Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022961.1 Corchorus olitorius cultivar O-4 contig22994, 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: 26803
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:545 original size:10 final size:10
Alignment explanation
Indices: 530--554 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
520 ACCTCCTGTA
530 ACATACCTTC
1 ACATACCTTC
540 ACATACCTTC
1 ACATACCTTC
550 ACATA
1 ACATA
555 ATTCTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (10 bp):
ACATACCTTC
Found at i:3028 original size:21 final size:21
Alignment explanation
Indices: 3004--3075 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
2994 TGCTAGGAAT
*
3004 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTTCAAGC
*
3025 TCATTGGAGAAAGTTTCAAGC
1 TCATTGGAGAAGGTTTCAAGC
3046 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTTCAAGC
3067 TCATTGGAG
1 TCATTGGAG
3076 TTGCCTAAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTTCAAGC
Found at i:5853 original size:21 final size:21
Alignment explanation
Indices: 5827--5898 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
5817 TGCTAGGAAT
*
5827 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTTCAAGC
* *
5848 TAATTGGAGAAAGTTTCAAGC
1 TCATTGGAGAAGGTTTCAAGC
5869 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTTCAAGC
5890 TCATTGGAG
1 TCATTGGAG
5899 TTGCCTAAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTTCAAGC
Found at i:9983 original size:76 final size:76
Alignment explanation
Indices: 9846--9997 Score: 177
Period size: 76 Copynumber: 2.0 Consensus size: 76
9836 ACAAGGGCCT
* **
9846 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCA-AG
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGACCACCCAGA-
9910 TGGGCGGTGTCA
65 TGGGCGGTGTCA
* * *
9922 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGACCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGACCACCCA
*
9984 GATGGGCTGTGTCA
63 GATGGGCGGTGTCA
9998 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
75 4 0.06
76 54 0.83
77 7 0.11
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGACCACCCAGAT
GGGCGGTGTCA
Found at i:14626 original size:13 final size:13
Alignment explanation
Indices: 14608--14633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14598 TTAGAAGTAC
14608 TTTGGTCAGTGTT
1 TTTGGTCAGTGTT
14621 TTTGGTCAGTGTT
1 TTTGGTCAGTGTT
14634 AGTTAGTTCG
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:0.08, C:0.08, G:0.31, T:0.54
Consensus pattern (13 bp):
TTTGGTCAGTGTT
Found at i:14657 original size:24 final size:24
Alignment explanation
Indices: 14630--14691 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
14620 TTTTGGTCAG
* *
14630 TGTTAGTTAGTTCGTTTTGACTTT
1 TGTTAGTTAGTCCATTTTGACTTT
*
14654 TGTTAGTTAGTCCATTTTGGCTTT
1 TGTTAGTTAGTCCATTTTGACTTT
*
14678 TGTCAAGTTAGTCC
1 TGT-TAGTTAGTCC
14692 TTGTAGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.52
Consensus pattern (24 bp):
TGTTAGTTAGTCCATTTTGACTTT
Found at i:17857 original size:66 final size:66
Alignment explanation
Indices: 17501--18094 Score: 572
Period size: 66 Copynumber: 9.0 Consensus size: 66
17491 CTCTTCCCAG
* * *
17501 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTT-GCATTTAAGTGT-AGTATTTT-CATT
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGT-TCA--ATTTTGC-TT
17563 TCCAA
62 TCCAA
* * * * * *
17568 AAATGCCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTT-GCAT-TCAAGTTTAGTATTTTGATT
1 AAATACCCTTTCGGTCGAAGGGTCAGT-TTCATATTTTTCGCATCT-AAGTTCA--ATTTTGCTT
17630 TCCAA
62 TCCAA
* * ** * *
17635 AAATGCCCTTTCGGTCGAAGGGTCGGTTTTGTCTTTTT-GCAT-TCAAGTTCAGTACTTTTGATT
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCT-AAGTTCA--A-TTTTGCTT
17698 TCCAA
62 TCCAA
* * * * * * *
17703 AAATACCATTTCGGT-GAAAGGGTCATTTTCATCA-TTTCCGCATTTAAGTT-TATTCTGTTTTC
1 AAATACCCTTTCGGTCG-AAGGGTCAGTTTCAT-ATTTTTCGCATCTAAGTTCAATTTTGCTTTC
17765 C-A
64 CAA
*
17767 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGTTCAATTTTGCTTTCCA
17832 A
66 A
* * * *
17833 AAATACCCTTCCGGTCGAATGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTTCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGTTCAATTTTGCTTTCCA
17898 A
66 A
* * * * * * *
17899 AAATACCCTTTCGAT-GAAAGGGTCAGTTTCATCATTTCT-GCATTTCAGTT-TATTCTGTTTTC
1 AAATACCCTTTCGGTCG-AAGGGTCAGTTTCAT-ATTTTTCGCATCTAAGTTCAATTTTGCTTTC
17961 C-A
64 CAA
* *
17963 AAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGTTCAATTTTGCTTTCCA
18028 A
66 A
* * * *
18029 AAATACCCTTCCGGGCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTCCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGTTCAATTTTGCTTTCCA
18094 A
66 A
