Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018494.1 Corchorus olitorius cultivar O-4 contig18527, 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: 28750
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1758 original size:22 final size:21
Alignment explanation
Indices: 1715--1758 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1705 GGGGGTCAGA
*
1715 ATGAGATGCAGAAAAATGACT
1 ATGAGATGCAGAAAAAGGACT
* *
1736 ATGAGGTGCTGAATAAAGGACT
1 ATGAGATGCAGAA-AAAGGACT
1758 A
1 A
1759 AAAGATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.09, G:0.27, T:0.20
Consensus pattern (21 bp):
ATGAGATGCAGAAAAAGGACT
Found at i:3428 original size:9 final size:9
Alignment explanation
Indices: 3386--3428 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
3376 TTTCCCATAA
3386 AAAAAGAATG
1 AAAAA-AATG
3396 -AAAAAATG
1 AAAAAAATG
*
3404 GAAAAAATG
1 AAAAAAATG
3413 AAAAAAATG
1 AAAAAAATG
3422 AAAAAAA
1 AAAAAAA
3429 AAGGCACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
8 4 0.13
9 27 0.87
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:3521 original size:14 final size:13
Alignment explanation
Indices: 3486--3530 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
3476 AGAATCATGG
* *
3486 TTTTCAAAATTGC
1 TTTTCAAAAATGA
*
3499 TTTTCAAAAATGT
1 TTTTCAAAAATGA
3512 TTTTCAAAAAATGA
1 TTTTC-AAAAATGA
3526 TTTTC
1 TTTTC
3531 GGAAACTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:5292 original size:69 final size:69
Alignment explanation
Indices: 5210--5350 Score: 201
Period size: 69 Copynumber: 2.0 Consensus size: 69
5200 TTGCATAAGT
* * **
5210 CAAACTCGTTTCCATACGAGTTAGTTCAAGTTTTGGTTCCATCCAAACAGCTTGGGCTTTTCCAC
1 CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
5275 AAGC
66 AAGC
* * * * *
5279 CAAACTCGTTTCCATATGAGATAGTTTAAGCTTTGGTTCCATCCAACCATCAAGGGCTTTTCCAT
1 CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
5344 AAGC
66 AAGC
5348 CAA
1 CAA
5351 GTTAAACGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (69 bp):
CAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAACAGCAAGGGCTTTTCCAC
AAGC
Found at i:5810 original size:149 final size:150
Alignment explanation
Indices: 5618--5925 Score: 447
Period size: 149 Copynumber: 2.1 Consensus size: 150
5608 ATTAATAAAA
* *
5618 CCTCCGGGTATCATGTCATTTCATCAAAAATTTTTCATCAAAGATTCATGTTTAAGTTTAAAATC
1 CCTCCGGGTACCATGTCATTTCATC-AAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATC
* * * *
5683 CTTGGTCAAGGTCTCTATTTAAAGTTTGCATTAGTAAGTCCTCCCGGCGCAAATTCAGAAACCTC
65 CTTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTC
5748 CAGGTATTAATTCTGATAAGT
130 CAGGTATTAATTCTGATAAGT
* * *
5769 CCTCCGGGTACCATTTCATTTCATC-AAGTTTTTCATCAAAGATTCATGTTTAAGTTCAGAATCC
1 CCTCCGGGTACCATGTCATTTCATCAAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATCC
* * * * *
5833 TTGTTCAAGGTCTCTATTCAGAGTTTGCATTGGTAAGACCTCCAGGCACAATTTCAGAAGCCTCC
66 TTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTCC
* * *
5898 GGGTATTAGTTTTGATAAGT
131 AGGTATTAATTCTGATAAGT
5918 CCTCCGGG
1 CCTCCGGG
5926 CATTTCATAT
Statistics
Matches: 140, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
149 117 0.84
151 23 0.16
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (150 bp):
CCTCCGGGTACCATGTCATTTCATCAAAATTTTTCATCAAAGATTCATGTTTAAGTTCAAAATCC
TTGGTCAAGGTCTCTATTCAAAGTTTGCATTAGTAAGACCTCCAGGCACAAATTCAGAAACCTCC
AGGTATTAATTCTGATAAGT
Found at i:6022 original size:38 final size:38
Alignment explanation
Indices: 5970--6426 Score: 290
Period size: 38 Copynumber: 12.2 Consensus size: 38
5960 ATCGGTTTCT
* * *
5970 TTTCGAATCCTGGTTTAGGATCATTGCTTTATGACTTAA
1 TTTC-AATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* * * * *
6009 TTTCAGTCTTGGTTTAGGATCATTGTTTTATGAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6047 TTTCAATCCCGATTTAGGATCTTTGC-TT-T-A-TT-A
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6080 GTT-AATCCTGATTTAGGATCATTGCTTCATCAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6117 TTTCAATCCTGATTTAGGATTATTGGTTTATCAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* *
6155 TTTCAGAATCCT-ATTGAGGATCATCGC-TTAGT-AGTTAA
1 TTTC--AATCCTGATTTAGGATCATTGCTTTA-TCAGTTAA
* * * *
6193 TTTCATAT--TTATAATCAAGTTCATTG-TTT-TC--TTAA
1 TTTCA-ATCCTGAT--TTAGGATCATTGCTTTATCAGTTAA
*
6228 TTTCAAAAT-CTCG-TTTAGGATCATTGCTTTATCAGTTTAC
1 TTTC--AATCCT-GATTTAGGATCATTGCTTTATCAG-TTAA
* * * *
6268 TTTCAATCTTGATTTAGGATTATCGCATTT-TGAGTTAA
1 TTTCAATCCTGATTTAGGATCATTGC-TTTATCAGTTAA
* *
6306 TTTCGATCCTGATTTAGGATCATTG-TTATATGAGTTAAA
1 TTTCAATCCTGATTTAGGATCATTGCTT-TATCAGTT-AA
* * * * * *
6345 TTTCAATCCTG-TTGAAGATCATTGCGTTATTAATTGA
1 TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
* * * *
6382 TTTCAAAATCCTG-TTCAAGATTATTGCTTTGTCAGTTAA
1 TTTC--AATCCTGATTTAGGATCATTGCTTTATCAGTTAA
6421 TTTCAA
1 TTTCAA
6427 AGTCTTGGTT
Statistics
Matches: 331, Mismatches: 54, Indels: 68
0.73 0.12 0.15
Matches are distributed among these distances:
32 20 0.06
33 4 0.01
34 3 0.01
35 20 0.06
36 14 0.04
37 20 0.06
38 159 0.48
39 75 0.23
40 16 0.05
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (38 bp):
TTTCAATCCTGATTTAGGATCATTGCTTTATCAGTTAA
Found at i:6093 original size:32 final size:32
Alignment explanation
Indices: 6051--6117 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
6041 AGTTAATTTC
* * *
6051 AATCCCGATTTAGGATCTTTGCTTTATTAGTT
1 AATCCCGATTTAGGATCATTGCTTCATCAGTT
*
6083 AATCCTGATTTAGGATCATTGCTTCATCAGTT
1 AATCCCGATTTAGGATCATTGCTTCATCAGTT
6115 AAT
1 AAT
6118 TTCAATCCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.43
Consensus pattern (32 bp):
AATCCCGATTTAGGATCATTGCTTCATCAGTT
