Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017631.1 Corchorus olitorius cultivar O-4 contig17664, 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: 61875
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2977 original size:21 final size:21
Alignment explanation
Indices: 2947--2993 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2937 TAGACCTTCA
2947 GGTCTCGAGTTCAAGTCTTAC
1 GGTCTCGAGTTCAAGTCTTAC
*
2968 GGTCTTGAGTTCAAGTCTTAC
1 GGTCTCGAGTTCAAGTCTTAC
2989 GGTCT
1 GGTCT
2994 ATGGTTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (21 bp):
GGTCTCGAGTTCAAGTCTTAC
Found at i:10408 original size:42 final size:43
Alignment explanation
Indices: 10357--10450 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
10347 AGTGCATTAC
*
10357 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
10398 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
10443 CTAATATT
1 CTAATATT
10451 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:11427 original size:3 final size:3
Alignment explanation
Indices: 11421--11469 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
11411 ATAATAATGA
*
11421 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11469 T
1 T
11470 GTAGACACCC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11590 original size:28 final size:28
Alignment explanation
Indices: 11544--11617 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
11534 GATCACCGAG
* *
11544 GGGGCATTTTAGTCA-TTTGTACATCCA
1 GGGGCATTTTGGTCATTTTGCACATCCA
* ** *
11571 GGGGCATTCTGGTCATTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTGCACATCCA
*
11599 GGGGCGTTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
11618 AAGTTCATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.15, C:0.16, G:0.28, T:0.41
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCACATCCA
Found at i:18446 original size:68 final size:69
Alignment explanation
Indices: 18284--18510 Score: 316
Period size: 68 Copynumber: 3.3 Consensus size: 69
18274 ATTTCCCGCA
* *
18284 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTC-A
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
18348 -AGC
66 CAGC
* ** * *
18351 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTC-TAACCTGTAATTTGCGCTCTTCAA
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
18415 CAGC
66 CAGC
* * *
18419 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCATGTCTTGTCCTGTATTTTTGCATTCCTCA
1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCGTTCCTCA
18484 ACAGC
65 ACAGC
* *
18489 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCGGGACAGGACTTGG
18511 CCAAGATCTG
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
66 18 0.13
67 38 0.27
68 41 0.29
69 7 0.05
70 35 0.25
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (69 bp):
ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
CAGC
Found at i:18829 original size:16 final size:16
Alignment explanation
Indices: 18808--18838 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18798 GCGAATGCAT
18808 TCATGCAAAGCATCAG
1 TCATGCAAAGCATCAG
*
18824 TCATGCAAATCATCA
1 TCATGCAAAGCATCA
18839 TAAGTATCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (16 bp):
TCATGCAAAGCATCAG
Found at i:21407 original size:2 final size:2
Alignment explanation
Indices: 21400--21426 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21390 TTCCATTATG
21400 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 T
21427 TACTGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23405 original size:35 final size:36
Alignment explanation
Indices: 23359--23441 Score: 141
Period size: 35 Copynumber: 2.3 Consensus size: 36
23349 GTTGCTAAAG
*
23359 ATTTATTTCAGTTGATCCAGGGCGATC-TTTCTTCA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACA
23394 ATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACA
1 ATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACA
*
23430 GTTTATTTCAGT
1 ATTTATTTCAGT
23442 CTACCGCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 27 0.60
36 18 0.40
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (36 bp):
