Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003895.1 Hibiscus syriacus cultivar Beakdansim tig00008417_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: 71404
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3973 original size:28 final size:28
Alignment explanation
Indices: 3913--3985 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
3903 GAGTTTATGC
* *
3913 TTTTTTGGGATTTTTAGGAATTTAGGAG
1 TTTTTTGAGATTTTTAGGAATTTAAGAG
*
3941 TTTTTTGAGATTTTCT-GGAATTTAAGATA
1 TTTTTTGAGATTTT-TAGGAATTTAAGA-G
* *
3970 TTTTTTGGGAATTTTA
1 TTTTTTGAGATTTTTA
3986 ATAATTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 24 0.65
29 13 0.35
ACGTcount: A:0.23, C:0.01, G:0.22, T:0.53
Consensus pattern (28 bp):
TTTTTTGAGATTTTTAGGAATTTAAGAG
Found at i:4115 original size:27 final size:26
Alignment explanation
Indices: 4069--4126 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
4059 GATTTTATAT
*
4069 TTTTTGAGATTTTTAAAAATTTAGGAG
1 TTTTTGAGATTTTTAAAAATTTAAG-G
*
4096 TTTTTGAGATTTTCT-GAAATTTAAGG
1 TTTTTGAGATTTT-TAAAAATTTAAGG
4122 TTTTT
1 TTTTT
4127 TTTTAGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 21 0.75
28 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (26 bp):
TTTTTGAGATTTTTAAAAATTTAAGG
Found at i:4127 original size:27 final size:27
Alignment explanation
Indices: 4067--4158 Score: 78
Period size: 29 Copynumber: 3.3 Consensus size: 27
4057 ACGATTTTAT
4067 ATTTTTTGAGATTTTTAAAAATTTAGG
1 ATTTTTTGAGATTTTTAAAAATTTAGG
* *
4094 AGTTTTTGAGATTTTCT-GAAATTTAAGG
1 ATTTTTTGAGATTTT-TAAAAATTT-AGG
* * * *
4122 TTTTTTTTTAGAATTTTAATAATTTCATGG
1 -ATTTTTTGAGATTTTTAAAAATTT-A-GG
4152 ATTTTTT
1 ATTTTTT
4159 AGAAAGTAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
27 20 0.40
28 5 0.10
29 23 0.46
30 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.55
Consensus pattern (27 bp):
ATTTTTTGAGATTTTTAAAAATTTAGG
Found at i:4140 original size:154 final size:157
Alignment explanation
Indices: 3854--4148 Score: 445
Period size: 154 Copynumber: 1.9 Consensus size: 157
3844 TCAAAAAATT
* * *
3854 ATAAACTCCCTAAAAAATGAATCTTATGATTTTTAGGGATTATGATTTAGAGTTTATGCTTTTTT
1 ATAAACTCCCTAAAAAATGAATCTTATGATTTTTAGAGATTACGATTTAGAGTTTATGATTTTTT
* ** * *
3919 GGGATTTTTAGGAATTTAGGAGTTTTTTGAGATTTTCTGGAATTTAAGATATTTTTTGGGAATTT
66 GAGATTTTTAAAAATTTAGGAGTTTTTTGAGATTTTCTGAAATTTAAGATATTTTTTGAGAATTT
3984 TAATAATTTCAAGGGGTTTTTTTAGAA
131 TAATAATTTCAAGGGGTTTTTTTAGAA
*
4011 ATAAACTCCCT-AAAAATGAATCTTATGATTTTTAGAGATTACGA-TTACGATTTTAT-ATTTTT
1 ATAAACTCCCTAAAAAATGAATCTTATGATTTTTAGAGATTACGATTTA-GAGTTTATGATTTTT
* * *
4073 TGAGATTTTTAAAAATTTAGGAG-TTTTTGAGATTTTCTGAAATTTAAGGTTTTTTTTTAGAATT
65 TGAGATTTTTAAAAATTTAGGAGTTTTTTGAGATTTTCTGAAATTTAAGATATTTTTTGAGAATT
4137 TTAATAATTTCA
130 TTAATAATTTCA
4149 TGGATTTTTT
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
154 48 0.38
155 28 0.22
156 38 0.30
157 11 0.09
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (157 bp):
ATAAACTCCCTAAAAAATGAATCTTATGATTTTTAGAGATTACGATTTAGAGTTTATGATTTTTT
GAGATTTTTAAAAATTTAGGAGTTTTTTGAGATTTTCTGAAATTTAAGATATTTTTTGAGAATTT
TAATAATTTCAAGGGGTTTTTTTAGAA
Found at i:10324 original size:15 final size:16
Alignment explanation
Indices: 10304--10338 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
10294 TCTCAAATTC
10304 AAATAAAAT-ATAATA
1 AAATAAAATCATAATA
*
10319 AAATAAAATCATATTA
1 AAATAAAATCATAATA
10335 AAAT
1 AAAT
10339 TCGTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAATCATAATA
Found at i:16789 original size:3 final size:3
Alignment explanation
Indices: 16781--16809 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16771 TTAATCTTAT
16781 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16810 TGGTTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20217 original size:2 final size:2
Alignment explanation
Indices: 20212--20242 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20202 TAAGTGTGTG
20212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20243 GCATGAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30518 original size:28 final size:28
Alignment explanation
Indices: 30453--30519 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
30443 AATAACATAA
* *
30453 TGTAAATTTAAAATTACATTTTGATCCC
1 TGTAAATTAAAAATTACATTTTGACCCC
* *
30481 T-AAAGTATTAAAAATTGCATTTTGACCCC
1 TGTAA--ATTAAAAATTACATTTTGACCCC
30510 TGTAAATTAA
1 TGTAAATTAA
30520 CTTTTATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 21 0.68
30 2 0.06
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (28 bp):
TGTAAATTAAAAATTACATTTTGACCCC
Found at i:33432 original size:2 final size:2
Alignment explanation
