Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012172.1 Corchorus olitorius cultivar O-4 contig12205, 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: 8198
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:2966 original size:26 final size:27
Alignment explanation
Indices: 2914--2980 Score: 100
Period size: 26 Copynumber: 2.5 Consensus size: 27
2904 CAGACTCTGG
* *
2914 ATTTTGAGTTTCGAACATGACATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
2941 ATTTTGAGTTTTGAA-ATGAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
2967 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
2981 CTTTTGAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:3028 original size:14 final size:14
Alignment explanation
Indices: 3019--3152 Score: 169
Period size: 14 Copynumber: 9.6 Consensus size: 14
3009 GGTTTTGAAA
*
3019 TTTGAATTTTGAGC
1 TTTGAATTTTGAGT
** *
3033 CATGAATTTTGAAT
1 TTTGAATTTTGAGT
3047 TTTGAATTTTGAGT
1 TTTGAATTTTGAGT
*
3061 TTTGAGTTTTGAGT
1 TTTGAATTTTGAGT
*
3075 TTTGAGTTTTGAGT
1 TTTGAATTTTGAGT
*
3089 TTTGAGTTTTGAGT
1 TTTGAATTTTGAGT
*
3103 TTTGAGTTTTGAGT
1 TTTGAATTTTGAGT
* *
3117 TTTGAGTTTTGAAT
1 TTTGAATTTTGAGT
*
3131 TTTGAATTTTGAAT
1 TTTGAATTTTGAGT
3145 TTTGAATT
1 TTTGAATT
3153 GCCTATTTGG
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 110 1.00
ACGTcount: A:0.21, C:0.01, G:0.22, T:0.55
Consensus pattern (14 bp):
TTTGAATTTTGAGT
Found at i:3038 original size:43 final size:43
Alignment explanation
Indices: 2957--3038 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
2947 AGTTTTGAAA
* * *
2957 TGAAATGCAAATTTTGAATTTTGACTTTTGAGGAATGAAATGT
1 TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAAATGT
** *
3000 TGAAATGCAGGTTTTGAAATTTGAATTTTGAGCCATGAA
1 TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAA
3039 TTTTGAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (43 bp):
TGAAATGCAAATTTTGAAATTTGAATTTTGAGCAATGAAATGT
Found at i:3063 original size:21 final size:21
Alignment explanation
Indices: 3010--3152 Score: 178
Period size: 21 Copynumber: 6.8 Consensus size: 21
3000 TGAAATGCAG
**
3010 GTTTTGAAATTTGAATTTTGA
1 GTTTTGAGTTTTGAATTTTGA
*** *
3031 GCCATGAATTTTGAATTTTGA
1 GTTTTGAGTTTTGAATTTTGA
* *
3052 ATTTTGAGTTTTGAGTTTTGA
1 GTTTTGAGTTTTGAATTTTGA
*
3073 GTTTTGAGTTTTGAGTTTTGA
1 GTTTTGAGTTTTGAATTTTGA
*
3094 GTTTTGAGTTTTGAGTTTTGA
1 GTTTTGAGTTTTGAATTTTGA
3115 GTTTTGAGTTTTGAATTTTGA
1 GTTTTGAGTTTTGAATTTTGA
* *
3136 ATTTTGAATTTTGAATT
1 GTTTTGAGTTTTGAATT
3153 GCCTATTTGG
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 108 1.00
ACGTcount: A:0.22, C:0.01, G:0.22, T:0.55
Consensus pattern (21 bp):
GTTTTGAGTTTTGAATTTTGA
Found at i:3152 original size:7 final size:7
Alignment explanation
Indices: 3039--3149 Score: 177
Period size: 7 Copynumber: 15.9 Consensus size: 7
3029 GAGCCATGAA
*
3039 TTTTGAA
1 TTTTGAG
*
3046 TTTTGAA
1 TTTTGAG
3053 TTTTGAG
1 TTTTGAG
3060 TTTTGAG
1 TTTTGAG
3067 TTTTGAG
1 TTTTGAG
3074 TTTTGAG
1 TTTTGAG
3081 TTTTGAG
1 TTTTGAG
3088 TTTTGAG
1 TTTTGAG
3095 TTTTGAG
1 TTTTGAG
3102 TTTTGAG
1 TTTTGAG
3109 TTTTGAG
1 TTTTGAG
3116 TTTTGAG
1 TTTTGAG
*
3123 TTTTGAA
1 TTTTGAG
*
3130 TTTTGAA
1 TTTTGAG
*
3137 TTTTGAA
1 TTTTGAG
3144 TTTTGA
1 TTTTGA
3150 ATTGCCTATT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 102 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (7 bp):
TTTTGAG
Found at i:3348 original size:33 final size:33
Alignment explanation
Indices: 3306--3383 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
3296 AGAAACTGTG
* * *
3306 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
3339 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
3372 AATTTTGAACTT
1 GATTTTGAACTT
3384 CCTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:3482 original size:56 final size:55
Alignment explanation