ATTTATTTCAGTTGATCCAGGGCGATCTTTTCTACA
Found at i:23691 original size:69 final size:69
Alignment explanation
Indices: 23600--23768 Score: 275
Period size: 69 Copynumber: 2.4 Consensus size: 69
23590 GAATGCTTTG
* * * *
23600 GGCTTCTCCATAAGCCAAACTCGTTTCCATGCGAGTCAGTTTAAGCCTTGGTTCCACCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTTAAGCCTTGGTTCCACCCAAGCCA
23665 CATA
66 CATA
*
23669 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTTAAGCCTTGGTTCCATCCAAGCCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTTAAGCCTTGGTTCCACCCAAGCCA
*
23734 TATA
66 CATA
*
23738 AGCTTTTCCACAAGCCAAACTCGTTTCCATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATA
23769 TGAGTCAAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 93 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.28
Consensus pattern (69 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAATCAGTTTAAGCCTTGGTTCCACCCAAGCCA
CATA
Found at i:24189 original size:30 final size:30
Alignment explanation
Indices: 24153--25049 Score: 909
Period size: 30 Copynumber: 29.7 Consensus size: 30
24143 ATTCAATTCC
* *
24153 AATCCTGATTTAGGATTATTG-TTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTT-ATTTT
* * *
24183 AATCCT-GTTTGAGTATCATTACTTCATTTTT
1 AATCCTGGTTT-AGGATCATTGCTTTA-TTTT
* *
24214 AATCCTGGTTGAGGATCATTGCTTTATGTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
24244 AATCCTGGTTGAGGATCTTTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
24274 AATCAT-GTTTGAGGATCATTGCTTTATATT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
* *
24304 AATTCT-GTTTGAGGATCGTTGCTTTATTTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
* *
24334 AATCCT-GTTTGAAGATCATTGCTTTATGTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
*
24364 AATCCT-GTTTGAGGATCATTGCTTTATGTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
24394 AATCCT-GTTTGAGGATCATTGCTTTATTTTT
1 AATCCTGGTTT-AGGATCATTGCTTTA-TTTT
*
24425 AATCCT-GTTTGAGGATCATTACTTTATTTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
24455 AATCCT-GTTTGAGGATCATTGCTTTATTTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
* *
24485 AATCCTGGTTGAGGATCATTGCTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
24515 AATCCTGGTTTAGGATCATTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
24545 TATCCTGGTTAAGGATCATTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* * * *
24575 GATCCTGGTTGAGGATCATCGCTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
*
24605 AATCCTGGTTGAGGATC---G--TTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* * * *
24630 AATCCTGGTTGAGAACCATCGCTTTATTTTTT
1 AATCCTGGTTTAGGATCATTGCTTTA--TTTT
* * *
24662 TATCCTGGTTAAAGATCATTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
*
24692 AATCCTGATTTAGGATCATTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
24722 AATCCTGGTTTAGGATCATTGCTTTATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
24752 AATCCTGGTTGT-GGATCATTGCTTTATTGCTTTGTTTT
1 AATCCTGGTT-TAGGATCATTGCTTTA--------TTTT
*
24790 AATCCT-GTTTGAGGATCATTGCTCTATTTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
* * *
24820 -ATCCTGGTTGAGGAT-ATTTGCTATATGTT
1 AATCCTGGTTTAGGATCA-TTGCTTTATTTT
* * *
24849 AATCCTGGCTTAGGATCATTACTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
24879 AATCCT-TTTTGAGGATCATTGCTTCATTTTT
1 AATCCTGGTTT-AGGATCATTGCTTTA-TTTT
* * *
24910 AATCC-CGTTTGATGATCATTGCTTCATTTT
1 AATCCTGGTTT-AGGATCATTGCTTTATTTT
* *
24940 AATCCTGTTTTAGGATCATTGCTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* * *
24970 AATCCTGGTTGAGGATCATTACTTCATTTT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
25000 AATCCTGGTTGAGGATCATTGCTTTATTCT
1 AATCCTGGTTTAGGATCATTGCTTTATTTT
* *
25030 AATCC-AGCTTAGGATCATTG
1 AATCCTGGTTTAGGATCATTG
25050 TTTCATCGGT
Statistics
Matches: 754, Mismatches: 80, Indels: 67
0.84 0.09 0.07
Matches are distributed among these distances:
25 21 0.03
27 1 0.00
28 2 0.00
29 40 0.05
30 549 0.73
31 87 0.12
32 27 0.04
36 1 0.00
37 3 0.00
38 23 0.03
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (30 bp):
