Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006955.1 Hibiscus syriacus cultivar Beakdansim tig00017880_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: 75184
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1960 original size:21 final size:22
Alignment explanation
Indices: 1934--1994 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 22
1924 TATACTTTAA
1934 TGTTGAATCATTCAGCA-GTTT
1 TGTTGAATCATTCAGCAGGTTT
* *
1955 TGTTGAATCATACAACAGTGTTT
1 TGTTGAATCATTCAGCAG-GTTT
1978 TGTTGAATCATTCAGCA
1 TGTTGAATCATTCAGCA
1995 TGATCTTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 15 0.44
23 19 0.56
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTTGAATCATTCAGCAGGTTT
Found at i:1981 original size:23 final size:21
Alignment explanation
Indices: 1934--1988 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
1924 TATACTTTAA
* *
1934 TGTTGAATCATTCAGCAGTTT
1 TGTTGAATCATACAACAGTTT
1955 TGTTGAATCATACAACAGTGTTT
1 TGTTGAATCATACAACA--GTTT
1978 TGTTGAATCAT
1 TGTTGAATCAT
1989 TCAGCATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 15 0.50
23 15 0.50
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (21 bp):
TGTTGAATCATACAACAGTTT
Found at i:2962 original size:2 final size:2
Alignment explanation
Indices: 2955--3016 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
2945 AATTATAATC
*
2955 TA TA TA TA TA TA TC 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 TA TA TA TA TA TA
2997 -A TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3017 ATTTTAGTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4587 original size:24 final size:24
Alignment explanation
Indices: 4560--4657 Score: 72
Period size: 24 Copynumber: 4.1 Consensus size: 24
4550 TATATCAAAA
* *
4560 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
4584 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * *
4608 ATTC-GATCAGAATCCAGGTCAAGT
1 A-TCAAAACAAAATCCAGGTCAAGT
** * * *
4632 ATCCGATCAGAATCCAGGTCAGGT
1 ATCAAAACAAAATCCAGGTCAAGT
4656 AT
1 AT
4658 TATAATAGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:5688 original size:10 final size:10
Alignment explanation
Indices: 5662--5689 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5652 TCAAAGTTCT
5662 GGTCAACGCC
1 GGTCAACGCC
5672 GGTCAACGCC
1 GGTCAACGCC
5682 GGTCAACG
1 GGTCAACG
5690 GTCAACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.32, T:0.11
Consensus pattern (10 bp):
GGTCAACGCC
Found at i:7777 original size:35 final size:35
Alignment explanation
Indices: 7734--7834 Score: 184
Period size: 35 Copynumber: 2.9 Consensus size: 35
7724 CGTCAAGTCC
*
7734 AGTAAGGCCCTGAGCACACAGTCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
7769 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
*
7804 AGTAAGGCCCTGAGCACACAACCGAGGAGCC
1 AGTAAGGCCCTGAGCACACAGCCGAGGAGCC
7835 TCCAGGTATA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.33, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
Found at i:8012 original size:24 final size:24
Alignment explanation
Indices: 7915--8002 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
7905 ATCAAAACAT
7915 AATCCAGGTCAGGTATCCGATCAG
1 AATCCAGGTCAGGTATCCGATCAG
* *
7939 AATCTAGGTCAGGTATTCGATCAG
1 AATCCAGGTCAGGTATCCGATCAG
*
7963 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAGGTATCCGATCAG
7987 AATCCAGGTCAGGTAT
1 AATCCAGGTCAGGTAT
8003 TATAATAGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAGGTATCCGATCAG
Found at i:16912 original size:19 final size:19
Alignment explanation
Indices: 16890--16935 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
16880 GTAGAGGCTG
16890 CGACGTGGTAGTGAGGTGT
1 CGACGTGGTAGTGAGGTGT
16909 CGACGTGGTAGTGAGGTGT
1 CGACGTGGTAGTGAGGTGT
*
16928 CAACGTGG
1 CGACGTGG
16936 GGTGGTTGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.13, G:0.46, T:0.24
Consensus pattern (19 bp):
CGACGTGGTAGTGAGGTGT
Found at i:21249 original size:20 final size:20
Alignment explanation
