Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005299.1 Hibiscus syriacus cultivar Beakdansim tig00011996_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: 80515
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2253 original size:6 final size:6
Alignment explanation
Indices: 2244--2276 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2234 TATGAACATG
*
2244 AAAACC AAAACC AAAACC AAAACC AAAAAC AAA
1 AAAACC AAAACC AAAACC AAAACC AAAACC AAA
2277 TGCTACAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:6276 original size:32 final size:32
Alignment explanation
Indices: 6235--6303 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
6225 AACCGGGTAT
*
6235 CGGGTACCCGATTCCCGGATACCCGCAAAATC
1 CGGGTACCCGATTACCGGATACCCGCAAAATC
* * *
6267 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGATACCCGCAAAATC
6299 CGGGT
1 CGGGT
6304 CGAGACACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGATACCCGCAAAATC
Found at i:6286 original size:15 final size:15
Alignment explanation
Indices: 6235--6291 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
6225 AACCGGGTAT
*
6235 CGGGTACCCGATTCC
1 CGGGTACCCGATTAC
* **
6250 CGGATACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
6267 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
6282 CGGGTACCCG
1 CGGGTACCCG
6292 TAACATCCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
15 20 0.61
16 3 0.09
17 10 0.30
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:8943 original size:27 final size:27
Alignment explanation
Indices: 8905--8958 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
8895 AGCCTTCATT
8905 GCTTGTTCCTTGGTAGCATGTGAATAG
1 GCTTGTTCCTTGGTAGCATGTGAATAG
8932 GCTTGTTCCTTGGTAGCATGTGAATAG
1 GCTTGTTCCTTGGTAGCATGTGAATAG
8959 CCTTCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (27 bp):
GCTTGTTCCTTGGTAGCATGTGAATAG
Found at i:9723 original size:14 final size:14
Alignment explanation
Indices: 9700--9736 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9690 CGAATTATAG
*
9700 TATTCTTCCCTTAT
1 TATTCCTCCCTTAT
9714 TATTCCTCCCTTAT
1 TATTCCTCCCTTAT
9728 TATTCCTCC
1 TATTCCTCC
9737 TTCCTCACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTCCTCCCTTAT
Found at i:12559 original size:23 final size:22
Alignment explanation
Indices: 12515--12559 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12505 AATGTCATGG
* *
12515 GGGAACTGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
12537 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
12560 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:13928 original size:121 final size:121
Alignment explanation
Indices: 13772--14135 Score: 638
Period size: 121 Copynumber: 3.0 Consensus size: 121
13762 CGAGGGTCTA
* *
13772 TGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGACTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
13837 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
13893 TGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
** * *
13958 GATCATTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
14014 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
14079 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
14135 T
1 T
14136 ATTATATGGC
Statistics
Matches: 228, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 228 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:14019 original size:18 final size:18
Alignment explanation
Indices: 13996--14031 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13986 AGGAATGATA
13996 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
14014 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
14032 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:14192 original size:23 final size:23
Alignment explanation
Indices: 14138--14210 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
14128 TGGACATTAT
14138 TATATGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
***
14161 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
14184 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
14205 TATATG
1 TATATG
14211 AGTTGTGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 34 0.79
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:18064 original size:23 final size:22
Alignment explanation
Indices: 18020--18064 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18010 AATGTCATGG
*
18020 GGGAACCAATACCCCCACAGGA
1 GGGAACCAATACCCCCAAAGGA
* *
18042 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCAATACCCCC-AAAGGA
18065 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.09
Consensus pattern (22 bp):
GGGAACCAATACCCCCAAAGGA
Found at i:19403 original size:18 final size:18
Alignment explanation
Indices: 19380--19415 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19370 AGGAATGATA
19380 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
19398 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
19416 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:19436 original size:121 final size:121
Alignment explanation
Indices: 19277--19640 Score: 656
Period size: 121 Copynumber: 3.0 Consensus size: 121
19267 CGAGGGTCTA
19277 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