Indices: 3421--3752 Score: 183
Period size: 54 Copynumber: 6.0 Consensus size: 55
3411 AATTCAACCT
* * *
3421 TGATCATGGAAATATTTCTTGGAACGACCGCACTGGATCAA-TTTAGAGATCAACTC
1 TGATCATCGAAA-ACTTCTTGGAACGACCACACTGGATCAACTTTA-AGATCAACTC
* *
3477 TGATCATCGTAAACTTCTTGGAATGACCACACTGGATCAACTTTAAGATCAACT-
1 TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACTC
** * * * ** *
3531 TAGATTTTTGAAAACTTCTATGGAA-GACCACACAGGGTCGTC-TGAAGATCAACT-
1 T-GATCATCGAAAACTTCT-TGGAACGACCACACTGGATCAACTTTAAGATCAACTC
* * * *
3585 TAGATC-TCTGAAAACTTCTAT-GAAAGACCACACTGGGTCATC-TTAAAATCAACT-
1 T-GATCATC-GAAAACTTCT-TGGAACGACCACACTGGATCAACTTTAAGATCAACTC
* * *
3639 TAGATC-TCTGAAAACTTCTATGAAAGACCAC-ACCGGCACTGGGTCATC-TTAAGATCAACT-
1 T-GATCATC-GAAAACTTCT-TG---GA--ACGACC-ACACTGGATCAACTTTAAGATCAACTC
* *
3699 TAAATC-TCTGAAAACTTCTAT-GAAAGACCACACTGGATCAAC-TTAAGATCAACT
1 T-GATCATC-GAAAACTTCT-TGGAACGACCACACTGGATCAACTTTAAGATCAACT
3753 TTCTAGAGAG
Statistics
Matches: 235, Mismatches: 28, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
53 4 0.02
54 98 0.42
55 63 0.27
56 21 0.09
58 2 0.01
59 3 0.01
60 44 0.19
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (55 bp):
TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAACTTTAAGATCAACTC
Found at i:3597 original size:54 final size:54
Alignment explanation
Indices: 3487--3753 Score: 320
Period size: 54 Copynumber: 4.8 Consensus size: 54
3477 TGATCATCGT
* * * * * *
3487 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAAAGACCACACAGGGTCATC-TTAAGATCAACTTAGATCTCTGA
* * *
3542 AAACTTCTATGGAAGACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
* *
3596 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAAATCAACTTAGATCTCTGA
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
*
3650 AAACTTCTATGAAAGACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGA
1 AAACTTCTATGAAAGACCACA----CA--GGGTCATCTTAAGATCAACTTAGATCTCTGA
* * *
3710 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTT
3754 TCTAGAGAGA
Statistics
Matches: 185, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
54 109 0.59
55 23 0.12
56 2 0.01
58 1 0.01
60 50 0.27
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (54 bp):
AAACTTCTATGAAAGACCACACAGGGTCATCTTAAGATCAACTTAGATCTCTGA
Found at i:3720 original size:114 final size:108
Alignment explanation
Indices: 3487--3753 Score: 365
Period size: 114 Copynumber: 2.4 Consensus size: 108
3477 TGATCATCGT
* * *
3487 AAACTTCT-TGGAATGACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTA
1 AAACTTCTAT-GAAAGACCACACTGGATCAAC-TTAAGATCAACTTAGATCTCTGAAAACTTCTA
* * *
3551 TGGAAGACCACACAGGGTCGTCTGAAGATCAACTTAGATCTCTGA
64 TGAAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
* * *
3596 AAACTTCTATGAAAGACCACACTGGGTCATCTTAAAATCAACTTAGATCTCTGAAAACTTCTATG
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
*
3661 AAAGACCACACCGGCACTGGGTCATCTTAAGATCAACTTAAATCTCTGA
66 AAAGACCACA----CA--GGGTCATCTGAAGATCAACTTAAATCTCTGA
3710 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
1 AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTT
3754 TCTAGAGAGA
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
108 40 0.29
109 26 0.19
110 1 0.01
112 2 0.01
114 69 0.50
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (108 bp):
AAACTTCTATGAAAGACCACACTGGATCAACTTAAGATCAACTTAGATCTCTGAAAACTTCTATG
AAAGACCACACAGGGTCATCTGAAGATCAACTTAAATCTCTGA
Found at i:3879 original size:37 final size:37
Alignment explanation
Indices: 3832--4349 Score: 492
Period size: 37 Copynumber: 13.9 Consensus size: 37
3822 AAACTTTGAT
* *
3832 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAAC
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* *
3869 AGGGACCTTAAATAAGGA-TTTAATGAGAAACCTAAAC
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAAAC
* * * *
