Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004260.1 Hibiscus syriacus cultivar Beakdansim tig00009335_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: 57544
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Found at i:2388 original size:22 final size:22
Alignment explanation
Indices: 2363--2408 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2353 ATAAAATACT
*
2363 AAAAATAAAAAAATTTACTAAA
1 AAAAATAAAAAAATATACTAAA
* * *
2385 AAAATTAAATATATATACTAAA
1 AAAAATAAAAAAATATACTAAA
2407 AA
1 AA
2409 TACTATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAATAAAAAAATATACTAAA
Found at i:2498 original size:20 final size:20
Alignment explanation
Indices: 2473--2529 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2463 CTATAACTTA
2473 TTAAAAAAT-TAAATATATTT
1 TTAAAAAATAT-AATATATTT
*
2493 TTAAAATATATAATATATTT
1 TTAAAAAATATAATATATTT
*
2513 TTAAAATATATAATATA
1 TTAAAAAATATAATATA
2530 CATAATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 34 0.97
21 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAAAATATAATATATTT
Found at i:2508 original size:18 final size:20
Alignment explanation
Indices: 2484--2529 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2474 TAAAAAATTA
2484 AATATATTTTTAAAATATAT
1 AATATATTTTTAAAATATAT
2504 AATATATTTTTAAAATATAT
1 AATATATTTTTAAAATATAT
2524 AATATA
1 AATATA
2530 CATAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATATTTTTAAAATATAT
Found at i:3007 original size:29 final size:29
Alignment explanation
Indices: 2975--3043 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
2965 TTCTTAATGG
2975 TAATTTTAAATATAATATTTTAA-TAATTT
1 TAATTTTAAATATAA-ATTTTAATTAATTT
* *
3004 TAA-TTTAATTTATAAATTTTAATTTATTT
1 TAATTTTAA-ATATAAATTTTAATTAATTT
3033 T--TTTTAAATAT
1 TAATTTTAAATAT
3044 GTGAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 3 0.09
28 17 0.50
29 14 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TAATTTTAAATATAAATTTTAATTAATTT
Found at i:3084 original size:15 final size:15
Alignment explanation
Indices: 3047--3075 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3037 TAAATATGTG
3047 AATATTTATATTTTA
1 AATATTTATATTTTA
3062 AATATTTATATTTT
1 AATATTTATATTTT
3076 TTAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATATTTATATTTTA
Found at i:3230 original size:21 final size:21
Alignment explanation
Indices: 3204--3261 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
3194 TAAGAATCAC
3204 CACATCAATATCATAAAATGT
1 CACATCAATATCATAAAATGT
*
3225 CACATCAATATCATAAACTGT
1 CACATCAATATCATAAAATGT
3246 CACATCAATATCATAA
1 CACATCAATATCATAA
3262 TAGTCAACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (21 bp):
CACATCAATATCATAAAATGT
Found at i:5343 original size:18 final size:18
Alignment explanation
Indices: 5318--5378 Score: 74
Period size: 17 Copynumber: 3.5 Consensus size: 18
5308 ATTAATTTTG
5318 TTTT-ATTAAATAATATA
1 TTTTGATTAAATAATATA
*
5335 TTTTGATT--ATAATTATT
1 TTTTGATTAAATAA-TATA
*
5352 TTTTTATTAAATAATATA
1 TTTTGATTAAATAATATA
5370 TTTTGATTA
1 TTTTGATTA
5379 TAATTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 4 0.11
17 14 0.39
18 14 0.39
19 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTGATTAAATAATATA
Found at i:5357 original size:35 final size:35
Alignment explanation
Indices: 5310--5393 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
5300 GCGTGCCAAT
5310 TAATT-TTGTTTTATTAAATAATATATTTTGATTA
1 TAATTATTGTTTTATTAAATAATATATTTTGATTA
*
5344 TAATTATTTTTTTATTAAATAATATATTTTGATTA
1 TAATTATTGTTTTATTAAATAATATATTTTGATTA
5379 TAATTATTGTTTTAT
1 TAATTATTGTTTTAT
5394 CATCTCATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 5 0.11
35 42 0.89
