACAAGATAAAAATAAG-AT
2607736 AAAACAAGATAAAGAA-AAGAT
1 AAAACAAGATAAA-AATAAGAT
2607757 AAA
1 AAA
2607760 TGAATTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 16 0.70
23 2 0.09
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (21 bp):
AAAACAAGATAAAAATAAGAT
Found at i:2621341 original size:14 final size:15
Alignment explanation
Indices: 2621301--2621342 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
2621291 ACCTTAATGA
2621301 TTATT-AAAAATTTG
1 TTATTAAAAAATTTG
*
2621315 TTACTAAATAAATTT-
1 TTATTAAA-AAATTTG
2621330 TTATTAAAAAATT
1 TTATTAAAAAATT
2621343 CAAAGAGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 9 0.38
16 6 0.25
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TTATTAAAAAATTTG
Found at i:2624325 original size:32 final size:32
Alignment explanation
Indices: 2624253--2624328 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
2624243 CAATAGCTTC
* *
2624253 ATCAAAATATTATAAATTATTAATTACAATCT
1 ATCAAATTATTATAAATTAATAATTACAATCT
** * *
2624285 ATTGAATTATTATAGAA-TAATAATTACATTTT
1 ATCAAATTATTATA-AATTAATAATTACAATCT
2624317 ATCAAATTATTA
1 ATCAAATTATTA
2624329 CAAAATTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (32 bp):
ATCAAATTATTATAAATTAATAATTACAATCT
Found at i:2624418 original size:15 final size:14
Alignment explanation
Indices: 2624382--2624420 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
2624372 ACCATAATGA
2624382 TTATTAAAAATTTG
1 TTATTAAAAATTTG
* *
2624396 TTACTAAATAATTTT
1 TTATTAAA-AATTTG
2624411 TTATTAAAAA
1 TTATTAAAAA
2624421 ATTCAATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATTAAAAATTTG
Found at i:2626333 original size:22 final size:22
Alignment explanation
Indices: 2626301--2626386 Score: 118
Period size: 23 Copynumber: 3.8 Consensus size: 22
2626291 AAGGCAAATA
*
2626301 GGTATCGATACCCCTATGAATG
1 GGTATCAATACCCCTATGAATG
*
2626323 GGTATCAATACCCCTTATAAATG
1 GGTATCAATACCCC-TATGAATG
*
2626346 GGTATCAATACCACTTATGAATG
1 GGTATCAATACC-CCTATGAATG
*
2626369 GGTACCAATACCCCTATG
1 GGTATCAATACCCCTATG
2626387 GGTATCAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.32
23 37 0.66
24 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (22 bp):
GGTATCAATACCCCTATGAATG
Found at i:2626371 original size:46 final size:45
Alignment explanation
Indices: 2626296--2626383 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
2626286 GCAAAAAGGC
* *
2626296 AAATAGGTATCGATACCCCTATGAATGGGTATCAATACCCCTTAT
1 AAATAGGTATCAATACCCCTATGAATGGGTACCAATACCCCTTAT
* *
2626341 AAATGGGTATCAATACCACTTATGAATGGGTACCAATACCCCT
1 AAATAGGTATCAATACC-CCTATGAATGGGTACCAATACCCCT
2626384 ATGGGTATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 15 0.39
46 23 0.61
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (45 bp):
AAATAGGTATCAATACCCCTATGAATGGGTACCAATACCCCTTAT
Found at i:2626510 original size:33 final size:34
Alignment explanation
Indices: 2626468--2626533 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
2626458 ATGCAAAAAG
*
2626468 GGTATCGATACCCCT-ATGGGAATCAATACCCTT
1 GGTACCGATACCCCTAATGGGAATCAATACCCTT
*
2626501 GGTACCGATACCCCTACATGGGTATCAATACCC
1 GGTACCGATACCCCTA-ATGGGAATCAATACCC
2626534 CCTGGCTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.48
35 15 0.52
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (34 bp):
GGTACCGATACCCCTAATGGGAATCAATACCCTT
Found at i:2626961 original size:34 final size:34
Alignment explanation
Indices: 2626904--2626968 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2626894 TGTAAAACGA
* *
2626904 AAGGTTCTAGTTGAGCCCTTGAAAAGCTAGGAAT
1 AAGGTTCTAGTTGAGACCTTGAAAAACTAGGAAT
*
2626938 AAGGTTCTAGTTTA-ACCTGTGAAAAACTAGG
1 AAGGTTCTAGTTGAGACCT-TGAAAAACTAGG
2626969 GAGTTGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 3 0.11
34 24 0.89
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (34 bp):
AAGGTTCTAGTTGAGACCTTGAAAAACTAGGAAT
Found at i:2629054 original size:18 final size:18
Alignment explanation
Indices: 2629031--2629088 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
2629021 CAACAATTGG
*
2629031 TAACAATGGGTATCTTTT
1 TAACAATTGGTATCTTTT
2629049 TAACAATTGGTATCCTTTT
1 TAACAATTGGTAT-CTTTT
2629068 GTAAACAATTGGTATCTTTT
1 -T-AACAATTGGTATCTTTT
2629088 T
1 T
2629089 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 6 0.17
21 12 0.33
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:2629323 original size:22 final size:23
Alignment explanation
Indices: 2629298--2629387 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
2629288 CAAAAATGCA
* *
2629298 AATGAGTACCGATACCCC-TATG
1 AATGGGTACCAATACCCCTTATG
*
2629320 AAT-GGTATCAATACCCCTTATG
1 AATGGGTACCAATACCCCTTATG
*
2629342 AATGGGTATCAATACCCCTTATG
1 AATGGGTACCAATACCCCTTATG
*
2629365 AATGGGTACCGATA-CCCTTATG
1 AATGGGTACCAATACCCCTTATG
2629387 A
1 A
2629388 GTATCAATAC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
21 11 0.18
22 19 0.31
23 31 0.51
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (23 bp):
AATGGGTACCAATACCCCTTATG
Found at i:2629353 original size:23 final size:23
Alignment explanation
Indices: 2629309--2629387 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
2629299 ATGAGTACCG
2629309 ATACCCC-TATGAAT-GGTATCA
1 ATACCCCTTATGAATGGGTATCA
2629330 ATACCCCTTATGAATGGGTATCA
1 ATACCCCTTATGAATGGGTATCA
* *
2629353 ATACCCCTTATGAATGGGTACCG
1 ATACCCCTTATGAATGGGTATCA
2629376 ATA-CCCTTATGA
1 ATACCCCTTATGA
2629388 GTATCAATAC
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
21 7 0.13
22 16 0.30
23 31 0.57
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (23 bp):
ATACCCCTTATGAATGGGTATCA
Found at i:2631207 original size:3 final size:3
Alignment explanation
Indices: 2631199--2631234 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2631189 TTAACTTTTG
*
2631199 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA -AA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2631235 TAGCGAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2634328 original size:29 final size:29
Alignment explanation
Indices: 2634295--2634377 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
2634285 GGGCTTAGAG
2634295 TTTAGAGTTTATGGTTTATGGTTTA-AGAT
1 TTTAGAGTTTATGGTTTATGGTTTATAG-T
* *
2634324 TTTAGATTTTAGGGTTTATGGTTTATAGT
1 TTTAGAGTTTATGGTTTATGGTTTATAGT
* * *
2634353 TTAAG-GTTTAT-GTCTAGGGTTTATA
1 TTTAGAGTTTATGGTTTATGGTTTATA
2634378 TTGTAATCAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 12 0.26
28 4 0.09
29 28 0.61
30 2 0.04
ACGTcount: A:0.23, C:0.01, G:0.24, T:0.52
Consensus pattern (29 bp):
TTTAGAGTTTATGGTTTATGGTTTATAGT
Found at i:2634341 original size:36 final size:36
Alignment explanation
Indices: 2634289--2634357 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2634279 GATTTAGGGC
*
2634289 TTAGAGTTTAGAGTTTATGGTTTATGGTTTAAGATT
1 TTAGAGTTTAGAGTTTATGGTTTATAGTTTAAGATT
* *
2634325 TTAGATTTTAGGGTTTATGGTTTATAGTTTAAG
1 TTAGAGTTTAGAGTTTATGGTTTATAGTTTAAG
