Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000098.1 Hibiscus syriacus cultivar Beakdansim tig00000181_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: 59825
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7393 original size:16 final size:16
Alignment explanation
Indices: 7349--7393 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
7339 GTATAATTGT
*
7349 TTTTTTATAATTT--A
1 TTTTTTATTATTTAAA
7363 TTTTTTATTCA-TTAAA
1 TTTTTTATT-ATTTAAA
7379 TTTTTTATTATTTAA
1 TTTTTTATTATTTAA
7394 GTAATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
16 14 0.54
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTTATTATTTAAA
Found at i:10369 original size:6 final size:6
Alignment explanation
Indices: 10358--10388 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10348 TATGTTTTAG
*
10358 GTGTAT GTGTAT GTGTAT GTATAT GTGTAT G
1 GTGTAT GTGTAT GTGTAT GTGTAT GTGTAT G
10389 CTTTTATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
GTGTAT
Found at i:10539 original size:26 final size:27
Alignment explanation
Indices: 10488--10539 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
10478 GGTATGCTTC
*
10488 ATGTCATGTTTAATAGTTTGTTGTTTA
1 ATGTAATGTTTAATAGTTTGTTGTTTA
*
10515 ATGTAATGTTT-ATGGTTTGTTGTTT
1 ATGTAATGTTTAATAGTTTGTTGTTT
10540 TTATAGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (27 bp):
ATGTAATGTTTAATAGTTTGTTGTTTA
Found at i:12425 original size:64 final size:64
Alignment explanation
Indices: 12312--12472 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
12302 ATTGTTCAAG
* * * * * *
12312 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATAA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCGAAGGCAATAA
* * * * * * **
12376 GTGTATCGATGCAAAAGTAGTGCATCGATGC-GTCCCCTTAAGATTAAAACGTCGAAGGTAATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACT-CCCTTAAAATAAAAACATCGAAGGCAATAA
* *
12440 GTGTACCGATGCACAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC
12473 ACGTTATGGA
Statistics
Matches: 77, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
63 1 0.01
64 76 0.99
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCCTTAAAATAAAAACATCGAAGGCAATAA
Found at i:13177 original size:22 final size:22
Alignment explanation
Indices: 13149--13232 Score: 113
Period size: 22 Copynumber: 4.0 Consensus size: 22
13139 GTTATTAAGG
13149 AGTGGTCCTTCGGGACATATAT
1 AGTGGTCCTTCGGGACATATAT
* *
13171 AGTGGTCCTTCAGGACATATAC
1 AGTGGTCCTTCGGGACATATAT
13193 AGTGGTCCTTCGGGAC----AT
1 AGTGGTCCTTCGGGACATATAT
*
13211 AGTGGTCCTTCGGGACAAATAT
1 AGTGGTCCTTCGGGACATATAT
13233 TCAGTGCCCC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
18 17 0.31
22 37 0.69
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACATATAT
Found at i:13975 original size:83 final size:83
Alignment explanation
Indices: 13856--14135 Score: 411
Period size: 83 Copynumber: 3.4 Consensus size: 83
13846 AGGGAAAACA
* *
13856 TTTTCCATTATTATTCA-AAAATCTTTGCCATGTCATAGTGTTCAATCCCATCCGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCAATCCCATCCGAAATGAAAGG
* *
13920 TGCATTCCAAGGGATGCG
66 TGCGTTCCAAGGGAAGCG
* * * *
13938 TTTTCCATTATTATTTAGAGAATATCTGCCATATCATAGTGTTCAATCCCATCCAAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCAATCCCATCCGAAATGAAAGG
* *
14003 TGCGTTCTAAGGGAACCG
66 TGCGTTCCAAGGGAAGCG
* *
14021 TTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATAATGTTTC-ATCCCATCCGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTG-TTCAATCCCATCCGAAATGAAAG
*
14085 GTGCGTTCCAGGGGAAGCG
65 GTGCGTTCCAAGGGAAGCG
*
14104 TTTTCCATTATTATTCAGAGAATCTATGCCAT
1 TTTTCCATTATTATTCAGAGAATCTCTGCCAT
14136 TTCACATAAT
Statistics
Matches: 175, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
82 16 0.09
83 156 0.89
84 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (83 bp):
TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCAATCCCATCCGAAATGAAAGG
TGCGTTCCAAGGGAAGCG
Found at i:17799 original size:35 final size:35
Alignment explanation
Indices: 17753--17865 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
17743 AAAACAGTCC
* * *
17753 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
*
17788 TCAATTTCATTCTAAACCCTAAATTCTAAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTC-AAAAATAAT
** * * *
17824 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
17859 TCAATTT
1 TCAATTT
17866 AAGATTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 37 0.56
36 29 0.44
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCAAAAATAAT
Found at i:17840 original size:36 final size:35
Alignment explanation
Indices: 17761--17864 Score: 127
Period size: 36 Copynumber: 2.9 Consensus size: 35
17751 CCTCAATTTC
* * * **
17761 ATTCTAAACCCCAATTTCCAAAGTAATTCAATTTC
1 ATTCTAAACCCCAAATTCTAAAATAATTCAATTAA
*
17796 ATTCTAAACCCTAAATTCTAAAAATAATTCAATTAA
1 ATTCTAAACCCCAAATTCT-AAAATAATTCAATTAA
* *
17832 ATTTTAAACCCCAAATTCTAAAATACTTCAATT
1 ATTCTAAACCCCAAATTCTAAAATAATTCAATT
17865 TAAGATTTAG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 29 0.49
36 30 0.51
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (35 bp):
ATTCTAAACCCCAAATTCTAAAATAATTCAATTAA
Found at i:43129 original size:36 final size:36
Alignment explanation
Indices: 43082--43155 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
43072 CAAGCTGCCA
43082 CGCAATCTTGAGGCCTTCTAAAATGCCCCATAGCTC
1 CGCAATCTTGAGGCCTTCTAAAATGCCCCATAGCTC
43118 CGCAATCTTGAGGCCTTCTAAAATGCCCCATAGCTC
1 CGCAATCTTGAGGCCTTCTAAAATGCCCCATAGCTC
43154 CG
1 CG
43156 TTTCCAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (36 bp):
CGCAATCTTGAGGCCTTCTAAAATGCCCCATAGCTC
Found at i:51161 original size:183 final size:183
Alignment explanation
Indices: 50853--51389 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
50843 ATTAAATCCG
50853 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
50918 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
50983 TTGTCAGACCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTAATTTGTCCCTC
*
51036 TAAAGCTGAGATATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
51101 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
51166 TTGTCAGGCGAAAGACTTTGTGATGAGACGAACCCTTCAGTAATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTAATTTGTCCCTC
51219 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * *
51284 ATAGATTACATTCAAA-TCATGACATTGCTCAGACACTTGGTAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
51348 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
51390 TAAACCTGAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 337 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTAATTTGTCCCTC
Found at i:52585 original size:36 final size:35
Alignment explanation
Indices: 52545--52658 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 35
52535 CACTCAAATT
52545 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACATA-TTTGTCTCACTTGAGAC
* * * * ** *
52581 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACATATTTGTCTCACTTGAGAC
* *
52617 TATTTTTCTTAAAACAATATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-ATATTTGTCTCACTTGAGAC
*
52653 CGTTTT
1 TGTTTT
52659 CACTCGAAAG
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 46 0.82
37 5 0.09
38 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (35 bp):
TGTTTTTCTTAAAACATATTTGTCTCACTTGAGAC
Found at i:52623 original size:72 final size:76
Alignment explanation
Indices: 52529--52690 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 76
52519 ATGCAGATGA
* * * *
52529 TTATCTCACTCAA-ATTTGTTTTTCTTAAAAC-ATACTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTTATTTTTCTTAAAACAATA-TTTGTCTCACTTGAGACCGTTTTCACTC