AATCCTGGTTTAGGATCATTGCTTTATTTT
Found at i:24292 original size:60 final size:60
Alignment explanation
Indices: 24153--25049 Score: 1019
Period size: 60 Copynumber: 14.8 Consensus size: 60
24143 ATTCAATTCC
* * * * *
24153 AATCCTGATTT-AGGATTATTG-TTTCATTTTAATCCTGTTTGAGTATCATTACTTCATTTTT
1 AATCCTG-TTTGAGGATCATTGCTTT-ATTTTAATCCTGGTTGAGGATCATTGCTTTA-TTTT
* * *
24214 AATCCTGGTTGAGGATCATTGCTTTATGTTAATCCTGGTTGAGGATCTTTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * * *
24274 AATCATGTTTGAGGATCATTGCTTTATATTAATTCTGTTTGAGGATCGTTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * *
24334 AATCCTGTTTGAAGATCATTGCTTTATGTTAATCCTGTTTGAGGATCATTGCTTTATGTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* *
24394 AATCCTGTTTGAGGATCATTGCTTTATTTTTAATCCTGTTTGAGGATCATTACTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTA-TTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
*
24455 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* *
24515 AATCCTGGTTT-AGGATCATTGCTTTATTTTTATCCTGGTTAAGGATCATTGCTTTATTTT
1 AATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * *
24575 GATCCTGGTTGAGGATCATCGCTTCATTTTAATCCTGGTTGAGGATC---G--TTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * * * * *
24630 AATCCTGGTTGAGAACCATCGCTTTATTTTTTTATCCTGGTTAAAGATCATTGCTTTATTTT
1 AATCCTGTTTGAGGATCATTGCTTTA--TTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
*
24692 AATCCTGATTT-AGGATCATTGCTTTATTTTAATCCTGGTTTAGGATCATTGCTTTATTTT
1 AATCCTG-TTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * *
24752 AATCCTGGTTGTGGATCATTGCTTTATTGCTTTGTTTTAATCCTGTTTGAGGATCATTGCTCTAT
1 AATCCTGTTTGAGGATCATTGCTTTA--------TTTTAATCCTGGTTGAGGATCATTGCTTTAT
24817 TTT
58 TTT
* * * * *
24820 -ATCCTGGTTGAGGAT-ATTTGCTATATGTTAATCCTGGCTT-AGGATCATTACTTCATTTT
1 AATCCTGTTTGAGGATCA-TTGCTTTATTTTAATCCTGG-TTGAGGATCATTGCTTTATTTT
* * * * * *
24879 AATCCTTTTTGAGGATCATTGCTTCATTTTTAATCCCGTTTGATGATCATTGCTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTA-TTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * *
24940 AATCCTGTTTTAGGATCATTGCTTCATTTTAATCCTGGTTGAGGATCATTACTTCATTTT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
* * * *
25000 AATCCTGGTTGAGGATCATTGCTTTATTCTAATCCAGCTT-AGGATCATTG
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTG
25050 TTTCATCGGT
Statistics
Matches: 724, Mismatches: 84, Indels: 58
0.84 0.10 0.07
Matches are distributed among these distances:
55 29 0.04
57 19 0.03
59 40 0.06
60 399 0.55
61 153 0.21
62 29 0.04
63 2 0.00
66 1 0.00
67 21 0.03
68 31 0.04
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (60 bp):
AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTTTATTTT
Found at i:24356 original size:90 final size:90
Alignment explanation
Indices: 24153--25049 Score: 1030
Period size: 90 Copynumber: 9.9 Consensus size: 90
24143 ATTCAATTCC
* * * *
24153 AATCCTGATTT-AGGATTATTG-TTTCATTTTAATCCTGTTTGAGTATCATTACTTCATTTTTAA
1 AATCCTG-TTTGAGGATCATTGCTTT-ATTTTAATCCTGTTTGAGGATCATTGCTTTA-TTTTAA
*
24216 TCCTGGTTGAGGATCATTGCTTTATGTT
63 TCCTGGTTGAGGATCATTGCTTTATTTT
* * * * *
24244 AATCCTGGTTGAGGATCTTTGCTTTATTTTAATCATGTTTGAGGATCATTGCTTTATATTAATTC
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
* *
24309 TGTTTGAGGATCGTTGCTTTATTTT
66 TGGTTGAGGATCATTGCTTTATTTT
* * *
24334 AATCCTGTTTGAAGATCATTGCTTTATGTTAATCCTGTTTGAGGATCATTGCTTTATGTTAATCC
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
*
24399 TGTTTGAGGATCATTGCTTTATTTTT
66 TGGTTGAGGATCATTGCTTTA-TTTT
*
24425 AATCCTGTTTGAGGATCATTACTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
*
24490 TGGTTGAGGATCATTGCTTCATTTT
66 TGGTTGAGGATCATTGCTTTATTTT
* * * *
24515 AATCCTGGTTT-AGGATCATTGCTTTATTTTTATCCTGGTTAAGGATCATTGCTTTATTTTGATC
1 AATCCT-GTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATC
* *
24579 CTGGTTGAGGATCATCGCTTCATTTT
65 CTGGTTGAGGATCATTGCTTTATTTT
* * * * * *
24605 AATCCTGGTTGAGGATC---G--TTATTTTAATCCTGGTTGAGAACCATCGCTTTATTTTTTTAT
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTA--TTTTAAT
* *
24665 CCTGGTTAAAGATCATTGCTTTATTTT
64 CCTGGTTGAGGATCATTGCTTTATTTT