2634358 GTTTATGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (36 bp):
TTAGAGTTTAGAGTTTATGGTTTATAGTTTAAGATT
Found at i:2645917 original size:20 final size:19
Alignment explanation
Indices: 2645893--2645939 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2645883 CGATATACCA
2645893 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
2645913 TGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
2645933 GGTAAAA
1 GGTAAAA
2645940 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2646009 original size:159 final size:158
Alignment explanation
Indices: 2645705--2646014 Score: 428
Period size: 159 Copynumber: 1.9 Consensus size: 158
2645695 ATCCAAATTA
* * ***
2645705 AAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATAAAAC
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTACAAAAATAAAAC
* *
2645770 CGGTAAAGCGCTACCGGATACATTTAAAGTGTCGTACTTTAATATAAGGATCGACACTTCGTGAA
66 CGGTAAAACGCTACCGGATACATTGAAAGTGTCGTACTTT-ATATAAGGATCGACACTTCGTGAA
2645835 TTTAAAAGAGAAGCAGTTTTAAATCCTAT
130 TTTAAAAGAGAAGCAGTTTTAAATCCTAT
* * *
2645864 AAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCTGTAACAAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGT-ACAAAA--ATAA
* * * *
2645929 AACCGGTAAAACGTTACCGGATATATTGGAAGTGTCGATACTTT-TATAAGGATCGACACTTTGT
63 AACCGGTAAAACGCTACCGGATACATTGAAAGTGTCG-TACTTTATATAAGGATCGACACTTCGT
2645993 GAATTT-AAAGAG-AGCAGTTTTA
127 GAATTTAAAAGAGAAGCAGTTTTA
2646015 GCGCCTATAA
Statistics
Matches: 133, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
159 57 0.43
160 9 0.07
161 25 0.19
162 36 0.27
163 6 0.05
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (158 bp):
AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTACAAAAATAAAAC
CGGTAAAACGCTACCGGATACATTGAAAGTGTCGTACTTTATATAAGGATCGACACTTCGTGAAT
TTAAAAGAGAAGCAGTTTTAAATCCTAT
Found at i:2646117 original size:17 final size:19
Alignment explanation
Indices: 2646078--2646120 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2646068 CAGGTAAAAT
2646078 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
2646098 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
2646115 ATGATA
1 ATGATA
2646121 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:2648355 original size:21 final size:21
Alignment explanation
Indices: 2648329--2648393 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2648319 AAGACAATCA
*
2648329 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
2648350 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2648371 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2648392 AG
1 AG
2648394 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2648469 original size:33 final size:33
Alignment explanation
Indices: 2648427--2648492 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2648417 AAATAGATGG
*
2648427 AGTGGTGAAAGAA-TTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTT-GAGGTGTTAAGGGGTGA
*
2648460 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
2648493 TATTACGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
Found at i:2649104 original size:6 final size:6
Alignment explanation
Indices: 2649093--2649204 Score: 89
Period size: 6 Copynumber: 18.7 Consensus size: 6
2649083 CAAGCGATCA
* * * * *
2649093 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * ** * * * *
2649141 ATGACG ATGAAG CTGGCG ATGAAG ATGACG ATGAAG ATGATG ACGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
2649189 ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGA
2649205 TGATCCAAAC
Statistics
Matches: 85, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:2649208 original size:12 final size:12
Alignment explanation
Indices: 2649093--2649204 Score: 134
Period size: 12 Copynumber: 9.3 Consensus size: 12
2649083 CAAGCGATCA
*
2649093 ATGAAGATGAAG
1 ATGACGATGAAG
*
2649105 CTGACGATGAAG
1 ATGACGATGAAG
2649117 ATGACGATGAAG
1 ATGACGATGAAG
*
2649129 ATGACGATGATG
1 ATGACGATGAAG
2649141 ATGACGATGAAG
1 ATGACGATGAAG
* *
2649153 CTGGCGATGAAG
1 ATGACGATGAAG
2649165 ATGACGATGAAG
1 ATGACGATGAAG
* * *
2649177 ATGATGACGATG
1 ATGACGATGAAG
* *
2649189 ATGATGATGATG
1 ATGACGATGAAG
2649201 ATGA
1 ATGA
2649205 TGATCCAAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 87 1.00
ACGTcount: A:0.38, C:0.08, G:0.34, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2650722 original size:183 final size:183
Alignment explanation
Indices: 2650412--2651168 Score: 1351
Period size: 183 Copynumber: 4.2 Consensus size: 183
2650402 CAAAGTTTTC
* *
2650412 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
2650477 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
2650542 AACCGGTATAAATATACCGTTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
2650595 ATACTTTTTAATATTGTGTCAGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
2650660 CAAAAAGTGTCGACATTTACACATCAGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
2650725 AACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
2650778 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
2650843 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATATAATAGACAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
2650908 AACCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * * *
2650961 ACACTTTTTAATATTGTGTCGGCACTTTATGTCCAGATTAGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
2651026 CAAAAAGTGTCGACATTTACACATCGGAACCC--AATTATAATGTAATAGATAA-TTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
2651088 AACCGGTATAAATATACCGG-TTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
2651140 ACACTTTTTAATATTGTGTCGGTACTTTA
1 ACACTTTTTAATATTGTGTCGGTACTTTA
2651169 CAATAGGAGT
Statistics
Matches: 553, Mismatches: 21, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
179 60 0.11
180 29 0.05
181 18 0.03
183 446 0.81
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:2653577 original size:25 final size:25
Alignment explanation
Indices: 2653549--2653613 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
2653539 TTATCATTAA
*
2653549 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAAATACAT
2653574 ATTTAGGTATGTACAATAAATACAT
1 ATTTAGGTATGTACAATAAATACAT
2653599 ATTTAGGTATGTACA
1 ATTTAGGTATGTACA
2653614 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAAATACAT
Found at i:2653976 original size:23 final size:23
Alignment explanation
Indices: 2653945--2654017 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2653935 ATAGGTAAAA
* *
2653945 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
2653968 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
2653991 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
2654014 ATAT
1 ATAT
2654018 TGTAAAGTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:2654398 original size:23 final size:23
Alignment explanation
Indices: 2654367--2654439 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2654357 ATAGGTAAAA