19342 GATCCCTAGTATATGTATATGATTTTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
19398 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
19463 GATCCTTGGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
19519 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
19584 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
19640 T
1 T
19641 ATTATATGGC
Statistics
Matches: 231, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 231 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:19524 original size:18 final size:18
Alignment explanation
Indices: 19501--19536 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19491 AGGAATGATA
*
19501 TGTGGTCCTTCGGGACAT
1 TGTGGTCATTCGGGACAT
19519 TGTGGTCATTCGGGACAT
1 TGTGGTCATTCGGGACAT
19537 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCATTCGGGACAT
Found at i:19538 original size:62 final size:62
Alignment explanation
Indices: 19352--19538 Score: 153
Period size: 62 Copynumber: 3.1 Consensus size: 62
19342 GATCCCTAGT
*
19352 ATATGTATATGATTTTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * *
19414 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCTT-
1 ATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTC
19470 -GG-C
58 GGGAC
*
19473 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCATTCGGGAC
1 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
19535 ATAT
1 ATAT
19539 ATGTATTCTT
Statistics
Matches: 92, Mismatches: 14, Indels: 38
0.64 0.10 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 12 0.13
62 24 0.26
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:19715 original size:23 final size:23
Alignment explanation
Indices: 19647--19707 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
19637 CATTATTATA
*
19647 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
19670 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
19693 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
19708 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:20948 original size:2 final size:2
Alignment explanation
Indices: 20941--21006 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
20931 TAGAAGGTAA
20941 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
20983 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
21007 GTGTGTGTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21011 original size:2 final size:2
Alignment explanation
Indices: 21006--21034 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20996 TATATATATA
21006 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
21035 ATGAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22218 original size:18 final size:18
Alignment explanation
Indices: 22195--22235 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
22185 TTGATTAATA
22195 AACTAACATTATTCAAAG
1 AACTAACATTATTCAAAG
* *
22213 AACTAACTTTATTCAATG
1 AACTAACATTATTCAAAG
22231 AACTA
1 AACTA
22236 GATGCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (18 bp):
AACTAACATTATTCAAAG
Found at i:22384 original size:18 final size:18
Alignment explanation
Indices: 22361--22396 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
22351 AAATGCAATG
22361 AATTCT-ATGCAAACTTCA
1 AATTCTCATGCAAA-TTCA
22379 AATTCTCATGCAAATTCA
1 AATTCTCATGCAAATTCA
22397 TGCACAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (18 bp):
AATTCTCATGCAAATTCA
Found at i:30752 original size:30 final size:30
Alignment explanation
Indices: 30700--30775 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
30690 ACTTTATTTA
* * * *
30700 TAATATATATATATAATATTTTATTAATAATTT
1 TAATA-AT-TATAAAATCTTTTAATAA-AATAT
*
30733 TAA-AATTTTAAAATCTTTTAATAAAATAT
1 TAATAATTATAAAATCTTTTAATAAAATAT
30762 TAATAATTATAAAA
1 TAATAATTATAAAA
30776 ATAATATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 7 0.19
30 23 0.64
31 2 0.06
32 1 0.03
33 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATAATTATAAAATCTTTTAATAAAATAT
Found at i:30800 original size:19 final size:20
Alignment explanation
Indices: 30748--30802 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
30738 TTTTAAAATC
*
30748 TTTTAATAAAATATTAATAA
1 TTTTAAAAAAATATTAATAA
* * *
30768 TTATAAAAATAATATTTAT-T
1 TTTTAAAAA-AATATTAATAA
30788 TTTTAAAAAAATATT
1 TTTTAAAAAAATATT
30803 GTGTTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.21
20 15 0.52
21 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTAAAAAAATATTAATAA
Found at i:33952 original size:8 final size:8
Alignment explanation
Indices: 33939--33970 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
33929 CTAACAAAAT
33939 ACTAATAA
1 ACTAATAA
33947 ACTAATAA
1 ACTAATAA
*
33955 ACTGATAA
1 ACTAATAA
33963 ACTAATAA
1 ACTAATAA
33971 CATAATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (8 bp):
ACTAATAA
Found at i:43434 original size:13 final size:13
Alignment explanation
Indices: 43416--43443 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43406 TTTTGGATAA
43416 AAGAAATATTCAT
1 AAGAAATATTCAT
43429 AAGAAATATTCAT
1 AAGAAATATTCAT
43442 AA
1 AA
43444 ACAGAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAGAAATATTCAT
Found at i:43689 original size:52 final size:52
Alignment explanation
Indices: 43630--43734 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
43620 TCTCCTTCCC
43630 CCATTCTTGTCTTCTTCCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAA
1 CCATTCTTGTCTTCTTCCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAA
43682 CCATTCTTGTCTTCTTCCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAA
1 CCATTCTTGTCTTCTTCCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAA
43734 C
1 C
43735 GGAAATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.10, C:0.30, G:0.11, T:0.50
Consensus pattern (52 bp):
CCATTCTTGTCTTCTTCCTCTCTTCCTGCTTTTCTTTCTCTGTATGTAGGAA
Found at i:45800 original size:16 final size:16
Alignment explanation
Indices: 45779--45812 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
45769 AAAATAGTAC
45779 ACGTAATAACAATACA
1 ACGTAATAACAATACA
45795 ACGTAATAACAATACA
1 ACGTAATAACAATACA
45811 AC
1 AC
45813 AAGGACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.06, T:0.18
Consensus pattern (16 bp):
ACGTAATAACAATACA
Found at i:49161 original size:22 final size:21
Alignment explanation
Indices: 49122--49162 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
49112 GCTTCCATAA
* *
49122 ATTTTAAACCCCTTTAAACCG
1 ATTTTAAAACCCTATAAACCG
49143 ATTTTAAAACCCTAATAAAC
1 ATTTTAAAACCCT-ATAAAC
49163 GAACCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTTTAAAACCCTATAAACCG
Found at i:50040 original size:4 final size:4
Alignment explanation
Indices: 50026--50056 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
50016 TGATTTGTAG
50026 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
50057 AAGCCGGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:50926 original size:32 final size:32
Alignment explanation
Indices: 50885--50953 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
50875 AACCGGGTAT
*
50885 CGGGTACCCGATTCCCAGATACCCGCAAAATC
1 CGGGTACCCGATTACCAGATACCCGCAAAATC
* * * *
50917 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCAGATACCCGCAAAATC
50949 CGGGT
1 CGGGT
50954 CGGGACACGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATTACCAGATACCCGCAAAATC
Found at i:51008 original size:16 final size:16
Alignment explanation
Indices: 50984--51016 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50974 CGTCGACCTG
*
50984 AAAATTCCGGGTACCC
1 AAAAATCCGGGTACCC
51000 AAAAATCCGGGTACCC
1 AAAAATCCGGGTACCC
51016 A
1 A
51017 GATTTGCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAAATCCGGGTACCC
Found at i:54393 original size:17 final size:14
Alignment explanation
Indices: 54356--54392 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
54346 CAAATTAAAG
54356 TATTCCTCCCTTAT
1 TATTCCTCCCTTAT
54370 TATTCCTCCCTTAT
1 TATTCCTCCCTTAT
54384 TATTCCTCC
1 TATTCCTCC
54393 TTCCTCACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.14, C:0.38, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTCCTCCCTTAT
Found at i:57215 original size:23 final size:22
Alignment explanation
Indices: 57171--57215 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
57161 AATGTCATGG
*
57171 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
57193 GGGAACCGAGT-CCCCCTAAAGGA
1 GGGAACCGA-TACCCCC-AAAGGA
57216 AAATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.31, C:0.33, G:0.29, T:0.07
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:58478 original size:18 final size:18
Alignment explanation
Indices: 58455--58490 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
58445 AGGAATGATA
58455 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
58473 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
58491 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:58510 original size:121 final size:121
Alignment explanation
Indices: 58352--58715 Score: 638
Period size: 121 Copynumber: 3.0 Consensus size: 121
58342 CGAGGGTCTA
*
58352 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGACTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
58417 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
58473 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
** * * * *
58538 GATCATTGGCATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
58594 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
58659 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
58715 T
1 T
58716 ATTATATGGC
Statistics
Matches: 227, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 227 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:58599 original size:18 final size:18
Alignment explanation
Indices: 58576--58611 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58566 AGGAATAATA
*
58576 TGTGGTCTTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
58594 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
58612 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:58613 original size:62 final size:62
Alignment explanation
Indices: 58427--58613 Score: 151
Period size: 62 Copynumber: 3.1 Consensus size: 62
58417 GATCCCTAGT
* *
58427 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * * * *
58489 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGTCTGGT-GAGACACATACT-TGATCATT--
1 ATATGTATATGATTCTTAAGGAATAATATGTG--GTCT-TTCG-G-GACAT--TGTGGTCCTTCG
58545 GG-C
59 GGAC
58548 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
58610 ATAT
1 ATAT
58614 ATGTATTCTT
Statistics