24692 AATCCTGATTT-AGGATCATTGCTTTATTTTAATCCTGGTTT-AGGATCATTGCTTTATTTTAAT
1 AATCCTG-TTTGAGGATCATTGCTTTATTTTAATCCT-GTTTGAGGATCATTGCTTTATTTTAAT
*
24755 CCTGGTTGTGGATCATTGCTTTATTGCTTTGTTTT
64 CCTGGTTGAGGATCATTGCTTTA--------TTTT
* * * *
24790 AATCCTGTTTGAGGATCATTGCTCTATTTT-ATCCTGGTTGAGGAT-ATTTGCTATATGTTAATC
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCA-TTGCTTTATTTTAATC
* *
24853 CTGGCTT-AGGATCATTACTTCATTTT
65 CTGG-TTGAGGATCATTGCTTTATTTT
* * * * *
24879 AATCCTTTTTGAGGATCATTGCTTCATTTTTAATCCCGTTTGATGATCATTGCTTCATTTTAATC
1 AATCCTGTTTGAGGATCATTGCTTTA-TTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATC
* * *
24944 CTGTTTTAGGATCATTGCTTCATTTT
65 CTGGTTGAGGATCATTGCTTTATTTT
* * * * *
24970 AATCCTGGTTGAGGATCATTACTTCATTTTAATCCTGGTTGAGGATCATTGCTTTATTCTAATCC
1 AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
* *
25035 AGCTT-AGGATCATTG
66 TGGTTGAGGATCATTG
25050 TTTCATCGGT
Statistics
Matches: 696, Mismatches: 80, Indels: 62
0.83 0.10 0.07
Matches are distributed among these distances:
85 28 0.04
87 43 0.06
88 2 0.00
89 40 0.06
90 274 0.39
91 199 0.29
92 29 0.04
93 3 0.00
96 4 0.01
97 43 0.06
98 31 0.04
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (90 bp):
AATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCC
TGGTTGAGGATCATTGCTTTATTTT
Found at i:24790 original size:38 final size:38
Alignment explanation
Indices: 24739--24817 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
24729 GTTTAGGATC
* *
24739 ATTGCTTTATTTTAATCCTGGTTGTGGATCATTGCTTT
1 ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTCT
* *
24777 ATTGCTTTGTTTTAATCCTGTTTGAGGATCATTGCTCT
1 ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTCT
24815 ATT
1 ATT
24818 TTATCCTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (38 bp):
ATTGCTTTATTTTAATCCTGGTTGAGGATCATTGCTCT
Found at i:25618 original size:28 final size:28
Alignment explanation
Indices: 25572--25645 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
25562 GATCACCGAG
* *
25572 GGGGCATTTTAGTCA-TTTGTACATCCA
1 GGGGCATTTTGGTCATTTTGCACATCCA
** *
25599 GGGGCATTTTGGTCATTTTGCATGTTCA
1 GGGGCATTTTGGTCATTTTGCACATCCA
*
25627 GGGGCGTTTTGGTCATTTT
1 GGGGCATTTTGGTCATTTT
25646 AAGTTCATTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 14 0.35
28 26 0.65
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGCACATCCA
Found at i:28398 original size:39 final size:41
Alignment explanation
Indices: 28355--28433 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
28345 TTTCACCTTG
** *
28355 GTCCCCGATTTAG-GTTAT-TTTGTTAATTGATTCAATTTT
1 GTCCCCGATTTAGAGCAATATTTATTAATTGATTCAATTTT
* *
28394 GTCCCTGATTTAGAGCAATATTTATTTATTGATTCAATTT
1 GTCCCCGATTTAGAGCAATATTTATTAATTGATTCAATTT
28434 CCCCCTGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 12 0.36
40 3 0.09
41 18 0.55
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (41 bp):
GTCCCCGATTTAGAGCAATATTTATTAATTGATTCAATTTT
Found at i:33430 original size:20 final size:20
Alignment explanation
Indices: 33393--33431 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
33383 TACTATTATT
33393 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
33413 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
33432 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:33625 original size:22 final size:22
Alignment explanation
Indices: 33597--33806 Score: 106
Period size: 22 Copynumber: 9.5 Consensus size: 22
33587 TGTCTTTGTG
*
33597 TGGTTATCGAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
33619 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
*
33642 -GGTTATCAAAATTCCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
33661 TGGTTACCAAAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* **
33684 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
33705 AGGTTATCAAAAATACATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
33727 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** * *
33751 AGGTTATTGAAATTTTAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
33773 TGGTTATCACAATTTTATATAAA
1 TGGTTATCAAAATTTCATA-AGA