Found at i:6125 original size:70 final size:70
Alignment explanation
Indices: 6021--6155 Score: 200
Period size: 70 Copynumber: 1.9 Consensus size: 70
6011 TCAGTCTTGG
* * * *
6021 TTTAGGATCATTGTTTTATGAGTTAATTTCAATCCCGATTTAGGATCT-TTGCTTTATTAGTTAA
1 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGAT-TATTGCTTTATCAGTTAA
6085 TCCTGA
65 TCCTGA
* *
6091 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCTGATTTAGGATTATTGGTTTATCAGTTAAT
1 TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGATTATTGCTTTATCAGTTAAT
6156 TTCAGAATCC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 1 0.02
70 57 0.98
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (70 bp):
TTTAGGATCATTGCTTCATCAGTTAATTTCAATCCCGATTTAGGATTATTGCTTTATCAGTTAAT
CCTGA
Found at i:6190 original size:108 final size:108
Alignment explanation
Indices: 5975--6193 Score: 271
Period size: 108 Copynumber: 2.0 Consensus size: 108
5965 TTTCTTTTCG
* * * * * * *
5975 AATCCTGGTTTAGGATCATTGCTTTATGACTTAATTTCAGTCTTGGTTTAGGATCATTGTTTTAT
1 AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
* * * * *
6040 GAGTTAATTTCAATCCCGATTTAGGATCTTTGCTTTATTAGTT
66 CAGTTAATTTCAATCCCGATTGAGGATCATCGCTTTAGTAGTT
* *
6083 AATCCTGATTTAGGATCATTGCTTCATCAGTTAATTTCAATCCTGATTTAGGATTATTGGTTTAT
1 AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
*
6148 CAGTTAATTTCAGAAT-CCTATTGAGGATCATCGC-TTAGTAGTT
66 CAGTTAATTTC--AATCCCGATTGAGGATCATCGCTTTAGTAGTT
6191 AAT
1 AAT
6194 TTCATATTTA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 77 0.82
109 14 0.15
110 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (108 bp):
AATCCTGATTTAGGATCATTGCTTCATCACTTAATTTCAATCCTGATTTAGGATCATTGGTTTAT
CAGTTAATTTCAATCCCGATTGAGGATCATCGCTTTAGTAGTT
Found at i:6424 original size:39 final size:39
Alignment explanation
Indices: 6349--6427 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
6339 GTTAAATTTC
* * *
6349 AATCCTGTTGAAGATCATTGCGTTATTAATTGATTTCAA
1 AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
* * * *
6388 AATCCTGTTCAAGATTATTGCTTTGTCAGTTAATTTCAA
1 AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
6427 A
1 A
6428 GTCTTGGTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (39 bp):
AATCCTGTTCAAGATCATTGCGTTATCAATTAATTTCAA
Found at i:11773 original size:23 final size:22
Alignment explanation
Indices: 11747--11789 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
11737 TAGATCCTCG
*
11747 GACTCTCTCTCTACAAAAAAAGA
1 GACTCTCTCAC-ACAAAAAAAGA
11770 GACTCTCTCACACAAAAAAA
1 GACTCTCTCACACAAAAAAA
11790 TCTCTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (22 bp):
GACTCTCTCACACAAAAAAAGA
Found at i:11794 original size:19 final size:21
Alignment explanation
Indices: 11750--11795 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11740 ATCCTCGGAC
11750 TCTCTCTCTACAAAAAAAGAG