* *
2654367 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
2654390 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
2654413 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
2654436 ATAT
1 ATAT
2654440 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2661863 original size:85 final size:85
Alignment explanation
Indices: 2661781--2661946 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
2661771 AAGATAATTC
**
2661781 CTAAAATAATATCTTAAATACTAATTAAAACACTTAA-AATTATTTAAACTAAAATACCTAAAAC
1 CTAAAATAATATCCAAAATACTAATTAAAACAC-TAACAATTATTTAAACTAAAATACCTAAAAC
*
2661845 AAAGATAGAATAAAATAATAT
65 AAAGATAAAATAAAATAATAT
* * * * *
2661866 TTAAAATATTATCCAAAATCCTAATTAAAATACTAACATTTATTTAAACTAAAATACCTAAAACA
1 CTAAAATAATATCCAAAATACTAATTAAAACACTAACAATTATTTAAACTAAAATACCTAAAACA
*
2661931 AAGATAAAATATAATA
66 AAGATAAAATAAAATA
2661947 TTTAAAACAT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 3 0.04
85 68 0.96
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (85 bp):
CTAAAATAATATCCAAAATACTAATTAAAACACTAACAATTATTTAAACTAAAATACCTAAAACA
AAGATAAAATAAAATAATAT
Found at i:2668057 original size:16 final size:17
Alignment explanation
Indices: 2668019--2668059 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
2668009 TACGGGGTGA
2668019 ATTTTTCACCGCTAATT
1 ATTTTTCACCGCTAATT
2668036 ATTTTTCACCGCTAATT
1 ATTTTTCACCGCTAATT
2668053 ATTTTTC
1 ATTTTTC
2668060 TCACACTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTTTCACCGCTAATT
Found at i:2670086 original size:15 final size:15
Alignment explanation
Indices: 2670068--2670097 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2670058 TTTATTTTAC
2670068 TTATATTATTATATA
1 TTATATTATTATATA
*
2670083 TTATTTTATTATATA
1 TTATATTATTATATA
2670098 CATAATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:2671975 original size:29 final size:29
Alignment explanation
Indices: 2671920--2671975 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
2671910 AATCTTTTCG
*
2671920 ACTAACTTGATTCTTGTTGTATTGCTTCT
1 ACTAACTTGATTCTTGTTGTATCGCTTCT
* *
2671949 ACTAACATTGATTTTTTTTGTA-CGCTT
1 ACTAAC-TTGATTCTTGTTGTATCGCTT
2671976 TTATTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (29 bp):
ACTAACTTGATTCTTGTTGTATCGCTTCT
Found at i:2672901 original size:17 final size:19
Alignment explanation
Indices: 2672879--2672917 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2672869 TGCATTTACC
2672879 TTTATAC-CTT-ACTTATT
1 TTTATACGCTTAACTTATT
2672896 TTTATACGTCTTAACTTATT
1 TTTATACG-CTTAACTTATT
2672916 TT
1 TT
2672918 CTTTTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.23, C:0.15, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTATACGCTTAACTTATT
Found at i:2676598 original size:2 final size:2
Alignment explanation
Indices: 2676591--2676631 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2676581 CATTTATCCT
2676591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2676632 CTATTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2676899 original size:23 final size:24
Alignment explanation
Indices: 2676873--2676924 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 24
2676863 CAGAGAAAAT
*
2676873 AAGAAAAGAAGGAAAAAATA-T-AA
1 AAGAAAA-AAGAAAAAAATATTAAA
2676896 AAG-AAAAAGAAAAAAATATTAAA
1 AAGAAAAAAGAAAAAAATATTAAA
2676919 AAGAAA
1 AAGAAA
2676925 TAAAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.44
22 4 0.16
23 8 0.32
24 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (24 bp):
AAGAAAAAAGAAAAAAATATTAAA
Found at i:2676909 original size:20 final size:20
Alignment explanation
Indices: 2676884--2676933 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2676874 AGAAAAGAAG
2676884 GAAAAAATA-TAAAAGAAAAA
1 GAAAAAATATTAAAA-AAAAA
*
2676904 GAAAAAAATATTAAAAAGAAA
1 G-AAAAAATATTAAAAAAAAA
*
2676925 TAAAAAATA
1 GAAAAAATA
2676934 GAGAGAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 12 0.46
22 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (20 bp):
GAAAAAATATTAAAAAAAAA
Found at i:2678736 original size:42 final size:41
Alignment explanation
Indices: 2678670--2678777 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 41
2678660 AAGGGTTTCT
*
2678670 TGATGAGTAAGTCCTTTGGGCCATC-AGGAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCTA-GAAGTCTTTCGAGCA
* * *
2678712 TGATGCGTAAGTCATTCGGACCATCTATAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCTAGAAGTCTTTCGAGCA
* *
2678754 AGATGATAAGTCCTTCGGGCCATC
1 TGATGGTAAGTCCTTCGGGCCATC
2678778 CATAAGACCT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 16 0.29
42 39 0.70
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (41 bp):
TGATGGTAAGTCCTTCGGGCCATCTAGAAGTCTTTCGAGCA
Found at i:2679238 original size:42 final size:42
Alignment explanation
Indices: 2679192--2679305 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 42
2679182 AAGGGTTTCT
2679192 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCTA-TAAGTCTTTCGAGCA
* * *
2679234 TGATGCGTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
* *
2679276 AGATGA-TAAG-CCTTTCGGGCCATCCATAAG
1 TGATGAGTAAGTCC-TTCGGGCCATCTATAAG
2679306 ACCTTCGGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
40 2 0.03
41 18 0.29
42 41 0.66
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
Found at i:2679247 original size:247 final size:247
Alignment explanation
Indices: 2678806--2679280 Score: 656
Period size: 247 Copynumber: 1.9 Consensus size: 247
2678796 GATGTCTTCA
* ** *
2678806 AATGAGTTTTTAGAAACTAAGCCTAATTTTTATAGGTTTCTTGATGATTATCTCCAAAAAGTTTT
1 AATGAGTTTTTAGAAACTAAGCCTAATTTTTAGAGGTTTCTCAATGACTATCTCCAAAAAGTTTT
*
2678871 TAAAAGGAATCTAATCCTAATTTTTATGGGTTCCTTGAAAACTAAAAAACTGAGCTTGATTTTCA
66 TAAAAGGAAACTAATCCTAATTTTTATGGGTTCCTTGAAAACTAAAAAACTGAGCTTGATTTTCA
* * * *
2678936 AGAGTTTCTTGATGAGTAAGTACTTTGGGCCATCAGTAAGTCTTTTGAGCGTGATGCTTAAATCC
131 AGAGTTTCTTGATGAGTAAGTACTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCC
* *
2679001 TTCGAGTCATCTATGACTCTTTCGAGTAAGATGTTTGGGCATGATGTTTGCG
196 TTCGAGTCATCTATAACTCTTTCGAGCAAGATGTTTGGGCATGATGTTTGCG
* * * **
2679053 AATGAGTTTTTAGAAACTAAGTCTGATTTTTAGGGGTTTCTCAATGACTATCTGTAAAGAA-TTT
1 AATGAGTTTTTAGAAACTAAGCCTAATTTTTAGAGGTTTCTCAATGACTATCTCCAAA-AAGTTT
* *
2679117 TT-AAAGGAAACTAAGT-CT-A-TTTTA-GGTGTTTCTTGATGACAACTAAGAAACTGAGCTTGA
65 TTAAAAGGAAACTAA-TCCTAATTTTTATGG-GTTCCTTGA--A-AACTAAAAAACTGAGCTTGA
* *
2679177 TTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGT
125 TTTTCAAGAGTTTCTTGATGAGTAAGTACTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGT
* *
2679242 AAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG
190 AAATCCTTCGAGTCATCTATAACTCTTTCGAGCAAGATG
2679281 ATAAGCCTTT
Statistics
Matches: 200, Mismatches: 22, Indels: 12
0.85 0.09 0.05
Matches are distributed among these distances:
243 2 0.01
244 13 0.06
245 1 0.00
246 14 0.07
247 168 0.84