Indices: 21189--21239 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
21179 ACCTCGTGCA
21189 TTTGCATTTGCATTCTTATT
1 TTTGCATTTGCATTCTTATT
21209 TTTGCATTTGCATTCTTATT
1 TTTGCATTTGCATTCTTATT
21229 TTTGCATTTGC
1 TTTGCATTTGC
21240 TTATTAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.14, C:0.16, G:0.12, T:0.59
Consensus pattern (20 bp):
TTTGCATTTGCATTCTTATT
Found at i:22380 original size:3 final size:3
Alignment explanation
Indices: 22372--22434 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
22362 CGGGTCTTAT
22372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
22418 TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
22435 CATTTTACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:22446 original size:14 final size:14
Alignment explanation
Indices: 22380--22447 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
22370 ATTTATTATT
* *
22380 ATTATTATTATTATT
1 ATTATTAATATTA-C
* *
22395 ATTATTATTATT-T
1 ATTATTAATATTAC
* *
22408 ATTATTATTATTAT
1 ATTATTAATATTAC
22422 ATTATTAATATTAC
1 ATTATTAATATTAC
22436 ATT-TTACATATT
1 ATTATTA-ATATT
22448 TTTGCAGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
13 16 0.33
14 21 0.43
15 12 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTAATATTAC
Found at i:23921 original size:30 final size:30
Alignment explanation
Indices: 23886--23995 Score: 73
Period size: 30 Copynumber: 3.7 Consensus size: 30
23876 CTTCAAATGA
* *
23886 CTGTTTTTACTATTTTAGTCTTGTAA-ATT
1 CTGTTTTTACTATTTTAGTCCTATAACATT
* * * *
23915 CATGTTTATGCTATTTCAGTCCTATAACTTT
1 C-TGTTTTTACTATTTTAGTCCTATAACATT
* * * **
23946 CTG-TTTTACTATTTTTGCCCTGTAAGTTT
1 CTGTTTTTACTATTTTAGTCCTATAACATT
*
23975 CTG-TTTTATCTATTTTGGTCC
1 CTGTTTTTA-CTATTTTAGTCC
23996 CCTAATGGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
29 28 0.44
30 32 0.51
31 3 0.05
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.55
Consensus pattern (30 bp):
CTGTTTTTACTATTTTAGTCCTATAACATT
Found at i:26232 original size:3 final size:3
Alignment explanation
Indices: 26213--26269 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
26203 ATGTAAAATG
*
26213 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
26258 TAA TAA TAA TAA
1 TAA TAA TAA TAA
26270 ATAAGACCCG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27664 original size:30 final size:30
Alignment explanation
Indices: 27629--27738 Score: 73
Period size: 30 Copynumber: 3.7 Consensus size: 30
27619 CTTCGAATGA
* *
27629 CTGTTTTTACTATTTTAGTCTTGTAA-ATT
1 CTGTTTTTACTATTTTAGTCCTATAACATT
* * * *
27658 CATGTTTATGCTATTTCAGTCCTATAACTTT
1 C-TGTTTTTACTATTTTAGTCCTATAACATT
* * * **
27689 CTG-TTTTACTATTTTTGCCCTGTAAGTTT
1 CTGTTTTTACTATTTTAGTCCTATAACATT
*
27718 CTG-TTTTATCTATTTTGGTCC
1 CTGTTTTTA-CTATTTTAGTCC
27739 CCTAATGGTT
Statistics
Matches: 63, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
29 28 0.44
30 32 0.51
31 3 0.05
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.55
Consensus pattern (30 bp):
CTGTTTTTACTATTTTAGTCCTATAACATT
Found at i:29754 original size:31 final size:32
Alignment explanation
Indices: 29713--29774 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
29703 ATTTTACATG
*
29713 TACTAGCTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
29744 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
29775 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:31898 original size:11 final size:11
Alignment explanation
Indices: 31870--31907 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
31860 AAGAGCAAAG
31870 AGAAAAATCAA
1 AGAAAAATCAA
31881 AGCAAAAATCAA
1 AG-AAAAATCAA
*
31893 AGAAAAAGCAA
1 AGAAAAATCAA
31904 AGAA
1 AGAA
31908 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:33090 original size:4 final size:4
Alignment explanation
Indices: 33081--33162 Score: 105
Period size: 4 Copynumber: 21.0 Consensus size: 4
33071 AAGAGTATAC
* * * *
33081 ACAT ACAT ACAT ACGT ATAC ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