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (35 bp):
TAATTATTGTTTTATTAAATAATATATTTTGATTA
Found at i:5391 original size:18 final size:18
Alignment explanation
Indices: 5333--5391 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
5323 TTAAATAATA
5333 TATTTTGATTATAATTAT
1 TATTTTGATTATAATTAT
* *
5351 T-TTTTTATTA-AATAAT
1 TATTTTGATTATAATTAT
5367 ATATTTTGATTATAATTAT
1 -TATTTTGATTATAATTAT
*
5386 TGTTTT
1 TATTTT
5392 ATCATCTCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 5 0.15
17 9 0.27
18 14 0.42
19 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TATTTTGATTATAATTAT
Found at i:6001 original size:14 final size:15
Alignment explanation
Indices: 5970--6002 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5960 TTAATCATGA
5970 TATTGTTCATGATAT
1 TATTGTTCATGATAT
*
5985 TATTGTT-ATGGTAT
1 TATTGTTCATGATAT
5999 TATT
1 TATT
6003 ACCATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (15 bp):
TATTGTTCATGATAT
Found at i:6316 original size:45 final size:44
Alignment explanation
Indices: 6201--6320 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 44
6191 TTAATCAAAG
* * * *
6201 TCTTTTGATTATTGTGTTGCCAAAAGTAAAATCAAAGGATTAGTT
1 TCTTTTGATTATTGGGTTG-GAAAATTAAAATCAAAAGATTAGTT
* * * *
6246 CCTTTCGATTATTGGATTGCGAAAATTAAAATTAAAAGATTAGTT
1 TCTTTTGATTATTGGGTTG-GAAAATTAAAATCAAAAGATTAGTT
6291 TCTTTTGATTATTGGGTTGGTAAAATTAAA
1 TCTTTTGATTATTGGGTTGG-AAAATTAAA
6321 GGATTAATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.02
45 62 0.98
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (44 bp):
TCTTTTGATTATTGGGTTGGAAAATTAAAATCAAAAGATTAGTT
Found at i:6326 original size:39 final size:40
Alignment explanation
Indices: 6226--6338 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 40
6216 GTTGCCAAAA
* *
6226 GTAAAATCAAAGGATTAGTTCCTTTCGATTATTGGATTGC
1 GTAAAATTAAAGGATTAGTTCCTTTTGATTATTGGATTGC
* * *
6266 GAAAATTAAAATTAAAAGATTAGTTTCTTTTGATTATTGGGTTG-
1 G-----TAAAATTAAAGGATTAGTTCCTTTTGATTATTGGATTGC
*
6310 GTAAAATTAAAGGATTAATTCCTTTTGAT
1 GTAAAATTAAAGGATTAGTTCCTTTTGAT
6339 ATGTTTGTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
39 25 0.42
40 1 0.02
44 1 0.02
45 33 0.55
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.41
Consensus pattern (40 bp):
GTAAAATTAAAGGATTAGTTCCTTTTGATTATTGGATTGC
Found at i:6541 original size:58 final size:58
Alignment explanation
Indices: 6467--6763 Score: 332
Period size: 58 Copynumber: 5.1 Consensus size: 58
6457 AATATTGCAT
* * * *
6467 TGATCCTAACATTGTAAGGAAAATAGATTGTTGAATTTATATCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
*** *
6525 TGATTCTAACTTTGTAAGG-AAATTGGTTGTTGAATTTATATCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
*
6582 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTG-GATATCTTGAA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGA-ATCTTAAA
* * * ** * **
6640 TGATTTTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTATTGAAAAT-TGTGGA
1 TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCT-TAAA
* * ** * *
6698 TGATTCTATCCTT-TAAAAAGAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGGA-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
6756 TGATTCTA
1 TGATTCTA
6764 TTTTGTTAAA
Statistics
Matches: 207, Mismatches: 26, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
57 63 0.30
58 142 0.69
59 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
Found at i:6754 original size:23 final size:23
Alignment explanation
Indices: 6728--6801 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 23
6718 AAATAAATTG
6728 TTAAATTTATTTTCTTGAGAATC
1 TTAAATTTATTTTCTTGAGAATC
* **
6751 TTAAATGATTCTATTTTGTT-A-AAGGG
1 TT-AA--ATT-TATTTTCTTGAGAA-TC