Indices: 33425--33481 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
33415 AAAATACACA
33425 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33467 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
33482 AACTAGTTGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33732 original size:39 final size:39
Alignment explanation
Indices: 33647--33887 Score: 204
Period size: 39 Copynumber: 5.9 Consensus size: 39
33637 TTTGATTCAA
* *
33647 ATATTAACACTTGAATATAGCT-GAAAAAGAGAAGAAGAAG
1 ATATAAACACTTGAATATAGCTAG-AAGA-AGAAGAAGAAG
*
33687 ACATAAACACTTGAATATAGCTAGAAGAAGAAGAAGAAG
1 ATATAAACACTTGAATATAGCTAGAAGAAGAAGAAGAAG
* * * *
33726 ATATAAACAATTGAATACAGTTAGAGGAAGAAGAAGAAG
1 ATATAAACACTTGAATATAGCTAGAAGAAGAAGAAGAAG
* **
33765 ATATAAACACTTGCATGTATCTAGAAGAAGAAGAAGAAGAAGAAGAAGAAG
1 ATATAAACACTTG-A---A--T---A-TAG--CTAGAAGAAGAAGAAGAAG
*
33816 ATATAAACACTTGAATATAGCTAGAAGAACAAG-AG--G
1 ATATAAACACTTGAATATAGCTAGAAGAAGAAGAAGAAG
* *
33852 ATACAAACACTTGAATATAGCT-GACGAAGAAGAAGA
1 ATATAAACACTTGAATATAGCTAGAAGAAGAAGAAGA
33888 GCTCACGCCA
Statistics
Matches: 166, Mismatches: 20, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
35 8 0.05
36 24 0.14
38 2 0.01
39 67 0.40
40 24 0.14
41 3 0.02
42 1 0.01
43 1 0.01
45 2 0.01
47 1 0.01
48 1 0.01
49 2 0.01
50 1 0.01
51 29 0.17
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.17
Consensus pattern (39 bp):
ATATAAACACTTGAATATAGCTAGAAGAAGAAGAAGAAG
Found at i:33795 original size:3 final size:3
Alignment explanation
Indices: 33787--33816 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
33777 GCATGTATCT
33787 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
33817 TATAAACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:33811 original size:51 final size:51
Alignment explanation
Indices: 33752--33849 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
33742 ACAGTTAGAG
* * * *
33752 GAAGAAGAAGAAGATATAAACACTTGCATGTATCTAGAAGAAGAAGAAGAA
1 GAAGAAGAAGAAGATATAAACACTTGAATATAGCTAGAAGAACAAGAAGAA
33803 GAAGAAGAAGAAGATATAAACACTTGAATATAGCTAGAAGAACAAGA
1 GAAGAAGAAGAAGATATAAACACTTGAATATAGCTAGAAGAACAAGA
33850 GGATACAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.15
Consensus pattern (51 bp):
GAAGAAGAAGAAGATATAAACACTTGAATATAGCTAGAAGAACAAGAAGAA
Found at i:33860 original size:36 final size:37
Alignment explanation
Indices: 33802--33888 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 37
33792 AAGAAGAAGA
* *
33802 AGAAGAAGAAGAAGATATAAACACTTGAATATAGCT-
1 AGAAGAAGAAGAGGATACAAACACTTGAATATAGCTG
*
33838 AGAAGAACAAGAGGATACAAACACTTGAATATAGCTG
1 AGAAGAAGAAGAGGATACAAACACTTGAATATAGCTG
33875 ACGAAGAAGAAGAG
1 A-GAAGAAGAAGAG
33889 CTCACGCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 33 0.73
37 1 0.02
38 11 0.24
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (37 bp):
AGAAGAAGAAGAGGATACAAACACTTGAATATAGCTG
Found at i:41056 original size:52 final size:52
Alignment explanation
Indices: 40978--41080 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
40968 TTATAATATT
40978 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
41030 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
41081 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:44256 original size:18 final size:17
Alignment explanation
Indices: 44219--44257 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
44209 CAAAGAACAA
* *
44219 AATATTATTTTATATTT
1 AATATTATTTTACATAT
44236 AATATTATATTTACATAT
1 AATATTAT-TTTACATAT
44254 AATA
1 AATA
44258 GGTATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTATTTTACATAT
Found at i:44331 original size:16 final size:17
Alignment explanation
Indices: 44295--44332 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
44285 TATAAATTTG
*
44295 TTTAATTTTAATTTAATA
1 TTTAATTTT-ATTTAACA
44313 TTTAATTTT-TTTAACA
1 TTTAATTTTATTTAACA
44329 TTTA
1 TTTA
44333 TAGATTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTAATTTTATTTAACA
Found at i:46813 original size:12 final size:12
Alignment explanation
Indices: 46796--46820 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46786 ATAATCATCA
46796 TTTTATTTTATT
1 TTTTATTTTATT
46808 TTTTATTTTATT
1 TTTTATTTTATT
46820 T
1 T
46821 ATTCCTTAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:50892 original size:35 final size:35
Alignment explanation
Indices: 50845--50930 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
50835 AAAACAGTCA
* * *
50845 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
50880 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
50915 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