18095 GTTTAGCTTT
Statistics
Matches: 457, Mismatches: 50, Indels: 41
0.83 0.09 0.07
Matches are distributed among these distances:
63 6 0.01
64 79 0.17
65 41 0.09
66 169 0.37
67 110 0.24
68 42 0.09
69 9 0.02
70 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (66 bp):
AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCGCATCTAAGTTCAATTTTGCTTTCCA
A
Found at i:17863 original size:130 final size:131
Alignment explanation
Indices: 17501--18094 Score: 568
Period size: 130 Copynumber: 4.5 Consensus size: 131
17491 CTCTTCCCAG
* * *
17501 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATCTTTTTGCATTTAAGTGT-AGTATTTT-CATTT
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTGCATCTAAGT-TCA--ATTTTGC-TTT
* * * * * * *
17564 CCAAAAATGCCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTT-GCAT-TCAAGTTTAGTATTTT
62 CCAAAAATACCCTTCCGGTCGAAGGGTCAGT-TTCATATTTTTCACATCT-AAGTTCA--ATTTT
*
17626 GATTTCCAA
123 GTTTTCCAA
* * ** * *
17635 AAATGCCCTTTCGGTCGAAGGGTCGGTTTTGTCTTTTTGCAT-TCAAGTTCAGTACTTTTGATTT
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTGCATCT-AAGTTCA--A-TTTTGCTTT
* * * * * * * *
17699 CCAAAAATACCATTTCGGT-GAAAGGGTCATTTTCATCA-TTTCCGCATTTAAGTT-TATTCTGT
62 CCAAAAATACCCTTCCGGTCG-AAGGGTCAGTTTCAT-ATTTTTCACATCTAAGTTCAATTTTGT
17761 TTTCC-A
125 TTTCCAA
*
17767 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTT-GCATCTAAGTTCAATTTTGCTTTCCA
*
17832 AAAATACCCTTCCGGTCGAATGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTT-
65 AAAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTG-TTTTC
17896 CAA
129 CAA
* * * * * * *
17899 AAATACCCTTTCGAT-GAAAGGGTCAGTTTCATCATTTCTGCATTTCAGTT-TATTCTGTTTTCC
1 AAATACCCTTTCGGTCG-AAGGGTCAGTTTCAT-ATTTTTGCATCTAAGTTCAATTTTGCTTTCC
*
17962 -AAAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTC
64 AAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTC
18026 CAA
129 CAA
* * * *
18029 AAATACCCTTCCGGGCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTCCA
1 AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTT-GCATCTAAGTTCAATTTTGCTTTCCA
18094 A
65 A
18095 GTTTAGCTTT
Statistics
Matches: 386, Mismatches: 51, Indels: 48
0.80 0.11 0.10
Matches are distributed among these distances:
129 9 0.02
130 147 0.38
131 31 0.08
132 77 0.20
133 27 0.07
134 48 0.12
135 37 0.10
136 9 0.02
137 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (131 bp):
AAATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTGCATCTAAGTTCAATTTTGCTTTCCAA
AAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTCCA
A
Found at i:17931 original size:196 final size:195
Alignment explanation
Indices: 17501--18091 Score: 762
Period size: 196 Copynumber: 3.0 Consensus size: 195
17491 CTCTTCCCAG
* * * **
17501 AAATACCCTTTCGGTCAAAGGGTCAGTTTCATC-TTTTTGCATTTAAGTGTAGTATTTTCATTTC
1 AAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTCTGCATTTAAGT-T--TATTCTGTTTTC
* * * * * *
17565 CAAAAATGCCCTTTCGGTCAAAGGGTCAGTCTT-GTCTTTTT-GCAT-TCAAGTTTAGTATTTTG
63 C-AAAATACCCTTTCGGTCGAAGGGTCAGT-TTCATATTTTTCACATCT-AAGTTCA--ATTTTG
* * * * ** * *
17627 ATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCGGTTTTGTCTTTTT-GCAT-TCAAGTTCAGTAC
123 CTTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCT-AAGTTCA--A-
*
17690 TTTTGATTTCCAA
184 TTTTG-TTTTCAA
* * *
17703 AAATACCATTTCGGTGAAAGGGTCATTTTCATCATTTCCGCATTTAAGTTTATTCTGTTTTCCAA
1 AAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTATTCTGTTTTCCAA
17768 AATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCAA
66 AATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCAA
*
17833 AAATACCCTTCCGGTCGAATGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTTCA
131 AAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTG-TTTTCA
17898 A
195 A
* *
17899 AAATACCCTTTCGATGAAAGGGTCAGTTTCATCATTTCTGCATTTCAGTTTATTCTGTTTTCCAA
1 AAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTATTCTGTTTTCCAA
*
17964 AATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCAA
66 AATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCAA
*
18029 AAATACCCTTCCGGGCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTC
131 AAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTC
18092 CAAGTTTAGC
Statistics
Matches: 350, Mismatches: 33, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
195 5 0.01
196 191 0.55
197 1 0.00
198 46 0.13
199 42 0.12
200 20 0.06
201 1 0.00
202 31 0.09
203 13 0.04
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (195 bp):
AAATACCCTTTCGGTGAAAGGGTCAGTTTCATCATTTCTGCATTTAAGTTTATTCTGTTTTCCAA
AATACCCTTTCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGCTTTCCAA
AAATACCCTTCCGGTCGAAGGGTCAGTTTCATATTTTTCACATCTAAGTTCAATTTTGTTTTCAA