1 TCTCTCTCTACAAAAAAAGAG
*
11771 ACTCTCTC-ACACAAAAAA-A-
1 TCTCTCTCTACA-AAAAAAGAG
11790 TCTCTC
1 TCTCTC
11796 CCTTTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.23
20 4 0.18
21 13 0.59
ACGTcount: A:0.41, C:0.30, G:0.04, T:0.24
Consensus pattern (21 bp):
TCTCTCTCTACAAAAAAAGAG
Found at i:14963 original size:35 final size:35
Alignment explanation
Indices: 14924--15066 Score: 189
Period size: 35 Copynumber: 4.1 Consensus size: 35
14914 AAGCCCAAAA
*
14924 AAGTAAATTGGTCATCAACTTAATTCGGTGTAATT
1 AAGTAAATTGGTAATCAACTTAATTCGGTGTAATT
*
14959 AAGTAAATTGGTAATCAACTTAATTTGGTGTAATT
1 AAGTAAATTGGTAATCAACTTAATTCGGTGTAATT
* *
14994 AAGTAAATTGGTAATCAACTTAA-TCAGATGTAACT
1 AAGTAAATTGGTAATCAACTTAATTC-GGTGTAATT
* ** * *
15029 AGGTAAATCAGTAATTAACTTAATTCAGTGTAATT
1 AAGTAAATTGGTAATCAACTTAATTCGGTGTAATT
15064 AAG
1 AAG
15067 AATCAAGGAA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
34 1 0.01
35 90 0.97
36 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (35 bp):
AAGTAAATTGGTAATCAACTTAATTCGGTGTAATT
Found at i:14983 original size:16 final size:16
Alignment explanation
Indices: 14929--15017 Score: 61
Period size: 16 Copynumber: 5.2 Consensus size: 16
14919 CAAAAAAGTA
*
14929 AATTGGTCATCAACTT
1 AATTGGTAATCAACTT
* * *
14945 AATTCGGTGTAATTAAGTA
1 AATT--G-GTAATCAACTT
14964 AATTGGTAATCAACTT
1 AATTGGTAATCAACTT
* * *
14980 AATTTGGTGTAATTAAGTA
1 AA-TT-G-GTAATCAACTT
14999 AATTGGTAATCAACTT
1 AATTGGTAATCAACTT
15015 AAT
1 AAT
15018 CAGATGTAAC
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
16 25 0.46
17 4 0.07
18 4 0.07
19 21 0.39
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (16 bp):
AATTGGTAATCAACTT
Found at i:15002 original size:19 final size:19
Alignment explanation
Indices: 14945--15002 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
14935 TCATCAACTT
*
14945 AATTCGGTGTAATTAAGTA
1 AATTTGGTGTAATTAAGTA
* * *
14964 AA-TT-G-GTAATCAACTT
1 AATTTGGTGTAATTAAGTA
14980 AATTTGGTGTAATTAAGTA
1 AATTTGGTGTAATTAAGTA
14999 AATT
1 AATT
15003 GGTAATCAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 2 0.07
19 14 0.48
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (19 bp):
AATTTGGTGTAATTAAGTA
Found at i:15063 original size:19 final size:19
Alignment explanation
Indices: 14940--15065 Score: 56
Period size: 19 Copynumber: 7.1 Consensus size: 19
14930 ATTGGTCATC
*
14940 AACTTAATTCGGTGTAATT
1 AACTTAATTCAGTGTAATT
* * *
14959 AAGTAAATT--G-GTAATC
1 AACTTAATTCAGTGTAATT
**
14975 AACTTAATTTGGTGTAATT
1 AACTTAATTCAGTGTAATT
* * *
14994 AAGTAAATT--G-GTAATC
1 AACTTAATTCAGTGTAATT
*
15010 AACTTAA-TCAGATGTAACT
1 AACTTAATTCAG-TGTAATT
** *
15029 -AGGTAAATCA--GTAATT
1 AACTTAATTCAGTGTAATT
15045 AACTTAATTCAGTGTAATT
1 AACTTAATTCAGTGTAATT
15064 AA
1 AA
15066 GAATCAAGGA
Statistics
