Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001471.1 Hibiscus syriacus cultivar Beakdansim tig00002852_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: 68233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4379 original size:16 final size:16
Alignment explanation
Indices: 4358--4389 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4348 GAGGGATTAT
4358 CAGTGGTCCTTCAGGA
1 CAGTGGTCCTTCAGGA
*
4374 CAGTGGTCTTTCAGGA
1 CAGTGGTCCTTCAGGA
4390 TATAGTGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (16 bp):
CAGTGGTCCTTCAGGA
Found at i:4398 original size:18 final size:18
Alignment explanation
Indices: 4359--4417 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
4349 AGGGATTATC
*
4359 AGTGGTCCTTCAGGAC--
1 AGTGGTCATTCAGGACAT
* *
4375 AGTGGTCTTTCAGGATAT
1 AGTGGTCATTCAGGACAT
*
4393 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCAGGACAT
4411 AGTGGTC
1 AGTGGTC
4418 CTTTGGGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
16 14 0.39
18 22 0.61
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (18 bp):
AGTGGTCATTCAGGACAT
Found at i:6880 original size:17 final size:17
Alignment explanation
Indices: 6858--6892 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6848 CTATCAATAA
6858 TCATATTTTTAATAACT
1 TCATATTTTTAATAACT
6875 TCATATTTTTAATAACT
1 TCATATTTTTAATAACT
6892 T
1 T
6893 TTATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (17 bp):
TCATATTTTTAATAACT
Found at i:14078 original size:2 final size:2
Alignment explanation
Indices: 14071--14110 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
14061 ATAAGCCAAG
*
14071 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
14111 ACTGACATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17262 original size:22 final size:23
Alignment explanation
Indices: 17226--17268 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
17216 ATAAATAAAT
*
17226 CTCCCATTCTCCGATCTTTCTTC
1 CTCCCATTCCCCGATCTTTCTTC
17249 CTCCC-TTCCCCGATCTTTCT
1 CTCCCATTCCCCGATCTTTCT
17269 GGTTCTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.07, C:0.47, G:0.05, T:0.42
Consensus pattern (23 bp):
CTCCCATTCCCCGATCTTTCTTC
Found at i:19899 original size:31 final size:31
Alignment explanation
Indices: 19847--19905 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
19837 ATTATATGGT
* * *
19847 AAATTAGTTTAAATTTATGTTATTTTGTATG
1 AAATTAGTCTAAAGTTATGTTAATTTGTATG
19878 AAATTAGTCTAATAGTT-TGTTAATTTGT
1 AAATTAGTCTAA-AGTTATGTTAATTTGT
19906 TTTTTGCAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (31 bp):
AAATTAGTCTAAAGTTATGTTAATTTGTATG
Found at i:21987 original size:23 final size:27
Alignment explanation
Indices: 21944--22016 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
21934 GTATATATGG
* *
21944 ATATATTTGATTTTTTTATAATAAT-T
1 ATATATTTGATTTTATAATAATAATGT
*
21970 A-A-A-TTGATTTTATAATAATTTATGT
1 ATATATTTGATTTTATAATAA-TAATGT
21995 ATATATTTGATTTTATAATAAT
1 ATATATTTGATTTTATAATAAT
22017 TAACTTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 13 0.33
24 4 0.10
25 3 0.08
26 2 0.05
27 2 0.05
28 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
ATATATTTGATTTTATAATAATAATGT
Found at i:22056 original size:14 final size:15
Alignment explanation
Indices: 21980--22060 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 15
21970 AAATTGATTT
21980 TATAATAATTTA-TG
1 TATAATAATTTATTG
*
21994 TAT-AT-ATTTGATTT
1 TATAATAATTT-ATTG
* *
22008 TATAATAATTAACT-
1 TATAATAATTTATTG
* *
22022 TA-ATTAACTTTATTT
1 TATAATAA-TTTATTG
22037 TATAATAATTTA-TG
1 TATAATAATTTATTG
22051 TATAATAATT
1 TATAATAATT
22061 AACTTTATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
12 4 0.08
13 7 0.13
14 24 0.46
15 10 0.19
16 7 0.13