248 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (247 bp):
AATGAGTTTTTAGAAACTAAGCCTAATTTTTAGAGGTTTCTCAATGACTATCTCCAAAAAGTTTT
TAAAAGGAAACTAATCCTAATTTTTATGGGTTCCTTGAAAACTAAAAAACTGAGCTTGATTTTCA
AGAGTTTCTTGATGAGTAAGTACTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCC
TTCGAGTCATCTATAACTCTTTCGAGCAAGATGTTTGGGCATGATGTTTGCG
Found at i:2681355 original size:261 final size:263
Alignment explanation
Indices: 2680891--2681414 Score: 998
Period size: 261 Copynumber: 2.0 Consensus size: 263
2680881 GTTTTGTGTT
2680891 ATTTTAATTTAGTCCTCTATTGTATGTATTATTATTGTTTTGTTTTTTTGTTCGAAATGGGGTAC
1 ATTTTAATTTAGTCCTCTATTGTATGTATTATTATTGTTTTGTTTTTTTGTTCGAAATGGGGTAC
*
2680956 TGATGTTTATGCAATTCCATTTTAGTCCTATATTTATGGTTTTATTACGATTCTATTGCTCTTGT
66 TGATGTTTATGCAATTCCATTTTAGTCCTATATTTATGGTTTTATTACGATTCTAGTGCTCTTGT
2681021 TATGTGATTTTCTTGTTTCATGCCATGATATTTGTTTTTATTAATGTTTATAATCCTTAAATTAT
131 TATGTGATTTTCTTGTTTCATGCCATGATATTTGTTTTTATTAATGTTTATAATCCTTAAATTAT
2681086 TTTTCACTCATTTTTTTCACTAAGATATTAACGAATGCATATGAATA-TG-TTATTTATACCATT
196 TTTTCACTCATTTTTTTCACTAAGATATTAACGAATGCATATGAATATTGTTTATTTATACCATT
2681149 AAA
261 AAA
2681152 ATTTTAATTTAGTCCTCTATTGTATGTATTATTATTGTTTTGTTTTTTTGTTCGAAATGGGGTAC
1 ATTTTAATTTAGTCCTCTATTGTATGTATTATTATTGTTTTGTTTTTTTGTTCGAAATGGGGTAC
2681217 TGATGTTTATGCAATTCCATTTTAGTCCTATATTTATGGTTTTATTACGATTCTAGTGCTCTTGT
66 TGATGTTTATGCAATTCCATTTTAGTCCTATATTTATGGTTTTATTACGATTCTAGTGCTCTTGT
2681282 TATGTGATTTTCTTGTTTCATGCCATGATATTTGTTTTTATTAATGTTTATAATCCTTAAATTAT
131 TATGTGATTTTCTTGTTTCATGCCATGATATTTGTTTTTATTAATGTTTATAATCCTTAAATTAT
* * *
2681347 TTTTCACTCATTTTTTTCACTAAGATATTAATGAATGCATATGTATATTGTTTATTTGTACCATT
196 TTTTCACTCATTTTTTTCACTAAGATATTAACGAATGCATATGAATATTGTTTATTTATACCATT
2681412 AAA
261 AAA
2681415 GTATGTTTTA
Statistics
Matches: 257, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
261 239 0.93
262 2 0.01
263 16 0.06
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (263 bp):
ATTTTAATTTAGTCCTCTATTGTATGTATTATTATTGTTTTGTTTTTTTGTTCGAAATGGGGTAC
TGATGTTTATGCAATTCCATTTTAGTCCTATATTTATGGTTTTATTACGATTCTAGTGCTCTTGT
TATGTGATTTTCTTGTTTCATGCCATGATATTTGTTTTTATTAATGTTTATAATCCTTAAATTAT
TTTTCACTCATTTTTTTCACTAAGATATTAACGAATGCATATGAATATTGTTTATTTATACCATT
AAA
Found at i:2681464 original size:15 final size:15
Alignment explanation
Indices: 2681446--2681475 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2681436 TTTATTTTAC
2681446 TTATATTATTATATA
1 TTATATTATTATATA
*
2681461 TTATTTTATTATATA
1 TTATATTATTATATA
2681476 CATAATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATATTATTATATA
Found at i:2687086 original size:28 final size:28
Alignment explanation
Indices: 2687052--2687106 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
2687042 CTTAAGAAAA
2687052 AACTTTGCAAGGTAAAAGAAATTCGAAC
1 AACTTTGCAAGGTAAAAGAAATTCGAAC
2687080 AACTTTGCAAGGTAAAAGAAATTCGAA
1 AACTTTGCAAGGTAAAAGAAATTCGAA
2687107 TATTCTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (28 bp):
AACTTTGCAAGGTAAAAGAAATTCGAAC
Found at i:2689220 original size:2 final size:2
Alignment explanation
Indices: 2689213--2689293 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
2689203 TTTTTAAAAC
2689213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2689255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2689294 CCCCTATCCG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2689428 original size:35 final size:35
Alignment explanation
Indices: 2689355--2689429 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2689345 CGTCACGTCC
* **
2689355 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
*
2689390 AGTAAGGCCCTGAGCACACAACCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
2689425 AGTAA
1 AGTAA
2689430 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
Found at i:2689532 original size:24 final size:24
Alignment explanation
Indices: 2689505--2689595 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
2689495 CATAATTCAA
*
2689505 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
2689529 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
2689553 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
2689576 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
2689596 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:2689575 original size:47 final size:48
Alignment explanation
Indices: 2689505--2689595 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
2689495 CATAATTCAA
* * *
2689505 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
2689553 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
2689596 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:2692105 original size:15 final size:16
Alignment explanation
Indices: 2692075--2692108 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
2692065 AGTCAACAGT
2692075 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
2692092 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
2692107 GG
1 GG
2692109 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:2692116 original size:13 final size:13
Alignment explanation
Indices: 2692098--2692173 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
2692088 CAACGGTCAA
2692098 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
2692111 CGGGTCAACGTGT
1 CGGGTCAACGGGT
*
2692124 TGGGTCAACAGGTCGGGT
1 CGGGTC-A-A---CGGGT
2692142 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
2692155 CAGGTAAACGGGT
1 CGGGTCAACGGGT
2692168 CGGGTC
1 CGGGTC
2692174 GGGTTATGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
13 37 0.74
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 9 0.18
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2692144 original size:31 final size:31
Alignment explanation
Indices: 2692106--2692177 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
2692096 AACGGGTCAA
* ** *
2692106 CGGGTCGGGTCAACGTGTTGGGTCAACAGGT
1 CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
*
2692137 CGGGTCGGGTCAACGGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
2692168 CGGGTCGGGT
1 CGGGTCGGGT
2692178 TATGACCGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.19
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCAGGTAAACAGGT
Found at i:2697886 original size:13 final size:13
Alignment explanation
Indices: 2697870--2697910 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
2697860 CAAATTTTTT
2697870 ATTTATAATTTAA
1 ATTTATAATTTAA
2697883 ATTTATAATTTAA
1 ATTTATAATTTAA
2697896 ATTTATAATTATAA
1 ATTTATAATT-TAA
2697910 A
1 A
2697911 AAATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTATAATTTAA
Found at i:2697886 original size:20 final size:19
Alignment explanation
Indices: 2697870--2697909 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2697860 CAAATTTTTT
2697870 ATTTATAATTTAAATTTATA
1 ATTTA-AATTTAAATTTATA
2697890 ATTTAAATTTATAA-TTATA
1 ATTTAAATTTA-AATTTATA
2697909 A
1 A