Matches: 77, Mismatches: 19, Indels: 22
0.65 0.16 0.19
Matches are distributed among these distances:
15 1 0.01
16 27 0.35
17 10 0.13
18 5 0.06
19 34 0.44
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (19 bp):
AACTTAATTCAGTGTAATT
Found at i:18460 original size:42 final size:42
Alignment explanation
Indices: 18337--18461 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
18327 GGTTGATTAC
* **
18337 TGATGTTGAAACTATAAA-AGACCAGTTTGTGGTCGATATCAT
1 TGATGTTGAAACTA-AAAGAGACCAGTCTGTGGTCGATATTGT
* * * *
18379 TGATCTTGAAACTGAAAGAGACCATTCTGTGGTTGATATTGT
1 TGATGTTGAAACTAAAAGAGACCAGTCTGTGGTCGATATTGT
*
18421 TGATGTTGTAACTAAAAGAGACCAGTCTGTGGTCGATATTG
1 TGATGTTGAAACTAAAAGAGACCAGTCTGTGGTCGATATTG
18462 AAACTAAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 67 0.96
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (42 bp):
TGATGTTGAAACTAAAAGAGACCAGTCTGTGGTCGATATTGT
Found at i:18560 original size:62 final size:61
Alignment explanation
Indices: 18439--18691 Score: 310
Period size: 62 Copynumber: 4.1 Consensus size: 61
18429 TAACTAAAAG
* * * * * * *
18439 AGACCAGTCTGTGGTCGA-TATTGAAACTAAAAAATACCTGTCTGAGGTCTAAAACTGAAGA
1 AGACCAGTCTGTGGTCGACT-TTAAAAATAAGAAAGACATGTCTGAGGTCTGAAATTGAAGA
* *
18500 AGACCAGTCCGTGGTCGACTTTAAAAATTAAGAAAGACTTGTCTGAGGTCTGAAATTGAAGA
1 AGACCAGTCTGTGGTCGACTTTAAAAA-TAAGAAAGACATGTCTGAGGTCTGAAATTGAAGA
* * * *
18562 AGAGCAGTTTGTGGTCGACGTTGAAAAATAAGAAAGACATGTCTGAGGCCTGAAATTGAAGA
1 AGACCAGTCTGTGGTCGAC-TTTAAAAATAAGAAAGACATGTCTGAGGTCTGAAATTGAAGA
* * * *
18624 AGACCAGTCTGTGGTCGACTTTAAAAACTAGGAAAGACCTGTCTAAGGTCTGAAATTGAAAA
1 AGACCAGTCTGTGGTCGACTTTAAAAA-TAAGAAAGACATGTCTGAGGTCTGAAATTGAAGA
18686 AGACCA
1 AGACCA
18692 ATATGTGTTC
Statistics
Matches: 166, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
61 29 0.17
62 130 0.78
63 7 0.04
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (61 bp):
AGACCAGTCTGTGGTCGACTTTAAAAATAAGAAAGACATGTCTGAGGTCTGAAATTGAAGA
Found at i:18891 original size:33 final size:34
Alignment explanation
Indices: 18839--18919 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
18829 GTCTGAAACT
* * * *
18839 GAAGAAGATCAGTCTGTGGTCAACTGATA-CTTGA
1 GAAG-AGACCAGTCCGTGGTCAACTAAAAGCTTGA
*
18873 GAAGAGACCAGTCCGTGGTCAACTAAAAGTTTGA
1 GAAGAGACCAGTCCGTGGTCAACTAAAAGCTTGA
18907 GAAAGAGACCAGT
1 G-AAGAGACCAGT
18920 TTGTGATCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
33 20 0.50
34 9 0.22
35 11 0.28
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (34 bp):
GAAGAGACCAGTCCGTGGTCAACTAAAAGCTTGA
Found at i:18916 original size:158 final size:157
Alignment explanation
Indices: 18592--18895 Score: 411
Period size: 158 Copynumber: 1.9 Consensus size: 157
18582 TTGAAAAATA
* * *
18592 AGAAAGACATGTCTGAGGCCTGAAATTGAAGAAGACCAGTCTGTGGTCGACTTTAAAAACTAGGA