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (15 bp):
TATAATAATTTATTG
Found at i:22060 original size:34 final size:33
Alignment explanation
Indices: 21964--22087 Score: 133
Period size: 34 Copynumber: 4.0 Consensus size: 33
21954 TTTTTTTATA
*
21964 ATAATTAAATTGATTTTATAATAATTTATGTAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
21997 AT-A-T---TTGATTTTATAATAA-TTA---ACT
1 ATAATTAACTTGATTTTATAATAATTTATGTA-T
*
22022 -TAATTAACTTTATTTTATAATAATTTATGTAT
1 ATAATTAACTTGATTTTATAATAATTTATGTAT
*
22054 AATAATTAACTTTATTTTATAATAATTTATGTAT
1 -ATAATTAACTTGATTTTATAATAATTTATGTAT
22088 TTTTAGGAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 23
0.76 0.01 0.23
Matches are distributed among these distances:
24 2 0.03
25 2 0.03
26 1 0.01
27 3 0.04
28 15 0.19
29 14 0.18
30 3 0.04
31 1 0.01
32 2 0.03
33 3 0.04
34 32 0.41
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (33 bp):
ATAATTAACTTGATTTTATAATAATTTATGTAT
Found at i:22076 original size:20 final size:19
Alignment explanation
Indices: 22022--22080 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 19
22012 ATAATTAACT
22022 TAATTAACTTTATTT-T-A
1 TAATTAACTTTATTTATAA
*
22039 TAA-TAA-TTTATGTATAA
1 TAATTAACTTTATTTATAA
22056 TAATTAACTTTATTTTATAA
1 TAATTAACTTTA-TTTATAA
22076 TAATT
1 TAATT
22081 TATGTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 6 0.17
16 4 0.11
17 7 0.20
18 3 0.09
19 4 0.11
20 11 0.31
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTAACTTTATTTATAA
Found at i:22246 original size:29 final size:28
Alignment explanation
Indices: 22187--22264 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 28
22177 AAATAACAAT
* *
22187 AAAATATATATTTTATTGTTATTTATTA
1 AAAATATATATTTTATTCTTATTTAATA
*
22215 AAAATATA-ATTTTTTTCTTATTTAACATA
1 AAAATATATATTTTATTCTTATTT-A-ATA
22244 AAAATATATATTTTATCTCTT
1 AAAATATATATTTTAT-TCTT
22265 CTTAACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 13 0.31
28 9 0.21
29 10 0.24
30 6 0.14
31 4 0.10
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (28 bp):
AAAATATATATTTTATTCTTATTTAATA
Found at i:22270 original size:30 final size:29
Alignment explanation
Indices: 22187--22270 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
22177 AAATAACAAT
* * *
22187 AAAATATATATTTTATTGTTATTTA-TTA
1 AAAATATATATTTTATTCTTATTAACATA
*
22215 AAAATATA-ATTTTTTTCTTATTTAACATA
1 AAAATATATATTTTATTCTTA-TTAACATA
*
22244 AAAATATATATTTTATCTCTTCTTAAC
1 AAAATATATATTTTAT-TCTTATTAAC
22271 TTTTAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
27 10 0.22
28 11 0.24
29 10 0.22
30 11 0.24
31 4 0.09
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (29 bp):
AAAATATATATTTTATTCTTATTAACATA
Found at i:22420 original size:120 final size:122
Alignment explanation
Indices: 22253--22494 Score: 346
Period size: 120 Copynumber: 2.0 Consensus size: 122
22243 AAAAATATAT
* * *
22253 ATTTTATCTCTTCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTATG-TCACTTA
1 ATTTTATCTCATATTAACTTTTAAAATTTAATAAAATTCATATAATTACACATT-TGTTCACTTA
*
22317 TAC-TCTATCAATTTAGTCGTAATTTTAAACAA-TTAAAATTAATTTATGTATCTACC
65 TACTTCTATCAATTTAGTCGTAATTTTAAAAAATTTAAAATTAATTTATGTATCTACC
* * *
22373 ATTTTATCTCATATTAACTTTTTAAATTTAATAAAATTCATATAATTACATATTTGTTCTCTTAT
1 ATTTTATCTCATATTAACTTTTAAAATTTAATAAAATTCATATAATTACACATTTGTTCACTTAT
22438 ACTTTTATTCTATCAATTTAGTCGTAATTTTAAAAAATTTAAAATTAATTTATGTAT
66 AC-----TTCTATCAATTTAGTCGTAATTTTAAAAAATTTAAAATTAATTTATGTAT
22495 AATATTTTTT
Statistics
Matches: 107, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
119 2 0.02
120 58 0.54
126 28 0.26
127 19 0.18
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (122 bp):
ATTTTATCTCATATTAACTTTTAAAATTTAATAAAATTCATATAATTACACATTTGTTCACTTAT
ACTTCTATCAATTTAGTCGTAATTTTAAAAAATTTAAAATTAATTTATGTATCTACC