*
33796 AGGTTATCAAA
1 TGGTTATCAAA
33807 GAGATTATCA
Statistics
Matches: 140, Mismatches: 37, Indels: 21
0.71 0.19 0.11
Matches are distributed among these distances:
20 16 0.11
21 4 0.03
22 90 0.64
23 12 0.09
24 18 0.13
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:33671 original size:20 final size:20
Alignment explanation
Indices: 33642--33679 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33632 TTCATGAGGA
*
33642 GGTTATCAAAATTCCATAGT
1 GGTTACCAAAATTCCATAGT
*
33662 GGTTACCAAAATTTCATA
1 GGTTACCAAAATTCCATA
33680 AGGAAGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (20 bp):
GGTTACCAAAATTCCATAGT
Found at i:33697 original size:64 final size:64
Alignment explanation
Indices: 33596--33716 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
33586 TTGTCTTTGT
* * * * *
33596 GTGGTTATCGAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCATA
1 GTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTCCATA
33660 GTGGTTACCAAAATTTCATAAGGA-AGTTATCAAAATTTCATGGGAAGGTTATCAAAA
1 GTGGTTACCAAAATTTCATAA-GATAGTTATCAAAATTTCATGGGAAGGTTATCAAAA
33717 ATACATAGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.04
64 46 0.92
65 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGGAAGGTTATCAAAATTCCATA
Found at i:33836 original size:22 final size:22
Alignment explanation
Indices: 33811--34643 Score: 276
Period size: 22 Copynumber: 37.6 Consensus size: 22
33801 ATCAAAGAGA
* *
33811 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
33833 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
33855 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
** * * *
33877 TTA-CTAGTATTTTATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
33899 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
**
33921 TTATCAAAATTTTTTAGTGTA-G
1 TTATCAAAATTTCATAGTG-AGG
33943 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
33965 TTAT-AAAAGTCTCAATTTCA-TGAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
33990 AGTACCAAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
34012 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * *
34033 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
* *
34058 TTATCAAAATTT-ATACG-AAGA
1 TTATCAAAATTTCATA-GTGAGG
**
34079 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* **
34101 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
34123 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
34145 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * *
34167 TCAAT-AAAATTTTATAGAGAGG
1 T-TATCAAAATTTCATAGTGAGG
** *
34189 TTATCAAAATTTCATAAAGAGT
1 TTATCAAAATTTCATAGTGAGG
* * * * *
34211 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
34233 TTACCAAAATTTCATAGTG-GTAT
1 TTATCAAAATTTCATAGTGAG--G
* * ** * **
34256 TTCTGGCGAGGTTATCA-A--AATT
1 TTAT--CAAAATT-TCATAGTGAGG
**
34278 TTAT-AGTATGGTTACCACATTAG-GAAGG
1 TTATCAAAAT--TT----CA-TAGTG-AGG
* * *
34306 TTATTAAACTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGAG-G
* *
34328 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
34348 ATATCAAAATTTTACA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* *
34370 TTATCAAAATTTCATAGTTTAGA
1 TTATCAAAATTTCATAG-TGAGG
*
34393 TT-TCAAAATTTCATA-AGAGGG
1 TTATCAAAATTTCATAGTGA-GG
*
34414 TTATCAAAATTTCATAGT-ATG
1 TTATCAAAATTTCATAGTGAGG
* * *
34435 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATAGTGAGG
* *
34458 TTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* ** *
34480 TTATAAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
34502 TTATCAAAA-TT--T-GT-A-G
1 TTATCAAAATTTCATAGTGAGG
*
34518 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
34540 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
34562 TTTATCAAAATTTTATAG-GATGAT
1 -TTATCAAAATTTCATAGTGA-G-G
*
34586 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
34608 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGAGG
34630 TTATCAAAATTTCA
1 TTATCAAAATTTCA
34644 GGGTGTGATT
Statistics
Matches: 599, Mismatches: 143, Indels: 138
0.68 0.16 0.16
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 4 0.01