2697910 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTAAATTTAAATTTATA
Found at i:2697887 original size:6 final size:7
Alignment explanation
Indices: 2697870--2697909 Score: 59
Period size: 6 Copynumber: 6.1 Consensus size: 7
2697860 CAAATTTTTT
2697870 ATTTATA
1 ATTTATA
2697877 ATTTA-A
1 ATTTATA
2697883 ATTTATA
1 ATTTATA
2697890 ATTTA-A
1 ATTTATA
2697896 ATTTATA
1 ATTTATA
2697903 A-TTATA
1 ATTTATA
2697909 A
1 A
2697910 AAAATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 18 0.58
7 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATTTATA
Found at i:2698166 original size:17 final size:17
Alignment explanation
Indices: 2698144--2698182 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
2698134 AATTATCGAA
2698144 ATATTATATTACTTTAT
1 ATATTATATTACTTTAT
2698161 ATA-T-TATTACTTTAT
1 ATATTATATTACTTTAT
2698176 ATATTAT
1 ATATTAT
2698183 TGAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.70
16 2 0.10
17 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTATATTACTTTAT
Found at i:2698168 original size:15 final size:15
Alignment explanation
Indices: 2698150--2698183 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2698140 CGAAATATTA
2698150 TATTACTTTATATAT
1 TATTACTTTATATAT
2698165 TATTACTTTATATAT
1 TATTACTTTATATAT
2698180 TATT
1 TATT
2698184 GAAAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTACTTTATATAT
Found at i:2708449 original size:28 final size:28
Alignment explanation
Indices: 2708417--2708491 Score: 150
Period size: 28 Copynumber: 2.7 Consensus size: 28
2708407 CTAAGGGCTC
2708417 GTTTAGTACTTTATATATTATTGGAAAT
1 GTTTAGTACTTTATATATTATTGGAAAT
2708445 GTTTAGTACTTTATATATTATTGGAAAT
1 GTTTAGTACTTTATATATTATTGGAAAT
2708473 GTTTAGTACTTTATATATT
1 GTTTAGTACTTTATATATT
2708492 TTATTTAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (28 bp):
GTTTAGTACTTTATATATTATTGGAAAT
Found at i:2721574 original size:65 final size:63
Alignment explanation
Indices: 2721444--2721602 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
2721434 GAATAAATTG
* * *
2721444 AACATCGAATGCATTATATGCATCGATGCACATACCATGCATCGATGCACTCATGTTTTTATGAA
1 AACATCGAATGCATT-TATGCATCGATGCACATACCATGCATCGATGCAATCAGGTTGTTATG-A
* *
2721509 AACATCGAATACATTTGATGCATCGATGCACA-AGCCATGCATCGATGCAATCGGGCTTGTT-TG
1 AACATCGAATGCATTT-ATGCATCGATGCACATA-CCATGCATCGATGCAATCAGG-TTGTTATG
2721572 A
63 A
*
2721573 AACATCGAATGCACTTCATGCATC-ATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
2721603 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 6 0.07
64 22 0.27
65 51 0.61
66 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACATACCATGCATCGATGCAATCAGGTTGTTATGA
Found at i:2730082 original size:2 final size:2
Alignment explanation
Indices: 2730075--2730104 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2730065 TAAATTACAT
2730075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2730105 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2730304 original size:39 final size:38
Alignment explanation
Indices: 2730261--2730379 Score: 111
Period size: 39 Copynumber: 3.1 Consensus size: 38
2730251 TTTAAATAAT
*
2730261 AATTTAGAATATTAATGTGAAATAATTTAAGAAATTAAA
1 AATTTAGAATGTTAATGTGAAATAATTTAA-AAATTAAA
* *
2730300 AATTTAGAATGTT-ATGGTAGTAAAT--TTTAATTAATTAAG
1 AATTTAGAATGTTAAT-GT-G-AAATAATTTAA-AAATTAAA
* *
2730339 AATTTAGAATGTTAAAT-TGAAATAATTCAAAAATTATA
1 AATTTAGAATGTT-AATGTGAAATAATTTAAAAATTAAA
2730377 AAT
1 AAT
2730380 AAAAATTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
37 4 0.06
38 11 0.17
39 43 0.66
40 1 0.02
41 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.39
Consensus pattern (38 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAAAATTAAA
Found at i:2730415 original size:23 final size:24
Alignment explanation
Indices: 2730379--2730423 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2730369 AAATTATAAA
*
2730379 TAAAAATTTAATATAAAATAAAAT
1 TAAAAATATAATATAAAATAAAAT
*
2730403 TAAAAATAT-ATATATAATAAA
1 TAAAAATATAATATAAAATAAA
2730424 TTGGGTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAAAATATAATATAAAATAAAAT
Found at i:2730989 original size:16 final size:17
Alignment explanation
Indices: 2730968--2731007 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2730958 TAAAAATATT
*
2730968 TTTAAATTA-TTTATAA
1 TTTAAAATATTTTATAA
*
2730984 TTTAAAATATTTTATAT
1 TTTAAAATATTTTATAA
2731001 TTTAAAA
1 TTTAAAA
2731008 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATATTTTATAA
Found at i:2736622 original size:97 final size:96
Alignment explanation
Indices: 2736506--2736706 Score: 357
Period size: 97 Copynumber: 2.1 Consensus size: 96
2736496 ATCACTGATT
*
2736506 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATCTAGTTTCCTGTTTTCACTAAAAAAAT
1 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATATAGTTTCCTGTTTTCACT-AAAAAAT
2736571 ATGATTGTTCCTGATTTATGAATCATGGAATC
65 ATGATTGTTCCTGATTTATGAATCATGGAATC
* *
2736603 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGAAAAATA
1 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATATAGTTTCCTGTTTTCACTAAAAAATA
*
2736668 TGATTGTTCCTGATTTATGGATCATGGAATC
66 TGATTGTTCCTGATTTATGAATCATGGAATC
2736699 TACTGGTT
1 TACTGGTT
2736707 ATATCTTGAA
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
96 45 0.45
97 55 0.55
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (96 bp):
TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATATAGTTTCCTGTTTTCACTAAAAAATA
TGATTGTTCCTGATTTATGAATCATGGAATC
Found at i:2736868 original size:32 final size:32
Alignment explanation
Indices: 2736806--2736877 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
2736796 TAAGGTGAAC
* *
2736806 CTTGGGTAGGCTCCGAGACCCCCAGAAACTTT
1 CTTGGGTAAGCTCCGAGACCCCAAGAAACTTT
* *
2736838 CTTGGGTAAGCTCTC-AGGCCCCAAGGAACTTT
1 CTTGGGTAAGCTC-CGAGACCCCAAGAAACTTT
2736870 -TTGGGTAA
1 CTTGGGTAA
2736878 ATCATGGGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.23
32 26 0.74
33 1 0.03
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (32 bp):
CTTGGGTAAGCTCCGAGACCCCAAGAAACTTT
Found at i:2744136 original size:2 final size:2
Alignment explanation
Indices: 2744131--2744179 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2744121 TGTAGAACAA
2744131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2744173 AT AT AT A
1 AT AT AT A
2744180 CCTAATAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2744335 original size:16 final size:16
Alignment explanation
Indices: 2744310--2744342 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2744300 AGATATATAT
*
2744310 ATATATAATAATAATA
1 ATATAAAATAATAATA
2744326 ATATAAAATAATAATA
1 ATATAAAATAATAATA
2744342 A
1 A
2744343 AGACAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAATAATAATA
Found at i:2744428 original size:62 final size:62
Alignment explanation
Indices: 2744302--2744453 Score: 143
Period size: 62 Copynumber: 2.4 Consensus size: 62
2744292 GTTAGGTTAG