33129 ACAT ACAT ATAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
33163 GATACATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
2 2 0.03
4 64 0.97
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:33558 original size:36 final size:36
Alignment explanation
Indices: 33518--33616 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
33508 GATTTTTCTA
33518 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
33554 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
33590 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
33617 TTTTCCCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:33945 original size:101 final size:98
Alignment explanation
Indices: 33739--33972 Score: 242
Period size: 101 Copynumber: 2.3 Consensus size: 98
33729 TGAGAATTTT
** * *
33739 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* *
33804 AAAAACAAAATCTCACCTTAGATTGTTGTTTCTTTC
66 AAAAACAAAATCGCACCTTAGA-T-TCGTTTC-TTC
* * *
33840 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
33904 ATTAAACAAAGTTGATCGCA-CTTGAGA-TCGTTTC-TC
66 A-AAAACAAA----ATCGCACCTT-AGATTCGTTTCTTC
* *
33940 AAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 -AAAACAAATTTTGTCTCGCTTGAGACATTTTC
33973 TCTAAAAACA
Statistics
Matches: 113, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
100 3 0.03
101 93 0.82
102 6 0.05
104 3 0.03
105 8 0.07
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (98 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATCGCACCTTAGATTCGTTTCTTC
Found at i:33963 original size:35 final size:33
Alignment explanation
Indices: 33922--34036 Score: 131
Period size: 33 Copynumber: 3.3 Consensus size: 33
33912 AAGTTGATCG
33922 CACTTGAGATCGTTTCTCAAAAACAAACTTTGTCT
1 CACTTGAGA-C-TTTCTCAAAAACAAACTTTGTCT
* *
33957 CGCTTGAGACAATTTCTCTAAAAACAAATTTTGTCT
1 CACTTGAGAC--TTTCTC-AAAAACAAACTTTGTCT
* * *
33993 CATTTGAGACTATATCAAAAACAAACTTTGTCT
1 CACTTGAGACTTTCTCAAAAACAAACTTTGTCT
*
34026 CATTTGAGACT
1 CACTTGAGACT
34037 ATATCTTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
33 27 0.39
34 5 0.07
35 14 0.20
36 24 0.34
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (33 bp):
CACTTGAGACTTTCTCAAAAACAAACTTTGTCT
Found at i:34019 original size:69 final size:67
Alignment explanation
Indices: 33938--34069 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 67
33928 AGATCGTTTC
* * * *
33938 TCAAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTGTCTCATTTGAGAC
1 TCAAAAACAAACTTTGTCTCACTTGAGACAATATCT-T-AAAACAAATTTCGTCTCACTTGAGAC
34003 TATA
64 TATA
* * * *
34007 TCAAAAACAAACTTTGTCTCATTTGAGACTATATCTTAAAGCAAATTTCGTCTCGCTTGAGAC
1 TCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTTCGTCTCACTTGAGAC
34070 ATCATTTTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 22 0.40
68 1 0.02
69 32 0.58
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (67 bp):
TCAAAAACAAACTTTGTCTCACTTGAGACAATATCTTAAAACAAATTTCGTCTCACTTGAGACTA
TA
Found at i:34067 original size:34 final size:34
Alignment explanation
Indices: 33941--34069 Score: 136
Period size: 33 Copynumber: 3.8 Consensus size: 34
33931 TCGTTTCTCA
* * *
33941 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAACAAACTTTGTCTCACTTGAGACTATATCT-T
* * *
33976 AAAAACAAATTTTGTCTCATTTGAGACTATATC-A
1 -AAAACAAACTTTGTCTCACTTGAGACTATATCTT
*
34010 AAAACAAACTTTGTCTCATTTGAGACTATATCTT
1 AAAACAAACTTTGTCTCACTTGAGACTATATCTT
* *
34044 AAAGCAAA-TTTCGTCTCGCTTGAGAC
1 AAAACAAACTTT-GTCTCACTTGAGAC
34070 ATCATTTTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
33 34 0.43
34 19 0.24
36 27 0.34
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAACAAACTTTGTCTCACTTGAGACTATATCTT
Found at i:34364 original size:29 final size:28
Alignment explanation
Indices: 34322--34418 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 28
34312 TTTCTCTTGA
34322 AAAAATCTTTGAGTTTGTTCATTTTGAAT
1 AAAAATCTTTGAGTTTGTTC-TTTTGAAT
* *
34351 AAAAATCTTGGAGTTTGTTCCTTTTAAAT
1 AAAAATCTTTGAGTTTGTT-CTTTTGAAT
*
34380 AAATATCTTTGAG-TTGTTTCTTTTG---