20 23 0.04
21 53 0.09
22 392 0.65
23 58 0.10
24 9 0.02
25 23 0.04
26 11 0.02
27 6 0.01
28 5 0.01
29 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:34612 original size:45 final size:45
Alignment explanation
Indices: 34518--34643 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
34508 AAATTTGTAG
* * * * *
34518 TTATCAAGATTTCATAAG-GAGGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCAT-AGTGTGATTATCAAAATTTCATAGCGAGGT
*
34563 TTATCAAAATTTTATAG-GATGATTTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTCATAGTG-TGA-TTATCAAAATTTCATAGCGAGGT
*
34608 TTATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCA
34644 GGGTGTGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
44 17 0.24
45 32 0.46
46 21 0.30
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGCGAGGT
Found at i:34649 original size:22 final size:22
Alignment explanation
Indices: 34563--34653 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
34553 ATAGGGAGGT
* *
34563 TTATCAAAATTTTATAG-GATGA
1 TTATCAAAATTTCAGAGTG-TGA
* * * *
34585 TTTATCAAAATTTCATAGCGAGG
1 -TTATCAAAATTTCAGAGTGTGA
* *
34608 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
34630 TTATCAAAATTTCAGGGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
34652 TT
1 TT
34654 TCTAACTAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
22 39 0.68
23 17 0.30
24 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:34733 original size:52 final size:52
Alignment explanation
Indices: 34655--34755 Score: 202
Period size: 52 Copynumber: 1.9 Consensus size: 52
34645 GGTGTGATTT
34655 CTAACTAGGCCTGCTCATGGGCCGGGTCGGGCTGGGTTTGGGTCGGGCTGGG
1 CTAACTAGGCCTGCTCATGGGCCGGGTCGGGCTGGGTTTGGGTCGGGCTGGG
34707 CTAACTAGGCCTGCTCATGGGCCGGGTCGGGCTGGGTTTGGGTCGGGCT
1 CTAACTAGGCCTGCTCATGGGCCGGGTCGGGCTGGGTTTGGGTCGGGCT
34756 ATGACTATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.08, C:0.24, G:0.45, T:0.24
Consensus pattern (52 bp):
CTAACTAGGCCTGCTCATGGGCCGGGTCGGGCTGGGTTTGGGTCGGGCTGGG
Found at i:35058 original size:12 final size:12
Alignment explanation
Indices: 35041--35065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35031 TATATATTAT
35041 TTAGAAATAATA
1 TTAGAAATAATA
35053 TTAGAAATAATA
1 TTAGAAATAATA
35065 T
1 T
35066 AGGTATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TTAGAAATAATA
Found at i:35362 original size:44 final size:45
Alignment explanation
Indices: 35292--35376 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 45
35282 TTCTAACAAT
* * *
35292 TCATATGGAGGTTTTTAAATTTTCATA-TCG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAGT-GTTGGTTATCAATATA
35336 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAA
1 TCATATGGAGGTTATCAA-ATTCTCATAGTGTTGGTTATCAA
35377 AATTTTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
44 23 0.66
45 12 0.34
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAGTGTTGGTTATCAATATA
Found at i:35375 original size:23 final size:22
Alignment explanation
Indices: 35314--35376 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
35304 TTTTAAATTT
* *
35314 TCATATCGTGGTTATCAATATA
1 TCATATGGTGGTTATCAACATA
* *
35336 TCATATGGAGGTTATCAACATC
1 TCATATGGTGGTTATCAACATA
*
35358 TCATAGTGTTGGTTATCAA
1 TCATA-TGGTGGTTATCAA
35377 AATTTTATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
TCATATGGTGGTTATCAACATA
Found at i:35543 original size:22 final size:22
Alignment explanation
Indices: 35483--35532 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
35473 AAAGTTCTCG
* ** *
35483 AAATTTCATAGTATCGTTATTA
1 AAATTTCATAGGAAGGTTATCA
35505 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
35527 AAATTT
1 AAATTT
35533 TATAAGGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTATCA
Found at i:35551 original size:22 final size:22
Alignment explanation
Indices: 35504--35551 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
35494 TATCGTTATT
* *
35504 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
*
35526 AAAATTTTATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
35548 AAAA
1 AAAA