1 AGAAAGACCTGTCTGAGGCCTGAAATTGAAGAAGACCAGTCTGTGGTCCACTTTAAAAACTAAGA
* * * *
18657 AAGACCTGTCTAAGGTCTGAAATTGAAAAAGACCAATATGTGTTCGATGTTGAGATTGTAAATGA
66 AAGACCTGTCTAAGGTCTGAAACTGAAAAAGACCAATATGTGGTCAATGATGAGATTGTAAATGA
*
18722 AGACCAGTCTGTGGTCAACACTAAACTG
131 AGACCAGTCCGTGGTCAACAC-AAACTG
* *
18750 AGAAAGACCTGTCTGAGGTCTGAAATTGAAGAAGACCAGTGTGTGGTCCACTTTAAAAACTAAGA
1 AGAAAGACCTGTCTGAGGCCTGAAATTGAAGAAGACCAGTCTGTGGTCCACTTTAAAAACTAAGA
* * * * *
18815 AAGACCTGTCTAAGGTCTGAAACTGAAGAAGATCAGTCTGTGGTCAACTGAT-A-CTTG-AGAA-
66 AAGACCTGTCTAAGGTCTGAAACTGAAAAAGACCAATATGTGGTCAA-TGATGAGATTGTA-AAT
18876 G-AGACCAGTCCGTGGTCAAC
129 GAAGACCAGTCCGTGGTCAAC
18896 TAAAAGTTTG
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
155 18 0.14
156 2 0.02
157 5 0.04
158 101 0.78
159 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (157 bp):
AGAAAGACCTGTCTGAGGCCTGAAATTGAAGAAGACCAGTCTGTGGTCCACTTTAAAAACTAAGA
AAGACCTGTCTAAGGTCTGAAACTGAAAAAGACCAATATGTGGTCAATGATGAGATTGTAAATGA
AGACCAGTCCGTGGTCAACACAAACTG
Found at i:19161 original size:48 final size:48
Alignment explanation
Indices: 19075--19198 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
19065 AAGTGGAAGT
* * ** * * *
19075 GAGAAAAGACCAACTTCGATCAAAGGGATTGCAGACTCGCATTG-GAGC
1 GAGAAAAGACCAACTTTGGTCAAATAGAGTGCAAACTCGCA-TGAAAGC
*
19123 GGGAAAAGACCAACTTTGGTCAAATAGAGTGCAAACTCGCATGAAAGC
1 GAGAAAAGACCAACTTTGGTCAAATAGAGTGCAAACTCGCATGAAAGC
19171 GAGAAAAGACCAACTTTGGTCAAATAGA
1 GAGAAAAGACCAACTTTGGTCAAATAGA
19199 TGTCAATTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 2 0.03
48 64 0.97
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.17
Consensus pattern (48 bp):
GAGAAAAGACCAACTTTGGTCAAATAGAGTGCAAACTCGCATGAAAGC
Found at i:19616 original size:13 final size:13
Alignment explanation
Indices: 19598--19623 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19588 GATTTTGAAA
19598 GAAAATAACTTTG
1 GAAAATAACTTTG
19611 GAAAATAACTTTG
1 GAAAATAACTTTG
19624 AATCTGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
GAAAATAACTTTG
Found at i:20242 original size:53 final size:54
Alignment explanation
Indices: 19945--20555 Score: 711
Period size: 54 Copynumber: 11.4 Consensus size: 54
19935 CTTCCTTTAC
* * * *
19945 TGACCGCACTGGATTACTTGAAGATACACTTAAAAC-ACTGTG-AACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCT-AAACTGCTG-GAAACTTTCTTGAT
* * * *
19999 AGACCGCACTAGATTACTTGAAGATAAACCTAAACTGCTTGAAACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * *
20053 TGACCGCACTAGATCACTTGAAGATAAACTTAAAAC-ACTGTG-AACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCT-AAACTGCTG-GAAACTTTCTTGAT
* * *
20107 AGACCGCACTAGATTACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * * *
20161 TGACCGCACTGGATCACTTGAAGATAAACTTAAACTGTTGGAAACCTT-TTGAC
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * *
20214 CGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTAGAAACCTTTC--GAA
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAA-CTTTCTTGAT
* * *
20267 TGACCGCATTGGATCACTTGAAAATAAACATAAACTGCTGGAAACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* *
20321 TGACCGCACTAGATTACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * * * * *
20375 TGACTGCACTAGATCACTTTAAGATAAACCTAAACTGCTAGAAACCTT-TTGAC
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * * * * *
20428 CGACCGCACTGGATCACTTGATGATAACCCTAAACTGCAGGAAACCTT-TTGAC
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * *
20481 CGACTGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACCTT-TTGAT
1 TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
* * *
20534 CGACGGCATTGGATCACTTGAA
1 TGACCGCACTGGATCACTTGAA
20556 ATTCAGCTAA
Statistics
Matches: 487, Mismatches: 60, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
52 5 0.01
53 212 0.44
54 265 0.54
55 5 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (54 bp):
TGACCGCACTGGATCACTTGAAGATAAACCTAAACTGCTGGAAACTTTCTTGAT
Found at i:20335 original size:214 final size:212
Alignment explanation
Indices: 19945--20533 Score: 776
Period size: 214 Copynumber: 2.7 Consensus size: 212
19935 CTTCCTTTAC
* * * **
19945 TGACCGCACTGGATTACTTGAAGATACACTTAAAACACTGTG-AACTTTCTTGATAGACCGCACT
1 TGACCGCACTGGATCACTTGAAGATAAACTT--AA-ACTGTGAAACCTT-TTGACCGACCGCACT
* * * * *
20009 AGATTACTTGAAGATAAACCTAAACTGCTTGAAA-CTTTCTTGATTGACCGCACTAGATCACTTG
62 GGATCACTTGAAGATAAACCTAAACTGCTAGAAACCTTTC--GAATGACCGCACTGGATCACTTG
* *
20073 AAGATAAACTTAAAAC-ACTGTG-AACTTTCTTGATAGACCGCACTAGATTACTTGAAGATAAAC
125 AAGATAAACAT-AAACTGCTG-GAAACTTTCTTGATAGACCGCACTAGATTACTTGAAGATAAAC
20136 CTAAACTGCTGGAAACTTTCTTGAT
188 CTAAACTGCTGGAAACTTTCTTGAT
20161 TGACCGCACTGGATCACTTGAAGATAAACTTAAACTGTTGGAAACCTTTTGACCGACCGCACTGG
1 TGACCGCACTGGATCACTTGAAGATAAACTTAAACTG-T-GAAACCTTTTGACCGACCGCACTGG
* *
20226 ATCACTTGAAGATAAACCTAAACTGCTAGAAACCTTTCGAATGACCGCATTGGATCACTTGAAAA
64 ATCACTTGAAGATAAACCTAAACTGCTAGAAACCTTTCGAATGACCGCACTGGATCACTTGAAGA
*
20291 TAAACATAAACTGCTGGAAACTTTCTTGATTGACCGCACTAGATTACTTGAAGATAAACCTAAAC
129 TAAACATAAACTGCTGGAAACTTTCTTGATAGACCGCACTAGATTACTTGAAGATAAACCTAAAC
20356 TGCTGGAAACTTTCTTGAT
194 TGCTGGAAACTTTCTTGAT
* * * *
20375 TGACTGCACTAGATCACTTTAAGATAAACCTAAACTGCTAGAAACCTTTTGACCGACCGCACTGG
1 TGACCGCACTGGATCACTTGAAGATAAACTTAAACTG-T-GAAACCTTTTGACCGACCGCACTGG
* * * ** *
20440 ATCACTTGATGATAACCCTAAACTGC-AGGAAACCTTTTGACCGACTGCACTGGATCACTTGAAG
64 ATCACTTGAAGATAAACCTAAACTGCTA-GAAACCTTTCGAATGACCGCACTGGATCACTTGAAG
* *
20504 ATAAACCTAAACTGCTGGAAACCTT-TTGAT
128 ATAAACATAAACTGCTGGAAACTTTCTTGAT
20534 CGACGGCATT
Statistics
Matches: 335, Mismatches: 31, Indels: 17
0.87 0.08 0.04
Matches are distributed among these distances:
213 15 0.04