1 AAAAATCTTTGAGTTTG-TTCTTTTGAAT
34405 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
34419 CTATTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
25 12 0.20
28 8 0.14
29 38 0.64
30 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.47
Consensus pattern (28 bp):
AAAAATCTTTGAGTTTGTTCTTTTGAAT
Found at i:34509 original size:52 final size:53
Alignment explanation
Indices: 34431--34533 Score: 172
Period size: 52 Copynumber: 1.9 Consensus size: 53
34421 ATTTATTTTG
34431 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTCT
1 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTCT
* *
34483 GAAACAAGGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
34534 ATTGTTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 34 0.72
54 13 0.28
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (53 bp):
GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTCT
Found at i:34557 original size:27 final size:27
Alignment explanation
Indices: 34520--34576 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
34510 AATTTTGTGA
*
34520 AAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAATCTTTGAGATTGTTTCTTTGG
*
34547 AAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAATCTTTGAGATTGTTTCTTTGG
34574 AAA
1 AAA
34577 CAAAATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (27 bp):
AAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:34614 original size:37 final size:37
Alignment explanation
Indices: 34564--34690 Score: 126
Period size: 37 Copynumber: 3.6 Consensus size: 37
34554 CTTTGAGTTT
34564 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
34601 GTTTCTTTTGAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
34631 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
34668 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
34691 AATATGTTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
30 22 0.31
31 3 0.04
36 8 0.11
37 37 0.53
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:34627 original size:67 final size:65
Alignment explanation
Indices: 34532--34753 Score: 281
Period size: 67 Copynumber: 3.4 Consensus size: 65
34522 AAAATCTTTG
*
34532 AGATTGTTTCTTTTG-AAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
34596 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTTG-AA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
34661 TA
64 TA
* * * * *
34663 AGATAATTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCTT--AAA-ATGAATTTTGTATCTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCT
*
34725 TG
64 TA
* * **
34727 AGACAGTTTCTCTTGAAGTAAATCTTT
1 AGATAGTTTCTTTTGAAAAAAATCTTT
34754 AAATATGTTC
Statistics
Matches: 141, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 53 0.38
65 20 0.14
66 5 0.04
67 62 0.44
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
Found at i:34941 original size:120 final size:119
Alignment explanation
Indices: 34801--35025 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
34791 CTTAACAAAA
* * * *
34801 TCATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAA
34864 AACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGAT
64 AA--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
* ** **
34921 TCATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
* * *
34986 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
35026 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (119 bp):
TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGAT
Found at i:35002 original size:64 final size:63
Alignment explanation
Indices: 34923--35047 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
34913 GATGTGATTC
* *
34923 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
34987 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
35048 TACCACCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:35225 original size:15 final size:15
Alignment explanation
Indices: 35202--35260 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