35552 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:39723 original size:31 final size:31
Alignment explanation
Indices: 39683--39843 Score: 196
Period size: 31 Copynumber: 5.2 Consensus size: 31
39673 GCATGAGACA
*
39683 TGCCACATGTCACTTTTTGATACATATGGCG
1 TGCCACATGTCACTTTTTGGTACATATGGCG
*
39714 TGACACATGTCACTTTTTGGTACATATGGCG
1 TGCCACATGTCACTTTTTGGTACATATGGCG
* * *
39745 TGCCACGTGTCACTTTTTGGTACATGTGGCA
1 TGCCACATGTCACTTTTTGGTACATATGGCG
* * * **
39776 TGCTACGTGTCGCTTTTTGGTACACGTGGCG
1 TGCCACATGTCACTTTTTGGTACATATGGCG
** * *
39807 TGCCACATGTTGCTTTTTGGTACACATGGCA
1 TGCCACATGTCACTTTTTGGTACATATGGCG
39838 TGCCAC
1 TGCCAC
39844 GTCGGACAGC
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (31 bp):
TGCCACATGTCACTTTTTGGTACATATGGCG
Found at i:39792 original size:93 final size:91
Alignment explanation
Indices: 39652--39845 Score: 235
Period size: 93 Copynumber: 2.1 Consensus size: 91
39642 AAAAATGACA
* * *
39652 CGTGGCACGTGTCCTTTTTGTGCATGAGACATGCCACATGTCACTTTTTGATACATATGGCGTGA
1 CGTGCCACGTGTCCTTTTTGTACATGAGACATGCCACATGTCACTTTTTGATACACATGGCGTGA
*
39717 CACATGTCACTTTTTGGTACATATGG
66 CACATGTCACTTTTTGGTACACATGG
* * * * * * *
39743 CGTGCCACGTGTCACTTTTTGGTACATGTGGCATGCTACGTGTCGCTTTTTGGTACACGTGGCGT
1 CGTGCCACGTGTC-CTTTTT-GTACATGAGACATGCCACATGTCACTTTTTGATACACATGGCGT
* **
39808 GCCACATGTTGCTTTTTGGTACACATGG
64 GACACATGTCACTTTTTGGTACACATGG
*
39836 CATGCCACGT
1 CGTGCCACGT
39846 CGGACAGCGT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
91 12 0.14
92 6 0.07
93 68 0.79
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (91 bp):
CGTGCCACGTGTCCTTTTTGTACATGAGACATGCCACATGTCACTTTTTGATACACATGGCGTGA
CACATGTCACTTTTTGGTACACATGG
Found at i:40373 original size:29 final size:32
Alignment explanation
Indices: 40340--40404 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
40330 GAGCCTTTCA
40340 AGCTGACTCG-AGCT-TT-CGAGCCGAGCTCG
1 AGCTGACTCGAAGCTATTACGAGCCGAGCTCG
**
40369 AGCTGACTCGAATTTATTACGAGCCGAGCTCG
1 AGCTGACTCGAAGCTATTACGAGCCGAGCTCG
40401 AGCT
1 AGCT
40405 TGAAATTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 10 0.32
30 2 0.06
31 2 0.06
32 17 0.55
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.23
Consensus pattern (32 bp):
AGCTGACTCGAAGCTATTACGAGCCGAGCTCG
Found at i:41907 original size:69 final size:70
Alignment explanation
Indices: 41827--41968 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 70
41817 TTTTGCTTGA
*
41827 AGTGCATTTGTCTTTATATGTAATTTTAGCATTTG-GATGTAATTAACGGTG-TTCCTACCTTTT
1 AGTGCATTTGTCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAACGGTGCTTCC-ACCATTT
41890 TTTCCTT
64 TTTCCTT
* *
41897 AGTGCA-TTGTCTTTATATGTAATTTTATCATTGAGATGTAATTAATGGTGCTTCCACCATTTTT
1 AGTGCATTTGTCTTTATATGTAATTTTAGCATTGAGATGTAATTAACGGTGCTTCCACCATTTTT
41961 TCCTT
66 TCCTT
41966 AGT
1 AGT
41969 TGTTAGTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
68 3 0.04
69 54 0.81
70 10 0.15
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (70 bp):
AGTGCATTTGTCTTTATATGTAATTTTAGCATTGAGATGTAATTAACGGTGCTTCCACCATTTTT
TCCTT
Found at i:43803 original size:25 final size:25
Alignment explanation
Indices: 43760--43810 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
43750 TGATAAATTT
43760 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
43787 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
43810 T
1 T
43811 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:52092 original size:21 final size:20
Alignment explanation
Indices: 52068--52112 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
52058 AAGCACAATT
52068 GAAATCG-AAATTGAAAGTAAA
1 GAAATCGAAAATT-AAAG-AAA
52089 GAAATCGAAAATTAAAGAAA
1 GAAATCGAAAATTAAAGAAA
52109 GAAA
1 GAAA
52113 AGGGAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAATCGAAAATTAAAGAAA
Found at i:60227 original size:321 final size:317
Alignment explanation
Indices: 59422--60385 Score: 1240
Period size: 321 Copynumber: 3.0 Consensus size: 317
59412 ATTTATGTGT
* *
59422 TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTTATTTCTTGTTGAACTGGGACAGATTTGTATG