Found at i:18901 original size:22 final size:22
Alignment explanation
Indices: 18859--18901 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18849 TTTTCCGCAA
* * *
18859 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAAGACTTGTC
18881 CAAGTCCTGGACAAGACTTGT
1 CAAGTCCTGGACAAGACTTGT
18902 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAAGACTTGTC
Found at i:18957 original size:21 final size:21
Alignment explanation
Indices: 18931--18972 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
18921 TTCAACAGAC
18931 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
18952 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
18973 TCTGATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:18977 original size:71 final size:71
Alignment explanation
Indices: 18859--19043 Score: 289
Period size: 71 Copynumber: 2.6 Consensus size: 71
18849 TTTTCCGCAA
* * * *
18859 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAAGACTTGTTCTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTATC
18924 AACAGAC
65 AACAGAC
* *
18931 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTATCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTATCA
18996 ACAGAC
66 ACAGAC
* *
19002 CAGGTCCTGGGCAGGAGTTGTCAAATCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
19044 CCTGTTTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 83 0.80
72 21 0.20
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.30
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCGTCTATCA
ACAGAC
Found at i:21010 original size:66 final size:66
Alignment explanation
Indices: 20939--21065 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
20929 AGAATTTGTT
* * *
20939 TCATCACAAACAATACCTAAAACAGATTTAGTGTCATTGCAAACAATACTCAAATTAGGTTTAGT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATTACAAACAACACTCAAATTAGGTTTAGT
21004 A
66 A
* * *
21005 TCATCACTAACAACATCTAAAACAGATTTCGTGTCATTACAAACAACACTCAAATTAGGTT
1 TCATCACAAACAACACCTAAAACAGATTTAGTGTCATTACAAACAACACTCAAATTAGGTT
21066 CAGAATTACT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAGATTTAGTGTCATTACAAACAACACTCAAATTAGGTTTAGT
A
Found at i:21052 original size:33 final size:33
Alignment explanation
Indices: 20891--21052 Score: 114
Period size: 33 Copynumber: 4.9 Consensus size: 33
20881 ATGATCAACC
* ** * *
20891 AAAACAGATTT-GTTTTCATCACAATTAGCATCC
1 AAAACAGATTTAG-TGTCATCACAAACAACATCT
* * *
20924 AAAACAGAATTT-GTTTCATCACAAACAATACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACATCT
** *
20957 AAAACAGATTTAGTGTCATTGCAAACAATA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACATCT
** * * *
20989 CAAATTAGGTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACATCT
* *
21023 AAAACAGATTTCGTGTCATTACAAACAACA
1 AAAACAGATTTAGTGTCATCACAAACAACA
21053 CTCAAATTAG
Statistics
Matches: 101, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
32 6 0.06
33 88 0.87
34 7 0.07
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACATCT
Found at i:21465 original size:10 final size:10
Alignment explanation
Indices: 21450--21476 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21440 CCTTGATCTT
21450 CATGCTTTTC
1 CATGCTTTTC
21460 CATGCTTTTC
1 CATGCTTTTC
21470 CATGCTT
1 CATGCTT
21477 CCTTGCAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (10 bp):
CATGCTTTTC
Found at i:22255 original size:35 final size:35
Alignment explanation
Indices: 22163--22257 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 35
22153 CGAAAATGAC
22163 GGGAACTTTCCGTAAA-TTGAAAA-TTAAAACTTGAT
1 GGGAACTTTCC--AAATTTGAAAACTTAAAACTTGAT
* *
22198 GGGAACTTTCCCAATTTGAAAACTTAAAAAC-TGGT
1 GGGAACTTTCCAAATTTGAAAACTT-AAAACTTGAT
*
22233 GGGAACTTTCCAAATTTAAAAACTT
1 GGGAACTTTCCAAATTTGAAAACTT
22258 TGACCTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.04
34 7 0.13
35 39 0.74
36 5 0.09
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
GGGAACTTTCCAAATTTGAAAACTTAAAACTTGAT
Found at i:25640 original size:38 final size:38
Alignment explanation
Indices: 25588--25767 Score: 315
Period size: 38 Copynumber: 4.7 Consensus size: 38
25578 AAGACTAAGA
* * * **
25588 AAAGACGACTTGTTTCCAGTCAACTTTGATAACTATTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
25626 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
25664 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
25702 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
25740 AAAGATGACCTGTTTCCAGTCAACTTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTG
25768 TGTCGAAACG
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 137 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (38 bp):
AAAGATGACCTGTTTCCAGTCAACTTTGATAATTGCTG
Done.