35192 TTTTGAGTCG
*
35202 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
35217 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
35232 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
35247 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
35261 AGATCATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:35668 original size:28 final size:28
Alignment explanation
Indices: 35597--35678 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
35587 TAAAAATATC
* * *
35597 ATCTTTGAGTTTATTTTTCTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
** *
35625 ATCTTTGGGTTTGTTTCTTTTGAAACAA
1 ATCTTTGAATTTGTTTCTCTTGAAACAA
35653 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAATTT-GTTTCTCTTGAAAC
35679 CATAACTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 3 0.07
28 43 0.93
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.50
Consensus pattern (28 bp):
ATCTTTGAATTTGTTTCTCTTGAAACAA
Found at i:35794 original size:43 final size:44
Alignment explanation
Indices: 35736--35939 Score: 134
Period size: 43 Copynumber: 4.7 Consensus size: 44
35726 TCATCCCCAG
* * *
35736 ACCAGATCTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
* * * *
35779 ACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATA
* * * * * **
35825 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
* * * **
35866 ACCAGATCTCTTCATCACGTAGGAGCTGTGTCA-ACTGTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
* *
35909 ACTAG-CCGTCCTCATCACGTAGGAACCGTGT
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGT
35940 TATCACCTTA
Statistics
Matches: 123, Mismatches: 29, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
40 3 0.02
41 29 0.24
42 2 0.02
43 50 0.41
44 2 0.02
45 5 0.04
46 31 0.25
47 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (44 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCATACCATAGATA
Found at i:35854 original size:89 final size:83
Alignment explanation
Indices: 35697--35857 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
35687 CTACAGATGG
** *
35697 CCAGCCGTCCTCATCGTGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGC
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
35762 CGTGTCAACCATAGATAA
66 CGTGTCAACCATAGATAA
* *
35780 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGAACTCTTCATCACGT
35845 ATGAGCCGTGTCA
60 ATGAGCCGTGTCA
35858 TTCCCCAGAC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 31 0.46
84 2 0.03
86 3 0.04
89 31 0.46
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (83 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGAACTCTTCATCACGTATGAGC
CGTGTCAACCATAGATAA
Found at i:35923 original size:130 final size:130
Alignment explanation
Indices: 35721--36028 Score: 465
Period size: 130 Copynumber: 2.4 Consensus size: 130
35711 CGTGTAGGAA
*
35721 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCC
1 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
*
35786 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCTTCATCACGTATGAG
66 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGAG
* ** *
35850 CCGTGTCATTCCCCAGACCAGATCTCTTCATCACGTAGGAGCTGTGTCAACTGTAGATAACTAGC
1 CCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGC
35915 CGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGA
65 CGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGA
35980 G
130 G
* * ** * * * * *
35981 CAGTGTCAACCCTTGACCAGATTTCCTCATCACGCAGGAACCATGTCA
1 CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCA
36029 CCCTTAGACG
Statistics
Matches: 161, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
129 8 0.05
130 124 0.77
131 29 0.18
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (130 bp):
CCGTGTCATCCCCAGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCC
GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTCATCACGTATGAG
Found at i:36234 original size:3 final size:3
Alignment explanation
Indices: 36226--36303 Score: 131