Matches: 91, Mismatches: 17, Indels: 34
0.64 0.12 0.24
Matches are distributed among these distances:
57 6 0.07
58 5 0.05
59 20 0.22
60 12 0.13
61 12 0.13
62 25 0.27
63 5 0.05
64 6 0.07
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATAATATGTGGTCTTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:58790 original size:23 final size:23
Alignment explanation
Indices: 58722--58782 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
58712 CATTATTATA
*
58722 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
58745 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
58768 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
58783 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:62641 original size:23 final size:22
Alignment explanation
Indices: 62597--62641 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
62587 AATGTCATGG
*
62597 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
62619 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
62642 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:63938 original size:18 final size:18
Alignment explanation
Indices: 63915--63950 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
63905 AGGAATGATA
63915 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
63933 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
63951 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:63948 original size:121 final size:121
Alignment explanation
Indices: 63812--64175 Score: 647
Period size: 121 Copynumber: 3.0 Consensus size: 121
63802 CGAGGGTCTA
63812 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
63877 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
63933 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
** * * *
63998 GATCATTGGCATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTCGGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
64054 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTGTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
64119 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
64175 T
1 T
64176 ATTATATGGC
Statistics
Matches: 229, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 229 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:64059 original size:18 final size:18
Alignment explanation
Indices: 64036--64071 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64026 AGGAATAATA
64036 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
64054 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
64072 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:64073 original size:62 final size:62
Alignment explanation
Indices: 63887--64073 Score: 153
Period size: 62 Copynumber: 3.1 Consensus size: 62
63877 GATCCCTAGT
*
63887 ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
* * * * * * *
63949 ATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCATT-
1 ATATGTATATGATTCTTAAGGAATAATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTTC
64005 -GG-C
58 GGGAC
64008 ATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
1 ATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
64070 ATAT
1 ATAT
64074 ATGTATTCTT
Statistics
Matches: 92, Mismatches: 14, Indels: 38
0.64 0.10 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 19 0.21
60 12 0.13
61 12 0.13
62 23 0.25
63 7 0.08
64 6 0.07
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (62 bp):
ATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTCGGGACATTGTGGTCCTTCGGGAC
Found at i:64249 original size:23 final size:23
Alignment explanation
Indices: 64173--64250 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
64163 CCTTATGGAC
*
64173 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
64197 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
64220 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
64243 TTTATATG
1 ATTATATG
64251 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:65942 original size:18 final size:18
Alignment explanation
Indices: 65919--65959 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
65909 TTGATTAATA
65919 AACTAACATTATTCAAAG
1 AACTAACATTATTCAAAG
* *
65937 AACTAACTTTATTCAATG
1 AACTAACATTATTCAAAG
65955 AACTA
1 AACTA
65960 GATGCATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (18 bp):
AACTAACATTATTCAAAG
Found at i:66108 original size:18 final size:18
Alignment explanation
Indices: 66085--66120 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
66075 AAATGCAATG
66085 AATTCT-ATGCAAACTTCA
1 AATTCTCATGCAAA-TTCA
66103 AATTCTCATGCAAATTCA
1 AATTCTCATGCAAATTCA
66121 TGCACAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (18 bp):
AATTCTCATGCAAATTCA
Found at i:74475 original size:30 final size:30
Alignment explanation
Indices: 74423--74498 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
74413 ACTTTATTTA
* * * *
74423 TAATATATATATATAATATTTTATTAATAATTT
1 TAATA-AT-TATAAAATCTTTTAATAA-AATAT
*
74456 TAA-AATTTTAAAATCTTTTAATAAAATAT
1 TAATAATTATAAAATCTTTTAATAAAATAT
74485 TAATAATTATAAAA
1 TAATAATTATAAAA
74499 ATAATATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 7 0.19
30 23 0.64
31 2 0.06
32 1 0.03
33 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATAATTATAAAATCTTTTAATAAAATAT
Done.