214 236 0.70
215 45 0.13
216 39 0.12
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (212 bp):
TGACCGCACTGGATCACTTGAAGATAAACTTAAACTGTGAAACCTTTTGACCGACCGCACTGGAT
CACTTGAAGATAAACCTAAACTGCTAGAAACCTTTCGAATGACCGCACTGGATCACTTGAAGATA
AACATAAACTGCTGGAAACTTTCTTGATAGACCGCACTAGATTACTTGAAGATAAACCTAAACTG
CTGGAAACTTTCTTGAT
Found at i:20607 original size:36 final size:36
Alignment explanation
Indices: 20562--20633 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
20552 TGAAATTCAG
*
20562 CTAAGGAAAGATC-GCCCTAGATCAATATGAAACTAT
1 CTAAAGAAAGA-CAGCCCTAGATCAATATGAAACTAT
*
20598 CTAAAGAAAGACAGCCCTGGATCAATATGAAACTAT
1 CTAAAGAAAGACAGCCCTAGATCAATATGAAACTAT
20634 AAAAAAGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (36 bp):
CTAAAGAAAGACAGCCCTAGATCAATATGAAACTAT
Found at i:20656 original size:33 final size:35
Alignment explanation
Indices: 20562--20656 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 35
20552 TGAAATTCAG
* *
20562 CTAAGGAAAGATC-GCCCTAGATCAATATGAAACTA
1 CTAAAGAAAGA-CAGCCCTAGGTCAATATGAAACTA
20597 TCTAAAGAAAGACAGCCCT-GGATCAATATGAAACTA
1 -CTAAAGAAAGACAGCCCTAGG-TCAATATGAAACTA
*
20633 -TAAA-AAAGACCA-TCCTAGGTCAAT
1 CTAAAGAAAGA-CAGCCCTAGGTCAAT
20657 TAACTGAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
33 13 0.25
34 8 0.15
35 2 0.04
36 29 0.56
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (35 bp):
CTAAAGAAAGACAGCCCTAGGTCAATATGAAACTA
Found at i:27169 original size:14 final size:13
Alignment explanation
Indices: 27150--27205 Score: 60
Period size: 14 Copynumber: 4.2 Consensus size: 13
27140 CTCAAAACTC
27150 TTTTGAAAACTCAT
1 TTTTGAAAA-TCAT
*
27164 TTTTGAAAATCTT
1 TTTTGAAAATCAT
27177 TTCTTGAAAA-CATT
1 TT-TTGAAAATCA-T
*
27191 TTTTGAAAAACAT
1 TTTTGAAAATCAT
27204 TT
1 TT
27206 CTTGTTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 16 0.43
14 21 0.57
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (13 bp):
TTTTGAAAATCAT
Found at i:27198 original size:13 final size:12
Alignment explanation
Indices: 27143--27199 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 12
27133 TAAAAAACTC
*
27143 AAAACTCTTTTG
1 AAAACTTTTTTG
27155 AAAACTCATTTTTG
1 AAAACT--TTTTTG
27169 AAAATCTTTTCTTG
1 AAAA-CTTTT-TTG
27183 AAAACATTTTTTG
1 AAAAC-TTTTTTG
27196 AAAA
1 AAAA
27200 ACATTTCTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
12 6 0.15
13 11 0.28
14 20 0.51
15 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (12 bp):
AAAACTTTTTTG
Found at i:27300 original size:13 final size:13
Alignment explanation
Indices: 27262--27300 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
27252 CCTCGCTTTC
*
27262 TTTTTCTTTTCGT
1 TTTTTCTTTTCTT
*
27275 TTTTTCACTTTCTT
1 TTTTTC-TTTTCTT
27289 TTTTTCTTTTCT
1 TTTTTCTTTTCT
27301 AATAGGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Done.