Period size: 3 Copynumber: 26.0 Consensus size: 3
36216 GTCTTATTTT
36226 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
36274 TTA TTA TTTA TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
36304 CATTTTACAT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.93
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:43651 original size:37 final size:38
Alignment explanation
Indices: 43600--43752 Score: 233
Period size: 37 Copynumber: 4.1 Consensus size: 38
43590 ATGAGATTGG
*
43600 AGCAAAGTCAATCTTAAGCCTTCACCGAA-AAGGAGGGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGAAGAAGGAGTGA
43638 AGCAAATCAATCTTAAGCCTTCACC-AAGAAGGAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAAGGAGTGA
*
43675 AGCAAATCAATCTTAAGCCTTCA-CTAAGAAGGAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAAGGAGTGA
* *
43712 AGCAAATCAATCTTAAACCTTCACCGAAG-AGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAAGGAGTGA
43749 AGCA
1 AGCA
43753 CCACCTTAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
36 3 0.03
37 95 0.88
38 10 0.09
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.19
Consensus pattern (38 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAGAAGGAGTGA
Found at i:43767 original size:34 final size:36
Alignment explanation
Indices: 43607--43787 Score: 190
Period size: 37 Copynumber: 5.0 Consensus size: 36
43597 TGGAGCAAAG
* *
43607 TCAATCTTAAGCCTTCACCGAAAAGGAGGGAAGCAAA
1 TCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGC-AA
43644 TCAATCTTAAGCCTTCACC-AAGAAGGAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACCGAAG-AGGAGTGAAGC-AA
*
43681 TCAATCTTAAGCCTTCA-CTAAGAAGGAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACCGAAG-AGGAGTGAAGC-AA
* *
43718 TCAATCTTAAACCTTCACCGAAGAGTAGTGAAGC-A
1 TCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAA
* * * * **
43753 -CCACCTTAAGCCTTCACAGAATAATAGTGAAGCAA
1 TCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAA
43788 ACCCATCAGT
Statistics
Matches: 129, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
34 27 0.21
35 2 0.02
36 3 0.02
37 93 0.72
38 4 0.03
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (36 bp):
TCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAA
Found at i:43878 original size:41 final size:42
Alignment explanation
Indices: 43790--43888 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
43780 TGAAGCAAAC
* * * * *
43790 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
1 CCATCTGTAAGCCTTTAGAGCAAGATGCATAAATCCTTCGGG
* *
43832 TCATCTGTAAGCCTTTAGAGCAAGATG-ATAAGTCCTTCGGG
1 CCATCTGTAAGCCTTTAGAGCAAGATGCATAAATCCTTCGGG
*
43873 CCATCTATAAGACCTT
1 CCATCTGTAAG-CCTT
43889 CGGGTAGGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 21 0.45
42 26 0.55
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
CCATCTGTAAGCCTTTAGAGCAAGATGCATAAATCCTTCGGG
Found at i:44018 original size:20 final size:20
Alignment explanation
Indices: 43993--44062 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
43983 TCACAATTTA
43993 TAAGTCCTTCGGGTCATCAG
1 TAAGTCCTTCGGGTCATCAG
* * *
44013 TAAGTCTTTCGAG-CATGATG
1 TAAGTCCTTCGGGTCATCA-G
* *
44033 CTTAAATCCTTCGGGTCATCTG
1 --TAAGTCCTTCGGGTCATCAG
44055 TAAG-CCTT
1 TAAGTCCTT
44063 TAGAGCAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 9
0.67 0.16 0.16
Matches are distributed among these distances:
19 8 0.22
20 15 0.41
22 11 0.30
23 3 0.08
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (20 bp):
TAAGTCCTTCGGGTCATCAG
Found at i:44058 original size:42 final size:41
Alignment explanation
Indices: 43992--44093 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
43982 TTCACAATTT
* * * *
43992 ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATG
* *
44033 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATG
* *
44075 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGTCATC
44094 CATAAGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:44283 original size:219 final size:215