* * * *
2744302 ATATATATATATATAATAATAATAATATAAAATAATAATAAAGACAAAAGACTAAAAAAGAA
1 ATATATATATATATAATAATAATAAAAGAAAATAATAAGAAAGACAAAAGACTAAAAAAAAA
* *
2744364 ATATA-ATATA-ATAATAATGAATAAAACGAAAATAATAAGAAATATAGAAA-A-TAAAAAGAAA
1 ATATATATATATATAATAAT-AATAAAA-GAAAATAATAAGAAAGACA-AAAGACTAAAAA-AAA
2744425 A
62 A
* *
2744426 ATACACT-TATATATATATAATTATAAAA
1 ATATA-TATATATATA-ATAATAATAAAA
2744454 TATAATACTT
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
60 8 0.11
61 17 0.23
62 28 0.38
63 7 0.09
64 9 0.12
65 5 0.07
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.26
Consensus pattern (62 bp):
ATATATATATATATAATAATAATAAAAGAAAATAATAAGAAAGACAAAAGACTAAAAAAAAA
Found at i:2746129 original size:94 final size:94
Alignment explanation
Indices: 2745968--2746971 Score: 1575
Period size: 94 Copynumber: 10.4 Consensus size: 94
2745958 AAATCCGATT
* *
2745968 ATTGTTCT-GAGTCCAACATCCTCCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCA
1 ATTG-TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCA
2746032 GCGGTCCCTTCGTCGTGAAGTTGAACTTGC
65 GCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
2746062 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAACTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
2746127 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
2746156 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
2746221 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
2746250 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
2746315 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
2746344 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
*
2746409 CGGTCCCTTCGTCGTAAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
2746438 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
2746503 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
* * *
2746532 GTTGTCTGGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGGAAATTGTTAATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
*
2746597 TGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
2746626 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
* *
2746691 CGGTCCCTTCGTCGTGAACTTGAACCTGC
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
2746720 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAATGTTTG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAA-T------TG-TTG
*
2746785 -TTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGC
54 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
2746825 ATTGTCTGGAGTCCAATGTCCTTCGTTGTGAAGTCGAAATTGGCTCTGAAATTGAGAAATGTTTG
1 ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAA-T------TG-TTG
2746890 -TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
54 ATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
2746930 GTTGTCTGGAGTCCAATATCCTTCGTTGAT-TAGTTGAAATTG
1 ATTGTCTGGAGTCCAATATCCTTCGTTG-TGAAGTTGAAATTG
2746972 ACTCTGGGTA
Statistics
Matches: 868, Mismatches: 28, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
93 3 0.00
94 680 0.78
98 4 0.00
99 1 0.00
105 176 0.20
106 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (94 bp):
ATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTGATTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGC
Found at i:2746969 original size:105 final size:105
Alignment explanation
Indices: 2746660--2746977 Score: 505
Period size: 105 Copynumber: 3.0 Consensus size: 105
2746650 GTTGTGAAGT
* * *
2746660 TGAAATTGGGAAAT-TGTTGATTGACAACCAGCGGTCCCTTCGTCGTGAACTTGAACCTGCATTG
1 TGAAATTGAGAAATGT-TTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTG
*
2746724 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTC
64 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
2746766 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
* *
2746831 TGGAGTCCAATGTCCTTCGTTGTGAAGTCGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
2746871 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
* *
2746936 TGGAGTCCAATATCCTTCGTTGAT-TAGTTGAAATTGACTC
66 TGGAGTCCAATATCCTTCGTTG-TGAAGTTGAAATTGGCTC
2746976 TG
1 TG
2746978 GGTAAAACCT
Statistics
Matches: 197, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
105 179 0.91
106 17 0.09
107 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:2747734 original size:21 final size:21
Alignment explanation
Indices: 2747706--2747749 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2747696 ACCCACCTTA
2747706 TTTTCTCTTCTT-TTGTTCTT
1 TTTTCTCTTCTTCTTGTTCTT
* *
2747726 TTTTCCTCTTTTTCTTTTTCTT
1 TTTT-CTCTTCTTCTTGTTCTT
2747748 TT
1 TT
2747750 CTCAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTCTCTTCTTCTTGTTCTT
Found at i:2758338 original size:2 final size:2
Alignment explanation
Indices: 2758333--2758376 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2758323 TGTAGAACAA
2758333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2758374 AT A
1 AT A
2758377 ATAAACCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2758528 original size:18 final size:15
Alignment explanation
Indices: 2758507--2758540 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2758497 TTAGATATAT
*
2758507 ATATATATATATAATA
1 ATATATA-AAATAATA
2758523 ATATATAAAATAATA
1 ATATATAAAATAATA
2758538 ATA
1 ATA
2758541 AAGACAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATAAAATAATA
Found at i:2758530 original size:10 final size:10
Alignment explanation
Indices: 2758501--2758541 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2758491 GTTAGGTTAG
2758501 ATATATATATA
1 ATATATA-ATA
2758512 TATATATAATA
1 -ATATATAATA
2758523 ATATATAA-A
1 ATATATAATA
2758532 ATA-ATAATA
1 ATATATAATA
2758541 A
1 A
2758542 AGACAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.14
9 6 0.21
10 8 0.29
11 3 0.11
12 7 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATAATA
Found at i:2758608 original size:47 final size:47
Alignment explanation
Indices: 2758515--2758613 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
2758505 ATATATATAT
*
2758515 ATATAATAATATATAAAATAATAATAAAGACAAAAGAGTAAAAAGAA
1 ATATAATAATATATAAAATAATAATAAAAACAAAAGAGTAAAAAGAA
* *
2758562 ATATAAT-ATAATATAATAATAATGAATAAAAACGAAA-A-TAATAAGAA
1 ATATAATAAT-ATATAA-AATAAT-AATAAAAACAAAAGAGTAAAAAGAA
2758609 ATATA
1 ATATA
2758614 CAAAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
46 2 0.04
47 26 0.57
48 7 0.15
49 11 0.24
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (47 bp):
ATATAATAATATATAAAATAATAATAAAAACAAAAGAGTAAAAAGAA
Found at i:2758618 original size:19 final size:19
Alignment explanation
Indices: 2758596--2758634 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2758586 AATAAAAACG
* *
2758596 AAAATAATAAGAAATATAC
1 AAAATAAAAAGAAAAATAC
2758615 AAAATAAAAAGAAAAATAC
1 AAAATAAAAAGAAAAATAC
2758634 A
1 A
2758635 CTTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAATAAAAAGAAAAATAC
Found at i:2758778 original size:17 final size:18