52591 GAAAGAA-G-AT
65 GAAAGAAGGCAT
*
52601 TTATTTCACTCAAGA-TTATTTTTCTTAAAACAATATTTGTCTCGCTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTATTTTTCTTAAAACAATATTTGTCTCACTTGAGACCGTTTTCACTCG
52665 AAAGAAGGCAT
66 AAAGAAGGCAT
52676 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
52691 GCTGTTTTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
72 48 0.61
73 14 0.18
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTATTTTTCTTAAAACAATATTTGTCTCACTTGAGACCGTTTTCACTCG
AAAGAAGGCAT
Found at i:52905 original size:106 final size:104
Alignment explanation
Indices: 52709--53004 Score: 454
Period size: 106 Copynumber: 2.9 Consensus size: 104
52699 TTTTAAGAAG
*
52709 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
*
52774 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 CTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGA
* * *
52813 TTTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
1 --ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTT
*
52878 CTCTTGAAATATAAACATTGAAAACATTTCCCTTAAAATGA
64 CTCTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGA
* *
52919 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AATTTTGTCTCACTTGAGACAGTTTCT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
** *
52981 CTCCAAACATAAACTTTGAAAACA
66 CTTGAAACATAAACATTGAAAACA
53005 ATTTAACGAA
Statistics
Matches: 175, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
101 46 0.26
103 1 0.01
104 30 0.17
106 98 0.56
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAACATAAACATTGAAAACATTTCCCTTAAAATGA
Found at i:52957 original size:36 final size:36
Alignment explanation
Indices: 52904--52979 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
52894 ATTGAAAACA
* * *
52904 TTTCCCTTAAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTAAAACGAATTTTATCTCACTTGAGACAG
* *
52940 TTTCCCTTGAAACGAATTTTGTCTCACTTGAGACAG
1 TTTCCCTTAAAACGAATTTTATCTCACTTGAGACAG
52976 TTTC
1 TTTC
52980 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTAAAACGAATTTTATCTCACTTGAGACAG
Found at i:53387 original size:105 final size:105
Alignment explanation
Indices: 53179--53802 Score: 898
Period size: 105 Copynumber: 6.0 Consensus size: 105
53169 ATATCGTGAC
* * * * * * *
53179 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
*
53244 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGA
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
53285 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
53350 ATTTCAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
53390 ACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
53455 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
53495 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAAGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
53560 ATCTCAGAGCCAATTTCAACTTCACAACGAAGTATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
53600 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* **
53661 A-TTCAGAGTCAATTTCAACTTCACAGTGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
53700 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
53765 GGTTCCAGAGCCAATTTCAACTTCACGACGAAGGATAT
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
53803 ACAACTCAAA
Statistics
Matches: 470, Mismatches: 42, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
100 80 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 300 0.64
106 77 0.16
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:54393 original size:36 final size:37
Alignment explanation
Indices: 54294--54396 Score: 136
Period size: 36 Copynumber: 2.8 Consensus size: 37
54284 TTTTTGTCCT
* *
54294 ACTAGGATTCAAACTCCTAAAAATAGGATCAGATTTT
1 ACTAGGATTCAAACTCCTAAAAATAGGATCAGAGTTC