6777 TTAAATTTATTTTCTTGAGAATC
1 TTAAATTTATTTTCTTGAGAATC
6800 TT
1 TT
6802 GAATGAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 4 0.11
25 4 0.11
26 6 0.16
27 8 0.21
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (23 bp):
TTAAATTTATTTTCTTGAGAATC
Found at i:6915 original size:39 final size:39
Alignment explanation
Indices: 6845--6959 Score: 142
Period size: 39 Copynumber: 3.0 Consensus size: 39
6835 TATATGATTC
* * * **
6845 TATTTTTTAAATG-AAATAAATAGTTGGATTTATTTTCT
1 TATTTTGTAAAAGAAAATAAATTGTTAAATTTATTTTCT
* * *
6883 TGTTTTGTAAAAGGAAATAATTTGTTAAATTTATTTTCT
1 TATTTTGTAAAAGAAAATAAATTGTTAAATTTATTTTCT
*
6922 TATTTTGTAAAAGAAAATAAATTGTTGAATTTATTTTC
1 TATTTTGTAAAAGAAAATAAATTGTTAAATTTATTTTC
6960 CTCAGAATCT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
38 10 0.15
39 55 0.85
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (39 bp):
TATTTTGTAAAAGAAAATAAATTGTTAAATTTATTTTCT
Found at i:7073 original size:96 final size:98
Alignment explanation
Indices: 6888--7138 Score: 280
Period size: 96 Copynumber: 2.6 Consensus size: 98
6878 TTTCTTGTTT
* * * * * *
6888 TGTAAAAGGAAATAATTTGTTA-AATTTATTTTCTTATTTTGTAAAAGAAAATAAAT-TGTTGAA
1 TGTAAAAGGAAATAAATTG-TAGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATCAGTTAAA
* *
6951 TTTATTTTCCTCAGAATCTCACATGATTCTGATA
65 ATTATTTTCCTAAGAATCTCACATGATTCTGATA
*
6985 TGTAAAAGGAAATAAATTGTAGAATTTATTTTTCCTA-TTTG-AGAAGGAAATAAATCAG-TAAA
1 TGTAAAAGGAAATAAATTGTAGAATTTA-TTTTCCTATTTTGAAAAAGGAAATAAATCAGTTAAA
* * *
7047 ATTATTTTCCTAATAATCTTGA-ATGATTCTGGTA
65 ATTATTTTCCTAAGAATC-TCACATGATTCTGATA
* * * * *
7081 TATAAAAGAAAATAAATCGTTGGATTTATTTTCCTATTTTGAAAAAGGAAATAAATCA
1 TGTAAAAGGAAATAAATTGTAGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATCA
7139 TAGAATTTAG
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
95 8 0.06
96 70 0.53
97 46 0.35
98 7 0.05
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (98 bp):
TGTAAAAGGAAATAAATTGTAGAATTTATTTTCCTATTTTGAAAAAGGAAATAAATCAGTTAAAA
TTATTTTCCTAAGAATCTCACATGATTCTGATA
Found at i:7147 original size:39 final size:39
Alignment explanation
Indices: 7084--7175 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 39
7074 TCTGGTATAT
* * * * * *
7084 AAAAGAAAATAAATCGTTGGATTTATTTTCCTATTTTGA
1 AAAAGGAAATAAATCATAGAATTTAGTTTCCTAGTTTGA
* *
7123 AAAAGGAAATAAATCATAGAATTTAGTTTCCTGGTTTGT
1 AAAAGGAAATAAATCATAGAATTTAGTTTCCTAGTTTGA
7162 AAAAGGAAATAAAT
1 AAAAGGAAATAAAT
7176 TTCCTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (39 bp):
AAAAGGAAATAAATCATAGAATTTAGTTTCCTAGTTTGA
Found at i:7178 original size:26 final size:26
Alignment explanation
Indices: 7149--7202 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
7139 TAGAATTTAG
*
7149 TTTCCTGGTTTGTAAAAGGAAATAAA
1 TTTCCTAGTTTGTAAAAGGAAATAAA
* *
7175 TTTCCTATTTTGTCAAAGGAAATAAA
1 TTTCCTAGTTTGTAAAAGGAAATAAA
7201 TT
1 TT
7203 GAAACAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (26 bp):
TTTCCTAGTTTGTAAAAGGAAATAAA
Found at i:7286 original size:39 final size:39
Alignment explanation
Indices: 7232--7314 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
7222 TGTTTTATTT
* *
7232 ATTTTCCTATTTTGTAAAAGGAAATAAATCGTTGGATTC
1 ATTTTCCTATTTTGTAAAAGGAAATAAACCGTTGAATTC
* * * *
7271 ATTTTCTTGTTTTGTAAAAGGAAATATACCGTTGAATTT
1 ATTTTCCTATTTTGTAAAAGGAAATAAACCGTTGAATTC
7310 ATTTT
1 ATTTT
7315 TTAGGAAACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.46
Consensus pattern (39 bp):
ATTTTCCTATTTTGTAAAAGGAAATAAACCGTTGAATTC
Found at i:11187 original size:26 final size:27
Alignment explanation
Indices: 11151--11226 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 27
11141 AGAGTCGAGG
11151 GTTCTACGTGGTCCTTCGGGACT-TGT