Alignment explanation
Indices: 2758753--2758786 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2758743 ATACGTATAC
2758753 ATAACAAAATAA-ATAAA
1 ATAACAAAATAATATAAA
*
2758770 ATAATAAAATAATATAA
1 ATAACAAAATAATATAA
2758787 GGGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAACAAAATAATATAAA
Found at i:2787016 original size:14 final size:14
Alignment explanation
Indices: 2786992--2787025 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2786982 GCTTATAAAA
2786992 ATATAATATATATAC
1 ATAT-ATATATATAC
2787007 ATATATATATATAC
1 ATATATATATATAC
2787021 A-ATAT
1 ATATAT
2787026 GTTAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:2794587 original size:30 final size:32
Alignment explanation
Indices: 2794553--2794619 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
2794543 AATAAAATTA
** *
2794553 GAATATTTTATTTTTGTC-AAAAAA-AACTAT
1 GAATATTTTAGGTTTGTCAAAAAAATAACCAT
2794583 GAATA--TTAGGTTTGTCAAAAAAATAACCAT
1 GAATATTTTAGGTTTGTCAAAAAAATAACCAT
2794613 GAATATT
1 GAATATT
2794620 AGGATTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 9 0.30
29 6 0.20
30 15 0.50
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.37
Consensus pattern (32 bp):
GAATATTTTAGGTTTGTCAAAAAAATAACCAT
Found at i:2794596 original size:28 final size:30
Alignment explanation
Indices: 2794565--2794622 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2794555 ATATTTTATT
*
2794565 TTTGTC-AAAAAA-AACTATGAATATTAGG
1 TTTGTCAAAAAAATAACCATGAATATTAGG
2794593 TTTGTCAAAAAAATAACCATGAATATTAGG
1 TTTGTCAAAAAAATAACCATGAATATTAGG
2794623 ATTTTGTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 6 0.22
29 6 0.22
30 15 0.56
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.31
Consensus pattern (30 bp):
TTTGTCAAAAAAATAACCATGAATATTAGG
Found at i:2796715 original size:19 final size:21
Alignment explanation
Indices: 2796686--2796729 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
2796676 TTTATATCAA
2796686 AGATAAAAATAAAATA-AACG
1 AGATAAAAATAAAATAGAACG
2796706 AGAT-AAAATAAAATAGAACG
1 AGATAAAAATAAAATAGAACG
2796726 AGAT
1 AGAT
2796730 GATGAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.16
Consensus pattern (21 bp):
AGATAAAAATAAAATAGAACG
Found at i:2797770 original size:28 final size:30
Alignment explanation
Indices: 2797728--2797789 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
2797718 AACTAATCCA
*
2797728 TCATTATTTCATTCAACAGTGTTTAACCTT
1 TCATTATTTCATTCAACAGTGTTTAACCGT
2797758 TCATT-TTT-ATTCAACAGTGTTTAACCGT
1 TCATTATTTCATTCAACAGTGTTTAACCGT
2797786 TCAT
1 TCAT
2797790 CTAACTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 23 0.74
29 3 0.10
30 5 0.16
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (30 bp):
TCATTATTTCATTCAACAGTGTTTAACCGT
Found at i:2798015 original size:80 final size:81
Alignment explanation
Indices: 2797762--2798076 Score: 373
Period size: 81 Copynumber: 3.9 Consensus size: 81
2797752 AACCTTTCAT
* * * * ** * * *
2797762 TTTTATTCAACAGTGTTTAACCGTTCATCTAACTGGTATAATTGACACCTTTCAAACAATTGCAT
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGGTACCTTTCTACCAATTGCAC
2797827 AGTTAGGCTATTATTC
66 AGTTAGGCTATTATTC
* * * * ** * * *
2797843 ATTTACTCAACAGTATTAAATCGTTCATCTAATTGGCATAATTGGTAGTTTTGTGCTAATTGCAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGGTACCTTTCTACCAATTGCAC
* *
2797908 AATTAGACTATTATTC
66 AGTTAGGCTATTATTC
* *
2797924 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGAATAATTTGTACC-TTCTACCAATTGCAC
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGGTACCTTTCTACCAATTGCAC
2797988 AGTTAGGCTATTATTC
66 AGTTAGGCTATTATTC
* * *
2798004 TTTTACTCAACGGCATTAAACCGTTCATCTAACT-GACATAATTGGTACCTTTCTACCAGTTGCA
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGA-ATAATTGGTACCTTTCTACCAATTGCA
*
2798068 CAGTAAGGC
65 CAGTTAGGC
2798077 CTCAAAGGCA
Statistics
Matches: 196, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
79 2 0.01
80 70 0.36
81 124 0.63
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (81 bp):
TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGGTACCTTTCTACCAATTGCAC
AGTTAGGCTATTATTC
Found at i:2798069 original size:161 final size:162
Alignment explanation
Indices: 2797762--2798069 Score: 404
Period size: 161 Copynumber: 1.9 Consensus size: 162
2797752 AACCTTTCAT
* * * * *
2797762 TTTTATTCAACAGTGTTTAACCGTTCATCTAACTGGTATAATTGACACCTTTCAAACAATTGCAT
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGACACCTTTCAAACAATTGCAC
* * * * **
2797827 AGTTAGGCTATTATTCATTTACTCAACAGTATTAAATCGTTCATCTAATTGGCATAATTGGTAGT
66 AGTTAGGCTATTATTCATTTACTCAACAGCATTAAACCGTTCATCTAACTGACATAATTGGTACC
* * *
2797892 TTTGTGCTAATTGCACAATTAGACTATTATTC
131 TTTCTACCAATTGCACAATTAGACTATTATTC
* * * *
2797924 TTTTACTCAACGGTATTAAACCGTTCATCTAACTGGAATAATTTG-TACC-TTCTACCAATTGCA
1 TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAA-TTGACACCTTTCAAACAATTGCA
* *
2797987 CAGTTAGGCTATTATTCTTTTACTCAACGGCATTAAACCGTTCATCTAACTGACATAATTGGTAC
65 CAGTTAGGCTATTATTCATTTACTCAACAGCATTAAACCGTTCATCTAACTGACATAATTGGTAC
*
2798052 CTTTCTACCAGTTGCACA
130 CTTTCTACCAATTGCACA
2798070 GTAAGGCCTC
Statistics
Matches: 124, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
161 82 0.66
162 39 0.31
163 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (162 bp):
TTTTACTCAACAGTATTAAACCGTTCATCTAACTGGAATAATTGACACCTTTCAAACAATTGCAC
AGTTAGGCTATTATTCATTTACTCAACAGCATTAAACCGTTCATCTAACTGACATAATTGGTACC
TTTCTACCAATTGCACAATTAGACTATTATTC
Found at i:2798122 original size:68 final size:68
Alignment explanation
Indices: 2798027--2798227 Score: 206
Period size: 68 Copynumber: 3.0 Consensus size: 68
2798017 CATTAAACCG
* * ** ** *
2798027 TTCATCTAACTGACATAATTGGTACCTTTCTACCAGTTGCACAGTAAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCAAATGCACAGTAAGGCCTCAAAGACACTTAG
2798092 CCT
66 CCT
* ** * *
2798095 TTCATCTATCTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTGAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCAAATGCACAGTAAGGCCTCAAAGACACTTAG
*
2798160 TCT
66 CCT
* * ** * * *
2798163 TTCATTTAACTGGCATAAATGACACATTTCTGTCAAATGAACAGTTAGACCTCAAAGGA-ACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTACCAAATGCACAGTAAGGCCTCAAA-GACACTTA
2798227 G
65 G
2798228 TATGATTTCT
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
68 111 0.98
69 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTACCAAATGCACAGTAAGGCCTCAAAGACACTTAG
CCT
Found at i:2798228 original size:68 final size:68
Alignment explanation
Indices: 2798067--2798228 Score: 227
Period size: 68 Copynumber: 2.4 Consensus size: 68
2798057 TACCAGTTGC
* * * * *
2798067 ACAGTAAGGCCTCAAAGGCACTTAGCCTTTCATCTATCTGGCATAAATGACACCTTTCTGTCAAA
1 ACAGTTAGGCCTCAAAGGAACTTAGTCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAA
*
2798132 TGC
66 TGA
* *
2798135 ACAGTTAGGCCTGAAA-GACACTTAGTCTTTCATTTAACTGGCATAAATGACACATTTCTGTCAA