1 TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTTATTTCTTGTTGAACTGTGACAAATTTGTATG
*
59487 ATAAATAAATGAGTAGGATTAAAAGTTTTATTTGTTTACCTTCTTTCATCCACCACTTTTTAGTT
66 ATAAATAAATGAGTAGGATTAAAAG-TTT-TTTATTTACCTTCTTTCATCCACCACTTTTTAGTT
* * * * *
59552 CTTTATTTATTGCGCGCACAC-AAATATGTATGTAGGTAGGGTTTAAGAATTTAGAGATCAAACG
129 CTTTATTTATTGCGCGCACACAAAAT-TATATGTATGTA-CGTTTAGGAATTTAGAGATCAAATG
*
59616 TATGAATGGATGGAACTGATGGAGATTTGTATGTACAAGTATAGACATGAAAAAAAAAGGGAAAT
192 TATGAATGGA-GGAAC---TGGAGATTTGTATGTACAAATATAGACAT--AAAAAAAAGGGAAAT
* * * *
59681 TTGATATATTTTCCTAAGTATATTGTCT-ATTTTTTTCTGGGTAAAGATACCAAGTATAG-AATA
251 TTGATATATTTTCCTAAGTATATTGTCTGATTTTTTTTTTGGTAAAGACACCAAATAT-GCAATA
59744 ATA
315 ATA
* * * * *
59747 TTAAAGTTTAAGTTCATCGTATGCTAGCATGC----TTCTTTTTAAAC--TGACAAATTTTTATG
1 TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTTATTTCTTGTTGAACTGTGACAAATTTGTATG
* * *
59806 ATAAATAAATGAGTAGGATTAAAAGTTTTATTATTTACCTTCTTTCCTCGACCACATTTTAGTTC
66 ATAAATAAATGAGTAGGATTAAAAGTTTT-TTATTTACCTTCTTTCATCCACCACTTTTTAGTTC
* ** * *
59871 TTTATTTATTGCGTGTGCACATAGA-TATTTGTATGTACGTTTAGGAATTTAGAGATCAAATGTA
130 TTTATTTATTGCGCGCACACA-AAATTATATGTATGTACGTTTAGGAATTTAGAGATCAAATGTA
59935 -G-AT-G-GG-ACTGGAGATTTTTGTATGTACAAATATAGACAT-AAAAAAAGGGAAATTTGATA
194 TGAATGGAGGAACTGGAGA--TTTGTATGTACAAATATAGACATAAAAAAAAGGGAAATTTGATA
*
59994 TATTTTCCTTAGTATATTGTCTGAATTATCTTTTTTTGGTAAAGACACCAAATATGCAATAATA
257 TATTTTCCTAAGTATATTGTCTG-ATT-T-TTTTTTTGGTAAAGACACCAAATATGCAATAATA
60058 TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTTAATTTCTTGTTGAACTGTGACAAATTTGTAT
1 TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTT-ATTTCTTGTTGAACTGTGACAAATTTGTAT
*
60123 GATGAATAAATGAGTATATAGGATTAAAAGTTTTTTATTTACCTTCTTTCATCCACCACTTTTTA
65 GATAAATAAATGAG----TAGGATTAAAAGTTTTTTATTTACCTTCTTTCATCCACCACTTTTTA
* * *
60188 GTTCTTTATTTATTGCACGCACACAAAATTATATGTATGTATGTATAGGAATTTAGAGATCAAAT
126 GTTCTTTATTTATTGCGCGCACACAAAATTATATGTATGTACGTTTAGGAATTTAGAGATCAAAT
** *
60253 GTATGAATGGATGGAACTGGAGATTTGTATGTACGGATATAGACATGAAAGAAAAAAGGAAATTT
191 GTATGAATGGA-GGAACTGGAGATTTGTATGTACAAATATAGACAT-AAA-AAAAAGGGAAATTT
* *
60318 GATATATTTTCCCAAGTATATTGTCTGATTTTTTTTTTGGTAAAGACACCCAATATATACAATAA
253 GATATATTTTCCTAAGTATATTGTCTGATTTTTTTTTTGGTAAAGACA-CCAA-ATATGCAATAA
60383 TA
316 TA
60385 T
1 T
60386 CAATGATTAC
Statistics
Matches: 556, Mismatches: 50, Indels: 64
0.83 0.07 0.10
Matches are distributed among these distances:
307 41 0.07
308 6 0.01
309 3 0.01
310 24 0.04
311 60 0.11
312 2 0.00
314 1 0.00
315 2 0.00
316 11 0.02
317 25 0.04
318 86 0.15
319 37 0.07
320 4 0.01
321 95 0.17
322 17 0.03
323 2 0.00
324 1 0.00
325 68 0.12
326 7 0.01
327 26 0.05
328 38 0.07
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (317 bp):
TTAAAGTTTAAGTTCATTGTATGCTAGCTTGCTTATTTCTTGTTGAACTGTGACAAATTTGTATG
ATAAATAAATGAGTAGGATTAAAAGTTTTTTATTTACCTTCTTTCATCCACCACTTTTTAGTTCT
TTATTTATTGCGCGCACACAAAATTATATGTATGTACGTTTAGGAATTTAGAGATCAAATGTATG
AATGGAGGAACTGGAGATTTGTATGTACAAATATAGACATAAAAAAAAGGGAAATTTGATATATT
TTCCTAAGTATATTGTCTGATTTTTTTTTTGGTAAAGACACCAAATATGCAATAATA
Found at i:60855 original size:43 final size:43
Alignment explanation
Indices: 60808--60897 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
60798 TTGTTTCTAT
60808 TTTAATCCTTATGATATATAATATAGCTGCCAAATGGTGTGTA
1 TTTAATCCTTATGATATATAATATAGCTGCCAAATGGTGTGTA
60851 TTTAATCCTTATGATATATAATATAGCTGCCAAATGGTGTGTA
1 TTTAATCCTTATGATATATAATATAGCTGCCAAATGGTGTGTA
60894 TTTA
1 TTTA
60898 GCTTAATGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (43 bp):
TTTAATCCTTATGATATATAATATAGCTGCCAAATGGTGTGTA
Found at i:61219 original size:32 final size:31
Alignment explanation
Indices: 61166--61232 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
61156 TGACTCTAGA
* *
61166 GACTTATTTGAGCCGAGTTTGCAATGTTAGG
1 GACTGATTTGAGCCGAGTTTGCAAAGTTAGG
* *
61197 GACTGATTTGAGGCCGATTTTGCAAAGTTTGG
1 GACTGATTTGA-GCCGAGTTTGCAAAGTTAGG
61229 GACT
1 GACT
61233 TAATTAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.34
Consensus pattern (31 bp):
GACTGATTTGAGCCGAGTTTGCAAAGTTAGG
Done.