1 GTTCTACGTGGTCCTTCGGGACTATGT
*
11177 GTTCTACGTGGTCCTTCGGGATATATGT
1 GTTCTACGTGGTCCTTCGGGA-CTATGT
* * *
11205 GTTATATGTGGTCCTTTGGGAC
1 GTTCTACGTGGTCCTTCGGGAC
11227 ATAGTGGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.49
27 1 0.02
28 21 0.49
ACGTcount: A:0.12, C:0.18, G:0.30, T:0.39
Consensus pattern (27 bp):
GTTCTACGTGGTCCTTCGGGACTATGT
Found at i:11215 original size:28 final size:26
Alignment explanation
Indices: 11155--11225 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 26
11145 TCGAGGGTTC
* *
11155 TACGTGGTCCTTCGGGACTTGTGTTC
1 TACGTGGTCCTTCGGGAATTGTGTTA
11181 TACGTGGTCCTTCGGGATATATGTGTTA
1 TACGTGGTCCTTCGGGA-AT-TGTGTTA
* *
11209 TATGTGGTCCTTTGGGA
1 TACGTGGTCCTTCGGGA
11226 CATAGTGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 17 0.44
27 1 0.03
28 21 0.54
ACGTcount: A:0.13, C:0.17, G:0.31, T:0.39
Consensus pattern (26 bp):
TACGTGGTCCTTCGGGAATTGTGTTA
Found at i:14205 original size:19 final size:20
Alignment explanation
Indices: 14181--14218 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14171 GAAGAACATC
14181 TTAATG-GTGTATCAATACA
1 TTAATGAGTGTATCAATACA
*
14200 TTAATGAGTGTATCGATAC
1 TTAATGAGTGTATCAATAC
14219 CCCCTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (20 bp):
TTAATGAGTGTATCAATACA
Found at i:14908 original size:26 final size:26
Alignment explanation
Indices: 14872--14949 Score: 111
Period size: 26 Copynumber: 2.9 Consensus size: 26
14862 AGAGTCGAGG
14872 GTTCTACGTGGTCCTTCGGGACATGT
1 GTTCTACGTGGTCCTTCGGGACATGT
14898 GTTCTACGTGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCCTTCGGGAC--ATGT
* * *
14926 GTTATATGTGGTCCTTTGGGACAT
1 GTTCTACGTGGTCCTTCGGGACAT
14950 AGTGGTCCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
26 24 0.51
28 23 0.49
ACGTcount: A:0.14, C:0.19, G:0.29, T:0.37
Consensus pattern (26 bp):
GTTCTACGTGGTCCTTCGGGACATGT
Found at i:14936 original size:28 final size:28
Alignment explanation
Indices: 14876--14950 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
14866 TCGAGGGTTC
*
14876 TACGTGGTCCTTCGGGAC--ATGTGTTC
1 TACGTGGTCCTTCGGGACATATGTGTTA
14902 TACGTGGTCCTTCGGGACATATGTGTTA
1 TACGTGGTCCTTCGGGACATATGTGTTA
* *
14930 TATGTGGTCCTTTGGGACATA
1 TACGTGGTCCTTCGGGACATA
14951 GTGGTCCTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 18 0.41
28 26 0.59
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.36
Consensus pattern (28 bp):
TACGTGGTCCTTCGGGACATATGTGTTA
Found at i:15912 original size:3 final size:3
Alignment explanation
Indices: 15898--15935 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
15888 AGAGATATTA
*
15898 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
15936 ATGTACGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:17590 original size:31 final size:31
Alignment explanation
Indices: 17499--17605 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
17489 GAGTCGAGGG
*
17499 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTAAGGAACATATGGACAGAA
* *** *
17530 TTACCTATTTTCTTTCGAGACATAAGGACAGAA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGAA
**
17563 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGAA
*
17594 TACCTAGGTTCT
1 TACCTATGTTCT
17606 TCGAAACCTA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
31 22 0.36
32 26 0.43
33 13 0.21
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGAA
Found at i:21318 original size:64 final size:64
Alignment explanation
Indices: 21249--21405 Score: 155
Period size: 64 Copynumber: 2.5 Consensus size: 64
21239 TTGAAGGTGT
* **
21249 ATCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAA-A-AACATCGAATGCA-ATTAG