50931 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:50924 original size:21 final size:21
Alignment explanation
Indices: 50899--50941 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
50889 TTCTAAACCC
50899 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
50920 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
50941 T
1 T
50942 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:51099 original size:14 final size:16
Alignment explanation
Indices: 51063--51099 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
51053 TATTAATGTA
51063 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
51080 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
51095 T-AATA
1 TGAATA
51100 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:51766 original size:130 final size:130
Alignment explanation
Indices: 51563--51810 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
51553 AATTTTCTTC
* * *
51563 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
51628 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTATGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
51693 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
51758 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
51811 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:57145 original size:28 final size:30
Alignment explanation
Indices: 57088--57145 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
57078 ATGTTGGTCA
*
57088 GAATAGACTGAACTTGGGCTGTAACAGATG
1 GAATAGACTGAACTTGGACTGTAACAGATG
*
57118 GAATAGACTGAA-TT-TACTGTAACAGATG
1 GAATAGACTGAACTTGGACTGTAACAGATG
57146 AATTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.46
29 2 0.08
30 12 0.46
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (30 bp):
GAATAGACTGAACTTGGACTGTAACAGATG
Found at i:60339 original size:20 final size:20
Alignment explanation
Indices: 60314--60351 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
60304 ATCTTATTCC
*
60314 CTGGTAATCTTACATTCCCA
1 CTGGTAATCATACATTCCCA
60334 CTGGTAATCATACATTCC
1 CTGGTAATCATACATTCC
60352 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (20 bp):
CTGGTAATCATACATTCCCA
Found at i:61957 original size:19 final size:18
Alignment explanation
Indices: 61929--61974 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
61919 GGTCCTTGTA
61929 TTTATGTTTATTTTATTT
1 TTTATGTTTATTTTATTT
61947 TTTACTGTTTATTTTATTT
1 TTTA-TGTTTATTTTATTT
*
61966 GTTAT-TTTA
1 TTTATGTTTA
61975 ATTAAGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 17 0.65
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTATGTTTATTTTATTT
Found at i:63309 original size:25 final size:26
Alignment explanation
Indices: 63275--63327 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
63265 ATTTTAAATA
63275 AGGATGCAACTCAAAAAG-AAGCATC
1 AGGATGCAACTCAAAAAGAAAGCATC
63300 AGGATGCAACTCAAAAAGAAAGCATC
1 AGGATGCAACTCAAAAAGAAAGCATC
63326 AG
1 AG
63328 TCTCGTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (26 bp):
AGGATGCAACTCAAAAAGAAAGCATC
Found at i:64757 original size:24 final size:24
Alignment explanation
Indices: 64730--64778 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
64720 TTGCCACCTT
64730 CTCCTCCTAAGCAACAATCACCAC
1 CTCCTCCTAAGCAACAATCACCAC
* * * *
64754 CTCCTCTTGAGTAAGAATCACCAC
1 CTCCTCCTAAGCAACAATCACCAC
64778 C
1 C
64779 GACATCATCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.41, G:0.08, T:0.20
Consensus pattern (24 bp):
CTCCTCCTAAGCAACAATCACCAC
Found at i:66091 original size:22 final size:22
Alignment explanation
Indices: 66065--66124 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
66055 CCTATAAAAG
*
66065 AATGAACAGTACTGTGTACAAC
1 AATGAACAGTACCGTGTACAAC
**
66087 AATGAACAGTACCGTGTACAGT
1 AATGAACAGTACCGTGTACAAC
* *
66109 ATTAAACAGTACCGTG
1 AATGAACAGTACCGTG
66125 AATAGTACCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (22 bp):
AATGAACAGTACCGTGTACAAC
Found at i:70168 original size:20 final size:20
Alignment explanation
Indices: 70131--70169 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70121 AGATTGAGTG
* * *
70131 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
70151 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
70170 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:70316 original size:20 final size:20
Alignment explanation
Indices: 70291--70330 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
70281 GAGGATTTTG
*
70291 AAGGGGGAATCGGTTCCCTC
1 AAGGGGGAATCGATTCCCTC
*
70311 AAGGGGGGATCGATTCCCTC
1 AAGGGGGAATCGATTCCCTC
70331 TGCACCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCTC
Done.