*
54331 GCTAGGATTCAAACTCCTAAAAATAGGAT-AGAGTTC
1 ACTAGGATTCAAACTCCTAAAAATAGGATCAGAGTTC
* * * *
54367 ACTAAGATTTAAATTCCTAAAGATAGGATC
1 ACTAGGATTCAAACTCCTAAAAATAGGATC
54397 CACAAGCACT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 29 0.51
37 28 0.49
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (37 bp):
ACTAGGATTCAAACTCCTAAAAATAGGATCAGAGTTC
Found at i:54774 original size:17 final size:18
Alignment explanation
Indices: 54752--54787 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54742 ATATGGATAT
*
54752 TTATTCAT-TTATTTTTA
1 TTATTCATGTTATTATTA
54769 TTATTCATGTTATTATTA
1 TTATTCATGTTATTATTA
54787 T
1 T
54788 ATATGTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTCATGTTATTATTA
Found at i:55862 original size:22 final size:21
Alignment explanation
Indices: 55820--55862 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
55810 TTTAAGTTAG
* *
55820 TATTTTTTTTAAAATAGTTAT
1 TATTTTTATTAAAATAATTAT
*
55841 TATTTTATATTAATATAATTAT
1 TATTTT-TATTAAAATAATTAT
55863 AAATATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTTTTATTAAAATAATTAT
Found at i:55869 original size:28 final size:30
Alignment explanation
Indices: 55837--55911 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 30
55827 TTTAAAATAG
*
55837 TTATTATTTTATATT-AATATAATTATA-AA
1 TTATTATTTT-TATTAAAAATAATTATATAA
*
55866 -TATTATTTTTATTAAAAATATTTATATAA
1 TTATTATTTTTATTAAAAATAATTATATAA
*
55895 TTATTATTTTTTTTAAA
1 TTATTATTTTTATTAAA
55912 TTTATTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 19 0.47
29 2 0.05
30 15 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTATTATTTTTATTAAAAATAATTATATAA
Found at i:55870 original size:18 final size:18
Alignment explanation
Indices: 55847--55898 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
55837 TTATTATTTT
55847 ATATTAATATAATTATAA
1 ATATTAATATAATTATAA
* * * *
55865 ATATTATTTTTATTAAAA
1 ATATTAATATAATTATAA
*
55883 ATATTTATATAATTAT
1 ATATTAATATAATTAT
55899 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTAATATAATTATAA
Found at i:55925 original size:29 final size:30
Alignment explanation
Indices: 55828--55928 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
55818 AGTATTTTTT
* *
55828 TTAAAATAGTTATTATTTTATATT---AATA
1 TTAATATAATTATTATTTT-TATTAAAAATA
*
55856 -TAATTATAAATATTATTTTTATTAAAAATA
1 TTAA-TATAATTATTATTTTTATTAAAAATA
* * **
55886 TTTATATAATTATTATTTTTTTTAAATTTA
1 TTAATATAATTATTATTTTTATTAAAAATA
55916 TTAAT-TAATTATT
1 TTAATATAATTATT
55929 TTTGTTCTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
27 7 0.12
28 12 0.20
29 8 0.14
30 30 0.51
31 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TTAATATAATTATTATTTTTATTAAAAATA
Found at i:56805 original size:15 final size:15
Alignment explanation
Indices: 56785--56814 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56775 ATAAAAATAC
56785 ATAAAAATTTAAATT
1 ATAAAAATTTAAATT
*
56800 ATAAAATTTTAAATT
1 ATAAAAATTTAAATT
56815 TTTAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAAAATTTAAATT
Found at i:57477 original size:19 final size:19
Alignment explanation
Indices: 57453--57490 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
57443 TAAAAACTAA
*
57453 AAATATTTAAAATTATAAT
1 AAATATTTAAAAGTATAAT
*
57472 AAATATTTACAAGTATAAT
1 AAATATTTAAAAGTATAAT
57491 TGTGAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (19 bp):
AAATATTTAAAAGTATAAT
Found at i:58184 original size:20 final size:20
Alignment explanation
Indices: 58159--58208 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
58149 AATTTGACAA
*
58159 TTTCGCAACACGAA-TTTCTT
1 TTTCGCAACAC-AAGTTTCCT
58179 TTTCGCAACACAAGTTTCCT
1 TTTCGCAACACAAGTTTCCT
58199 TTTCGCAACA
1 TTTCGCAACA
58209 AGATTTCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (20 bp):
TTTCGCAACACAAGTTTCCT
Done.