1 ACAGTTAGGCCTCAAAGGA-ACTTAGTCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAA
2798199 ATGA
65 ATGA
*
2798203 ACAGTTAGACCTCAAAGGAACTTAGT
1 ACAGTTAGGCCTCAAAGGAACTTAGT
2798229 ATGATTTCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
67 1 0.01
68 79 0.96
69 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (68 bp):
ACAGTTAGGCCTCAAAGGAACTTAGTCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAA
TGA
Found at i:2798372 original size:58 final size:56
Alignment explanation
Indices: 2798222--2798373 Score: 211
Period size: 59 Copynumber: 2.7 Consensus size: 56
2798212 CCTCAAAGGA
*
2798222 ACTTAGTATG-ATTTCTT--ATTTCGCACACATAGTGCCCATACGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAAATTTTGCACACATAGTGCCCATACGGAAATTCATAC
* *
2798275 ACTTAGTATGAAGTTCTTAATATTTTAGCACACAAAGTGCCCAATACGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAA-ATTTT-GCACACATAGTGCCC-ATACGGAAATTCATAC
*
2798334 ACTTAGTATGAATTTCTTAACATTTTGCACACTTAGTGCC
1 ACTTAGTATGAATTTCTTAA-ATTTTGCACACATAGTGCC
2798374 ATTTGGTAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
53 10 0.12
54 6 0.07
57 4 0.05
58 26 0.30
59 40 0.47
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (56 bp):
ACTTAGTATGAATTTCTTAAATTTTGCACACATAGTGCCCATACGGAAATTCATAC
Found at i:2798835 original size:22 final size:22
Alignment explanation
Indices: 2798783--2798855 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
2798773 CGATGTTGCT
*
2798783 TGGTATCGATAC--CCTTACCA
1 TGGTATCGATACTACCCTACCA
*
2798803 TGGTATCGATACTACCCTACTA
1 TGGTATCGATACTACCCTACCA
2798825 TGGTA-CTGATACT-CCCTACC-
1 TGGTATC-GATACTACCCTACCA
2798845 -GGTATCGATAC
1 TGGTATCGATAC
2798856 CAAAATTAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 9 0.20
20 13 0.28
21 7 0.15
22 17 0.37
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (22 bp):
TGGTATCGATACTACCCTACCA
Found at i:2798853 original size:95 final size:96
Alignment explanation
Indices: 2798725--2798914 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 96
2798715 GATACTTCTA
* * * *
2798725 TACTATGGTACCGATACCCCCTTCGGGTATCGATACCAAAAATAGGTTCGATGTTGCTTGGTATC
1 TACTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTATC
*
2798790 GATA-CCCTTACCATGGTATCGATACTACCC
66 AATACCCCTTACCATGGTATCGATACTACCC
* * * * *
2798820 TACTATGGTACTGATACTCCCTACCGGTATCGATACCAAAATTAGATTTGATGTTTCATGGTATC
1 TACTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTATC
*
2798885 AATACCCCTTATCATGGTATCGATACTACC
66 AATACCCCTTACCATGGTATCGATACTACC
2798915 TCCTCGATAT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 59 0.71
96 24 0.29
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (96 bp):
TACTATGGTACCGATACCCCCTACCGGTATCGATACCAAAAATAGATTCGATGTTGCATGGTATC
AATACCCCTTACCATGGTATCGATACTACCC
Found at i:2803565 original size:81 final size:80
Alignment explanation
Indices: 2803439--2803738 Score: 429
Period size: 81 Copynumber: 3.7 Consensus size: 80
2803429 TCAATAGTGT
* * *
2803439 TTAACCGTTCATCTAACTAGCATAATTGGCACATTTCTACCAATTGCACAGTTAGGCTATTATTC
1 TTAAACGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCTATTATTC
2803504 TTTTACTCAACGGTA
66 TTTTACTCAACGGTA
* * * *
2803519 TTAAATCGTTCATCTAACTGGCATAATTGGTAAATTTCTTCTAATTGCAAAGTTAGGCTATTATT
1 TTAAA-CGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCTATTATT
2803584 CTTTTACTCAACGGTA
65 CTTTTACTCAACGGTA
* * * *
2803600 TTAAACTATTCATCTAACTGGCTTAATTAGTACATTTCTACCAATTGCACAGTTAGTCTATTATT
1 TTAAAC-GTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCTATTATT
* *
2803665 CTTTTACTCAACAGCA
65 CTTTTACTCAACGGTA
* * *
2803681 TTAAACCGTTCATCTAACTGGCATAGTTGGTACCTTTCTACCAGTTGCACAGTTAGGC
1 TTAAA-CGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTTAGGC
2803739 CTTAAAGACA
Statistics
Matches: 193, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
80 5 0.03
81 187 0.97
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (80 bp):
TTAAACGTTCATCTAACTGGCATAATTGGTACATTTCTACCAATTGCACAGTTAGGCTATTATTC
TTTTACTCAACGGTA
Found at i:2803808 original size:68 final size:68
Alignment explanation
Indices: 2803726--2803876 Score: 212
Period size: 68 Copynumber: 2.2 Consensus size: 68
2803716 TTCTACCAGT
* * ** *
2803726 TGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTATTTGGAATAAATGACACATTTCTGTT
1 TGCATAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGAATAAATGACACATTTCTGTC
2803791 AAA
66 AAA
* * * * *
2803794 TGCATAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGATACCTTTTTGTC
1 TGCATAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGAATAAATGACACATTTCTGTC
2803859 AAA
66 AAA
2803862 TGCATAGTTAGGCCT
1 TGCATAGTTAGGCCT
2803877 ATTAATCTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (68 bp):
TGCATAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAACTGGAATAAATGACACATTTCTGTC
AAA
Found at i:2804676 original size:95 final size:95
Alignment explanation
Indices: 2804510--2804730 Score: 216
Period size: 95 Copynumber: 2.3 Consensus size: 95
2804500 TGGCTCTATA
* * * *
2804510 GTATCGATACTAC-TACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCAGGTA
1 GTATCGATAC-CCTTACCATAGTATCGATACTTCTATACTATGGCACCGATACCCCCTTCAGGTA
* * * * *
2804574 TCGATACCAAAAATT-GGTTCGTTGTTTCTTT
65 TCAATACC-AAAATTAGATTCGATGTTTCATG
* * *
2804605 GTATCGATACCCTTACCATAGTATCGATACTATC-CTACTATGGCACCGATA-CTCCTTACTGGT
1 GTATCGATACCCTTACCATAGTATCGATACT-TCTATACTATGGCACCGATACCCCCTT-CAGGT
*
2804668 ATTAATACCAAAATTAGATTCGATGTTTCATG
64 ATCAATACCAAAATTAGATTCGATGTTTCATG
* * * *
2804700 GTATCAATACCCCTTATCATGGTATCAATAC
1 GTATCGATA-CCCTTACCATAGTATCGATAC
2804731 CCCTTATCAT
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
94 12 0.12
95 72 0.69
96 20 0.19
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (95 bp):
GTATCGATACCCTTACCATAGTATCGATACTTCTATACTATGGCACCGATACCCCCTTCAGGTAT
CAATACCAAAATTAGATTCGATGTTTCATG
Found at i:2804721 original size:21 final size:21
Alignment explanation
Indices: 2804695--2804757 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2804685 ATTCGATGTT
2804695 TCATGGTATCAATACCCCTTA
1 TCATGGTATCAATACCCCTTA
2804716 TCATGGTATCAATACCCCTTA
1 TCATGGTATCAATACCCCTTA
* *
2804737 TCATGGTATCGATACTCCTTA
1 TCATGGTATCAATACCCCTTA
2804758 CAGTTTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (21 bp):
TCATGGTATCAATACCCCTTA
Found at i:2806019 original size:32 final size:32
Alignment explanation
Indices: 2805947--2806036 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
2805937 GTTAGTTTGT
* *
2805947 ACAATAAAATAAAATGGTAGTAA-GTTAGTAAGA
1 ACAATAAAATAAAA-GTTA-TAATGTTAATAAGA
* *
2805980 ACAATAAAGTAAAAGTTATAATGTTAATATGA
1 ACAATAAAATAAAAGTTATAATGTTAATAAGA
*
2806012 ACAATAAAATAAAAGTTAGAATGTT
1 ACAATAAAATAAAAGTTATAATGTT
2806037 TGTAAGTTAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 3 0.06
32 34 0.68
33 13 0.26
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.28
Consensus pattern (32 bp):
ACAATAAAATAAAAGTTATAATGTTAATAAGA
Done.