Found at i:28934 original size:5 final size:5
Alignment explanation
Indices: 28908--28952 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
28898 ATAAATTAAG
*
28908 AAATA AAATT -AATT -AATT -AATT AAATT AAA-T AAATT AAATT AAAT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAAT
28953 AGTAGTAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
4 16 0.43
5 21 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:28936 original size:9 final size:9
Alignment explanation
Indices: 28913--28952 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
28903 TTAAGAAATA
28913 AAATTAATT
1 AAATTAATT
28922 -AATTAATT
1 AAATTAATT
*
28930 AAATTAAAT
1 AAATTAATT
28939 AAATTAAATT
1 AAATT-AATT
28949 AAAT
1 AAAT
28953 AGTAGTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 8 0.30
9 12 0.44
10 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATTAATT
Found at i:28945 original size:14 final size:14
Alignment explanation
Indices: 28908--28953 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
28898 ATAAATTAAG
28908 AAATAAAATT-AATT
1 AAAT-AAATTAAATT
*
28922 -AATTAATTAAATT
1 AAATAAATTAAATT
28935 AAATAAATTAAATT
1 AAATAAATTAAATT
28949 AAATA
1 AAATA
28954 GTAGTAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 4 0.14
13 7 0.25
14 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTAAATT
Found at i:28977 original size:5 final size:5
Alignment explanation
Indices: 28967--28995 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28957 GTAGTTTTAG
28967 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
28996 AAATATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:29001 original size:15 final size:15
Alignment explanation
Indices: 28968--29001 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28958 TAGTTTTAGT
**
28968 ATATTATATTATATT
1 ATATTATATTATAAA
28983 ATATTATATTATAAA
1 ATATTATATTATAAA
28998 ATAT
1 ATAT
29002 ACATTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATATTATAAA
Found at i:29985 original size:20 final size:21
Alignment explanation
Indices: 29957--30008 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
29947 AATAAACATT
*
29957 AATATTTATAATA-TTTAATA
1 AATAATTATAATATTTTAATA
*
29977 AATAATTATAATATTTTATTA
1 AATAATTATAATATTTTAATA
*
29998 AATAATAATAA
1 AATAATTATAA
30009 CACCATCGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATTATAATATTTTAATA
Found at i:30134 original size:17 final size:16
Alignment explanation
Indices: 30095--30134 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
30085 AATCTTTAGA
*
30095 AAAATTTAATAACATT
1 AAAATTTAATAACAAT
30111 AATAATTTAATAACACAT
1 AA-AATTTAATAACA-AT
30129 AAAATT
1 AAAATT
30135 GTTGCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTTAATAACAAT
Found at i:30711 original size:10 final size:10
Alignment explanation
Indices: 30686--30727 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
30676 GACTTTAACT
30686 TTCTTCTCTTC
1 TTCTT-TCTTC
30697 TTCTTTCTTC
1 TTCTTTCTTC
*
30707 CTCTTT-TGTC
1 TTCTTTCT-TC
30717 TTCTTTCTTC
1 TTCTTTCTTC
30727 T
1 T
30728 CCCCTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.04
10 20 0.74
11 6 0.22
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:31162 original size:16 final size:16
Alignment explanation
Indices: 31141--31176 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31131 TTTCGATACA
31141 AAGGGAAAACGCTGGG
1 AAGGGAAAACGCTGGG
*
31157 AAGGGAAGACGCTGGG
1 AAGGGAAAACGCTGGG
31173 AAGG
1 AAGG
31177 CACGATGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.47, T:0.06
Consensus pattern (16 bp):
AAGGGAAAACGCTGGG
Found at i:31692 original size:17 final size:18
Alignment explanation
Indices: 31672--31711 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