Alignment explanation
Indices: 43790--44552 Score: 1215
Period size: 219 Copynumber: 3.5 Consensus size: 215
43780 TGAAGCAAAC
43790 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
43855 GATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
66 GATGATAAATCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
43920 TGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAATAATGCGATTTTCAAAATTTC
131 T-AAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTC
43985 ACAATTTATAAGTCCTTCGGG
195 ACAATTTATAAGTCCTTCGGG
*
44006 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
44071 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGGTGTTTTC-CATGAATTTGAAAA
66 GATGATAAATCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* *
44135 TAAAAAAAAATGATGATGTTTTAAGAAGATGGAATTTTTTAAAACGAAGAATGCGATTTTTAAAA
131 T---AAAAAA--ATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA
*
44200 TTTCACAATTTATAAGTCTTTCGGG
191 TTTCACAATTTATAAGTCCTTCGGG
*
44225 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * * *
44290 GATGATAAATCCTTTGGGCCGTCCATAAGACCTGCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAATCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
* * *
44355 TGAGAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAAGGAAGAATGCGA-TTTCAAAATTTCA
131 TAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
44419 CAATTTATAAGTCCTTCGGG
196 CAATTTATAAGTCCTTCGGG
* * * * * **
44439 CCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATTTGTGAGTCTCTCCAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
44504 GATGATAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTT
66 GATGATAAATCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
44553 GCACCAAGGT
Statistics
Matches: 506, Mismatches: 36, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
214 132 0.26
215 57 0.11
216 112 0.22
217 10 0.02
219 181 0.36
220 14 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (215 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAATCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAA
TAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCA
CAATTTATAAGTCCTTCGGG
Found at i:44494 original size:42 final size:41
Alignment explanation
Indices: 44425--44526 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
44415 TTCACAATTT
* * * * *
44425 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGTCATCAGTAAGTCTCTCCAGCAAGATG
* ** *
44466 TTTAAATCCTTCGGGTCATTTGTGAGTCTCTCCAGCAAGATG
1 -ATAAATCCTTCGGGTCATCAGTAAGTCTCTCCAGCAAGATG
44508 ATAAATCCTTCGGGTCATC
1 ATAAATCCTTCGGGTCATC
44527 CATAAGACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 17 0.35
42 32 0.65
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGTCTCTCCAGCAAGATG
Found at i:44753 original size:57 final size:55
Alignment explanation
Indices: 44597--44777 Score: 236
Period size: 55 Copynumber: 3.2 Consensus size: 55
44587 GACTTCTCAG
* * *
44597 AAGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTACACTCCCTGA
1 AAGAATAGGGAGCGAACCCGTTTTCTGAAGATTTCTTGAGTTCTATACTCCCTGA
* * * *
44652 AAGAATAGGGAGCGGACACGTTTGCTGAAGATTTCTCGAGTTCTATACTCCCTGA
1 AAGAATAGGGAGCGAACCCGTTTTCTGAAGATTTCTTGAGTTCTATACTCCCTGA
* * *
44707 AAGAAATAGGGAGCGAACCCATTTTTCTGAAGATTTATTGAATTCTATACTCCCTGAA
1 AAG-AATAGGGAGCGAACCC-GTTTTCTGAAGATTTCTTGAGTTCTATACTCCCTG-A
*
44765 AAGAATAAGGAGC
1 AAGAATAGGGAGC
44778 AAATACGCTG
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
55 51 0.47
56 14 0.13
57 39 0.36
58 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (55 bp):
AAGAATAGGGAGCGAACCCGTTTTCTGAAGATTTCTTGAGTTCTATACTCCCTGA
Found at i:44820 original size:113 final size:110
Alignment explanation
Indices: 44597--44833 Score: 269
Period size: 113 Copynumber: 2.1 Consensus size: 110
44587 GACTTCTCAG
* * *
44597 AAGAATAGGGAGCAAACCCGTTTTCAGAAGATTTCTTGAGTTCTACACTCCCTGAAAGAATAGGG
1 AAGAATAGGGAGCAAACCCGTTTTCAGAAGATTTATTGAATTCTACACTCCCTGAAAGAATAAGG
** * * ** * *
44662 AGCGGACACGTTTGCTGAAGATTTCTCGAGTTCTATACTCCCTGA