1 ATCGATGCATAGGTAGTGCATCGATGCA-TC--CCAATAATAATACAACATCGAATGCATATTA-
21310 TGC
62 TGC
* * *
21313 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAATAATAATACAACATCGAATGTATTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCAATAATAATACAACATCGAATGCATATTATGC
*
21377 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
21406 ACCCTCATTG
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
61 2 0.03
62 5 0.06
63 5 0.06
64 60 0.77
65 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCAATAATAATACAACATCGAATGCATATTATGC
Found at i:22377 original size:31 final size:31
Alignment explanation
Indices: 22293--22416 Score: 119
Period size: 31 Copynumber: 4.0 Consensus size: 31
22283 GAGTCGAGGG
* *
22293 TACCTATGTTCTACGAAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* *
22324 TTATCTATG-TCTTTC-GAGACATATGGACAGTA
1 -TACCTATGTTC-TACGGA-ACATATGGACAGTA
*
22356 TACCTATGTTCTAAGGAACATATGGACAGT-
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
22386 TCACCTAGGTTCTTCGGAACCTATGGACAGT
1 T-ACCTATGTTCTACGGAACATATGGACAGT
22417 TGCCGAGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.01
31 49 0.64
32 26 0.34
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:25481 original size:3 final size:3
Alignment explanation
Indices: 25467--25498 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
25457 AGAGATATTC
*
25467 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
25499 ATGTACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:27161 original size:31 final size:31
Alignment explanation
Indices: 27077--27182 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 31
27067 GAGTCGAGGG
* *
27077 TACCTATGTTCTACGAAACATATGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
*
27108 TTACCTATG-TCTTTCGTG-ACATATGGACAGTA
1 -TACCTATGTTC-TACG-GAACATATGGACAGTA
*
27140 TACCTATGTTCTAAGGAACATATGGACAGT-
1 TACCTATGTTCTACGGAACATATGGACAGTA
*
27170 TCACCTAGGTTCT
1 T-ACCTATGTTCT
27183 TTTGAAACTA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
30 2 0.03
31 35 0.56
32 26 0.41
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:27184 original size:63 final size:61
Alignment explanation
Indices: 27077--27200 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 61
27067 GAGTCGAGGG
* * *
27077 TACCTATGTTCTACGAAACATATGGACAGAATTACCTATGTCTTTCGTGACA-TATGGACAGTA
1 TACCTATGTTCTAAGAAACATATGGACAG-ATTACCTAGGTCTTT--TGAAACTATGGACAGTA
*
27140 TACCTATGTTCTAAGGAACATATGGACAG-TTCACCTAGGTTCTTTTGAAACTATGGACAGT
1 TACCTATGTTCTAAGAAACATATGGACAGATT-ACCTAGG-TCTTTTGAAACTATGGACAGT
27201 TGCCGAGGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
61 6 0.11
62 16 0.30
63 32 0.59
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (61 bp):
TACCTATGTTCTAAGAAACATATGGACAGATTACCTAGGTCTTTTGAAACTATGGACAGTA
Found at i:27237 original size:30 final size:30
Alignment explanation
Indices: 27193--27259 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
27183 TTTGAAACTA
* * *
27193 TGGACAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCGTTATGACCTC
* * *
27223 TGGATAGTTACCGAGGTTCGTTGTGACCTT
1 TGGATAGTTACCGAGGATCGTTATGACCTC
27253 TGGATAG
1 TGGATAG
27260 GTCCTTCTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCGTTATGACCTC
Found at i:33932 original size:16 final size:16
Alignment explanation
Indices: 33831--33953 Score: 73
Period size: 16 Copynumber: 7.8 Consensus size: 16
33821 TGTGTGTGTA
33831 TATATAAAGTATA-A-
1 TATATAAAGTATATAT
33845 -ACTATAAAGTATATAT
1 TA-TATAAAGTATATAT
* *
33861 ATAAATATA-TATATAT
1 -TATATAAAGTATATAT
*
33877 ATATATATA-TATATAT
1 -TATATAAAGTATATAT
*
33893 ATATATATA-TATATAT
1 -TATATAAAGTATATAT
*
33909 AAGTATAAAGTATATAT
1 TA-TATAAAGTATATAT
* *
33926 TATAT-AAGCATAT-G