31662 ATTTTAATAG
31672 AAAATATATAA-AAATTT
1 AAAATATATAATAAATTT
*
31689 AAAATATATAATAATTTT
1 AAAATATATAATAAATTT
31707 AAAAT
1 AAAAT
31712 TTGATATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATATAATAAATTT
Found at i:34012 original size:15 final size:16
Alignment explanation
Indices: 33992--34030 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
33982 AATGTCATTT
33992 AAAATAATTTT-AAGA
1 AAAATAATTTTAAAGA
34007 AAAATAATTTTAAAGA
1 AAAATAATTTTAAAGA
34023 AAAA-AATT
1 AAAATAATT
34031 GGTCAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (16 bp):
AAAATAATTTTAAAGA
Found at i:37085 original size:3 final size:3
Alignment explanation
Indices: 37077--37143 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
37067 AAGGAAAACT
37077 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * *
37123 ATA TTA ATA TTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA
37144 TTAAATACCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:38852 original size:25 final size:24
Alignment explanation
Indices: 38809--38913 Score: 101
Period size: 24 Copynumber: 4.4 Consensus size: 24
38799 TTTCAAAAGG
* *
38809 TGAAAAAGTTTAATG-AAGAAGTTT
1 TGAAAATGTTTGATGAAAGAA-TTT
* *
38833 TGAAAATGTTTTATGAAAGATTTT
1 TGAAAATGTTTGATGAAAGAATTT
* *
38857 TGAAAACGTTTGAAGAAAGAATTT
1 TGAAAATGTTTGATGAAAGAATTT
38881 TGAAAAATGTTTGATG-AAG--TTT
1 TG-AAAATGTTTGATGAAAGAATTT
38903 TGAAAAATGTT
1 TG-AAAATGTT
38914 ACCCCTTACT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.20
24 41 0.59
25 15 0.21
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.37
Consensus pattern (24 bp):
TGAAAATGTTTGATGAAAGAATTT
Found at i:38861 original size:48 final size:46
Alignment explanation
Indices: 38809--38909 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 46
38799 TTTCAAAAGG
*
38809 TGAAAAAGTTT-AATG-AAGAAGTTTTG-AAAATGTTTTATGAAAGATTTT
1 TGAAAAAGTTTGAA-GAAAGAA-TTTTGAAAAATGTTTGATG-AAG--TTT
*
38857 TGAAAACGTTTGAAGAAAGAATTTTGAAAAATGTTTGATGAAGTTT
1 TGAAAAAGTTTGAAGAAAGAATTTTGAAAAATGTTTGATGAAGTTT
38903 TGAAAAA
1 TGAAAAA
38910 TGTTACCCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
46 9 0.19
48 19 0.40
49 19 0.40
ACGTcount: A:0.44, C:0.01, G:0.20, T:0.36
Consensus pattern (46 bp):
TGAAAAAGTTTGAAGAAAGAATTTTGAAAAATGTTTGATGAAGTTT
Found at i:39594 original size:107 final size:107
Alignment explanation
Indices: 39418--39613 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 107
39408 TTTGTTTGGC
** * * *
39418 TAGCTGAAGGAATCTATCTATAAAGCTAAGACTTTTAACCAATTACTTTAGAAGAATAACTCAGT
1 TAGCTGAAAAAATCTATCAATAAAGCTAAGACTTTTAACCAATTACTTTAGAAGAACAACTCAGA
39483 TTTATTGTATATATACATATATATTATTTGCTTTTACGTGGA
66 TTTATTGTATATATACATATATATTATTTGCTTTTACGTGGA
* * * * ** *
39525 TAGCTGAAAAAATCTATCAATAAAGCTAGGGCTTTTAACCAATTGCTTTAGAGGAACAGTTTAGA
1 TAGCTGAAAAAATCTATCAATAAAGCTAAGACTTTTAACCAATTACTTTAGAAGAACAACTCAGA
*
39590 TTTATTGTATATATATATATATAT
66 TTTATTGTATATATACATATATAT
39614 ATATATATAT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
107 76 1.00
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (107 bp):
TAGCTGAAAAAATCTATCAATAAAGCTAAGACTTTTAACCAATTACTTTAGAAGAACAACTCAGA
TTTATTGTATATATACATATATATTATTTGCTTTTACGTGGA
Found at i:39604 original size:2 final size:2
Alignment explanation
Indices: 39597--39672 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
39587 AGATTTATTG
39597 TA TA TA TA TA TA 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 TA TA TA TA TA TA
39639 TA TA 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 TA TA
39673 ATTACATTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43934 original size:2 final size:2
Alignment explanation
Indices: 43927--43951 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43917 ATTTTTGAAT