66 AGCAAACACGTCTGATGAAGATTAATCAAGTCCTATACTCCCTGA
* * * *
44707 AAGAAATAGGGAGCGAACCCATTTTTCTGAAGATTTATTGAATTCTATACTCCCTGAAAAGAATA
1 AAG-AATAGGGAGCAAACCC-GTTTTCAGAAGATTTATTGAATTCTACACTCCCTG-AAAGAATA
* *
44772 AGGAGCAAATACG-CTGATCGAAGATTAATCAAGTCCTATACTCTCTGA
63 AGGAGCAAACACGTCTGAT-GAAGATTAATCAAGTCCTATACTCCCTGA
*
44820 AAGAATAGGAAGCA
1 AAGAATAGGGAGCA
44834 TACATGTTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
110 3 0.03
111 15 0.14
112 42 0.40
113 44 0.42
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26
Consensus pattern (110 bp):
AAGAATAGGGAGCAAACCCGTTTTCAGAAGATTTATTGAATTCTACACTCCCTGAAAGAATAAGG
AGCAAACACGTCTGATGAAGATTAATCAAGTCCTATACTCCCTGA
Found at i:48525 original size:3 final size:3
Alignment explanation
Indices: 48517--48590 Score: 85
Period size: 3 Copynumber: 23.7 Consensus size: 3
48507 TATATTTATT
* *
48517 TAA TAA TAA TAA TAA TAAA TAA TTAA TAA TAA TGTA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA T-AA TAA TAA TAA TAA
* *
48565 TAA AAA TAA TAA AAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
48591 GTATGAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
3 53 0.87
4 8 0.13
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:51432 original size:19 final size:19
Alignment explanation
Indices: 51386--51433 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
51376 TATCACATGT
51386 AAAGTAAAAATAAATAATAA
1 AAAGT-AAAATAAATAATAA
* *
51406 AAACTAAAATAAGA-AATGA
1 AAAGTAAAATAA-ATAATAA
51425 AAAGTAAAA
1 AAAGTAAAA
51434 ATATGATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (19 bp):
AAAGTAAAATAAATAATAA
Found at i:56737 original size:2 final size:2
Alignment explanation
Indices: 56730--56754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56720 TAATTCAATG
56730 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 T
56755 TCCTTACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66309 original size:21 final size:22
Alignment explanation
Indices: 66283--66324 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
66273 TTAATTATTT
66283 ATTTTATTTATAATT-TTTTAA
1 ATTTTATTTATAATTATTTTAA
*
66304 ATTTTATTTATAGTTATTTTA
1 ATTTTATTTATAATTATTTTA
66325 TTTTAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTTATTTATAATTATTTTAA
Found at i:66320 original size:27 final size:26
Alignment explanation
Indices: 66269--66343 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 26
66259 AATTTACTTT
* *
66269 TTTTTTAATTATTTATTT-TATTTATAA
1 TTTTTTAAAT-TTTATTTATAGTTAT-A
*
66296 TTTTTTAAATTTTATTTATAGTTATT
1 TTTTTTAAATTTTATTTATAGTTATA
66322 TTATTTTAAAGTTTTATATTAT
1 TT-TTTTAAA-TTTTAT-TTAT
66344 TAAAATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 9 0.22
27 22 0.54
28 6 0.15
29 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTTTTAAATTTTATTTATAGTTATA
Found at i:72255 original size:30 final size:30
Alignment explanation
Indices: 72172--72272 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
72162 AATTCAGTGA
* *
72172 TCAAATTAATATTTTATCTAAAGTTTAAGAG
1 TCAAATTAATA-TTCATCTAAAATTTAAGAG
* * *
72203 TCAAAATAATATATCTTATAAAATTTAAGA-
1 TCAAATTAATAT-TCATCTAAAATTTAAGAG
* *
72233 TCAAATTAGTATTCCATCTAAAATTCAAGAG
1 TCAAATTAATATT-CATCTAAAATTTAAGAG
*
72264 TTAAATTAA
1 TCAAATTAA
72273 AAATTCATTC
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
29 1 0.02
30 24 0.44
31 30 0.55
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
TCAAATTAATATTCATCTAAAATTTAAGAG
Found at i:72858 original size:16 final size:17
Alignment explanation
Indices: 72825--72881 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
72815 GGATGGTATC
72825 ATTTTAGAATTTATATT
1 ATTTTAGAATTTATATT
72842 ATTTTAG-ATTTGA-ATT
1 ATTTTAGAATTT-ATATT
** *
72858 ATTTT-TTATTTATCTT
1 ATTTTAGAATTTATATT
72874 ATTTTAGA
1 ATTTTAGA
72882 CTTAAAATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 1 0.03
16 23 0.72
17 8 0.25
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (17 bp):
ATTTTAGAATTTATATT
Done.