1 TATATAAAGTATATAT
33940 TATATACAAGTATA
1 TATATA-AAGTATA
33954 CACATAACTA
Statistics
Matches: 91, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.01
14 16 0.18
15 9 0.10
16 52 0.57
17 12 0.13
18 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (16 bp):
TATATAAAGTATATAT
Found at i:33945 original size:2 final size:2
Alignment explanation
Indices: 33529--33931 Score: 224
Period size: 2 Copynumber: 204.0 Consensus size: 2
33519 TTGAAACAAT
33529 TA TA -A 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
* *
33570 TA GA TA TA TA TA TA T- TA TG T- TA TA TA -A TA TA -A 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
* * * *
33608 TGA TGA -A TG T- TA TGA TA -A TA TGA TG CA TG TA TA TA TA TCA TA
1 T-A T-A TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA TA TA T-A TA
* * * * * *
33650 -A TA TA CA T- TA TA TT TA TG CA TA CA -A TA TA AA TA TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
33689 TA TA -A GTA TA TA TA TA -A GTA TA CA T- TA TA CT- TA TA -A TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* *
33727 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A GA -A TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
33766 TA TA TA TA TA TA TA TA TA GTA TA AA GTA TA TA TA TA -A GTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA
** * * * * * *
33808 TA -A CTA TA TA GCG TG TG TG TG TA TA TA TA AA GTA TA AA CTA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* *
33851 AA GTA TA TA TA TA AA 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
*
33894 TA TA TA TA TA TA TA TA -A GTA TA AA GTA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
33932 AGCATATGTA
Statistics
Matches: 318, Mismatches: 41, Indels: 84
0.72 0.09 0.19
Matches are distributed among these distances:
1 24 0.08
2 270 0.85
3 24 0.08
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:34453 original size:2 final size:2
Alignment explanation
Indices: 34446--34473 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34436 ACTCATGTGA
34446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34474 CATTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34715 original size:27 final size:23
Alignment explanation
Indices: 34663--34731 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 23
34653 CATGTTCAAT
34663 ATATAAATTATT-TAATTAAATTA
1 ATAT-AATTATTATAATTAAATTA
34686 ATATAATTATTATAATTAAGATTTACA
1 ATATAATTATTATAATTAA-A-TT--A
*
34713 ATATAATGATTATAATTAA
1 ATATAATTATTATAATTAA
34732 TATAGAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 7 0.17
23 11 0.28
24 1 0.03
25 2 0.05
27 19 0.47
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (23 bp):
ATATAATTATTATAATTAAATTA
Found at i:34852 original size:19 final size:19
Alignment explanation
Indices: 34828--34869 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
34818 TATTATATAT
*
34828 TCAAAATCTCACAACTTCA
1 TCAAAATCTCACAACTACA
*
34847 TCAAAATCTTACAACTACA
1 TCAAAATCTCACAACTACA
34866 TCAA
1 TCAA
34870 TTGTAACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
TCAAAATCTCACAACTACA
Found at i:36366 original size:2 final size:2
Alignment explanation
Indices: 36359--36388 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36349 GAGTTTTCTT
36359 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
36389 AAAGTTACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52864 original size:2 final size:2
Alignment explanation
Indices: 52857--52881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52847 ATAAAATTAT
52857 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
52882 TATTTAGCTT
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
Done.