43927 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
43952 TAAATATAAC
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:47738 original size:18 final size:19
Alignment explanation
Indices: 47715--47764 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 19
47705 ATGCTTTAAA
47715 CTTAACTTTCTAACA-CAT
1 CTTAACTTTCTAACATCAT
*
47733 CTTAACTTTC---CATGAT
1 CTTAACTTTCTAACATCAT
47749 CTTAACTTTCTAACAT
1 CTTAACTTTCTAACAT
47765 GCTTATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
18 10 0.37
19 3 0.11
ACGTcount: A:0.30, C:0.26, G:0.02, T:0.42
Consensus pattern (19 bp):
CTTAACTTTCTAACATCAT
Found at i:50176 original size:20 final size:20
Alignment explanation
Indices: 50140--50178 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50130 GAAGAACAAG
*
50140 TATCGATATTATCCCTATAT
1 TATCGATATTATACCTATAT
50160 TATCGATACTT-TACCTATA
1 TATCGATA-TTATACCTATA
50179 AAAGTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (20 bp):
TATCGATATTATACCTATAT
Found at i:51209 original size:17 final size:17
Alignment explanation
Indices: 51183--51221 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
51173 TCAGTGCCAC
* *
51183 ACTAACAACAGAATCAT
1 ACTAACAACAAAACCAT
*
51200 ACTAATAACAAAACCAT
1 ACTAACAACAAAACCAT
51217 ACTAA
1 ACTAA
51222 AAGTTTTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.23, G:0.03, T:0.18
Consensus pattern (17 bp):
ACTAACAACAAAACCAT
Found at i:59536 original size:17 final size:17
Alignment explanation
Indices: 59516--59555 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
59506 TTAATTAATT
59516 AAACTAGTTCATTCATC
1 AAACTAGTTCATTCATC
* *
59533 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
59550 AAACTA
1 AAACTA
59556 ACTCTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:61112 original size:14 final size:14
Alignment explanation
Indices: 61093--61131 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
61083 CCCAGGTTAG
61093 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
61107 TAAAAAAAT-AAAA
1 TAAAAAAATAAAAA
61120 -AAAAAAATAAAA
1 TAAAAAAATAAAA
61132 GGAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 7 0.29
14 9 0.38
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:61137 original size:14 final size:12
Alignment explanation
Indices: 61094--61146 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 12
61084 CCAGGTTAGT
61094 AAAAAAATAAAAA
1 AAAAAAAT-AAAA
61107 TAAAAAAATAAAA
1 -AAAAAAATAAAA
61120 AAAAAAATAAAA
1 AAAAAAATAAAA
*
61132 GGAAAAAATAGAAA
1 -AAAAAAATA-AAA
61146 A
1 A
61147 TTTTAAAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 12 0.34
13 12 0.34
14 11 0.31
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAAAATAAAA
Found at i:61146 original size:20 final size:18
Alignment explanation
Indices: 61094--61147 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
61084 CCAGGTTAGT
61094 AAAAAAATAAAAATAAAAA
1 AAAAAAATAAAAAT-AAAA
*
61113 AATAAAAAAAAAAATAAAA
1 AA-AAAAATAAAAATAAAA
*
61132 GGAAAAAATAGAAAAT
1 -AAAAAAATA-AAAAT
61148 TTTAAAGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAAAATAAAAATAAAA
Found at i:63328 original size:17 final size:17
Alignment explanation
Indices: 63250--63333 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 17
63240 CATATTTAGA
* * *
63250 TCATTTAGTAAGCTACT
1 TCATTTATTAAACTAGT
* * *
63267 TCATTCATTCATCTAGT
1 TCATTTATTAAACTAGT
* * *
63284 TCATTGAATAAAGTTAGT
1 TCATTTATTAAA-CTAGT
* *
63302 TAATTAATTAAACTAGT
1 TCATTTATTAAACTAGT
63319 TCATTTATTAAACTA
1 TCATTTATTAAACTA
63334 ACTCTTAATT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
17 37 0.74
18 13 0.26
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (17 bp):
TCATTTATTAAACTAGT
Done.