3906 AGGAATCTTGAACAAGATTTTGATGAGACACCTAAAC
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* *
3943 AGGGACCTTAAATAAGGA-TTTGATAAGAAACCTAAAC
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAAAC
* * * *
3980 AGTGATCTTAAACAAAAATTTTG-TCAAGAAACCTAAAC
1 AGGGATCTTAAA-TAAGATTTTGAT-GAGAAACCTAAAC
* * *
4018 AGGCATCTTAAATAAGGA-TTTGATAAGAAGCCTAAAC
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAAAC
* *
4055 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAAC
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* *
4092 AGGGACCTTAAATAAGGA-TTTAATGAGAAACCTAAAC
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAAAC
* * * *
4129 AGGAATCTTGAACAAGATTTTGATGAGACACCTAAAC
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* *
4166 AGGGACCTTAAATAAGAATTTTGATAAGAAACCTAAAC
1 AGGGATCTTAAATAAG-ATTTTGATGAGAAACCTAAAC
* * * * *
4204 AGGAATCTTGAATAAGGTTTTGATGAGACACCTAAAT
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* * **
4241 AGGGACCTTAAATAAGGA-TTTGATAAGAAATATAAAC
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAAAC
* ** * * * *
4278 AGGAATCTTGGACAAGGTTTTGGTGAGACACCTAAAC
1 AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
* * *
4315 AGGGACCTTAAATAAGGA-TTTGATAAGTAACCTAA
1 AGGGATCTTAAATAA-GATTTTGATGAGAAACCTAA
4350 TTAGAAATCT
Statistics
Matches: 383, Mismatches: 83, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
36 7 0.02
37 305 0.80
38 71 0.19
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (37 bp):
AGGGATCTTAAATAAGATTTTGATGAGAAACCTAAAC
Found at i:3931 original size:74 final size:74
Alignment explanation
Indices: 3836--4380 Score: 788
Period size: 74 Copynumber: 7.3 Consensus size: 74
3826 TTTGATAGGG
* * *
3836 ATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGAAACC
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
3901 TAAACAGGA
66 TAAACAGGA
3910 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
3975 TAAACAGTG-
66 TAAACAG-GA
* * * * * * *
3984 ATCTTAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCATCTTAAATAAGGATTTGATAAGAAG
1 ATCTTGAAC-AAGATTTTGAT-GAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAA
*
4048 CCTAAACAGGG
64 CCTAAACAGGA
* * *
4059 ATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGAAACC
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
4124 TAAACAGGA
66 TAAACAGGA
*
4133 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGAATTTTGATAAGAAAC
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAGAAAC
4198 CTAAACAGGA
65 CTAAACAGGA
* * * **
4208 ATCTTGAATAAGGTTTTGATGAGACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAATA
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
4273 TAAACAGGA
66 TAAACAGGA
* * * *
4282 ATCTTGGACAAGGTTTTGGTGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGTAACC
1 ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
** *
4347 TAATTAGAA
66 TAAACAGGA
*
4356 ATCTTGAACAAGGTTTTGATGAGAC
1 ATCTTGAACAAGATTTTGATGAGAC
4381 TGAATTTTGT
Statistics
Matches: 424, Mismatches: 41, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
74 290 0.68
75 134 0.32
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (74 bp):
ATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACC
TAAACAGGA
Found at i:4239 original size:223 final size:223
Alignment explanation
Indices: 3832--4380 Score: 825
Period size: 223 Copynumber: 2.5 Consensus size: 223
3822 AAACTTTGAT
3832 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
1 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
*
3897 AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGAT
66 AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGAAT
*
3962 TTGATAAGAAACCTAAACAGTGATCTTAAACAAAAATTTTGTCAAGAAACCTAAACAGGCATCTT
131 TTGATAAGAAACCTAAACAGTGATCTTAAACAAAAATTTTGTCAAGAAACCTAAACAGGCACCTT
* *
4027 AAATAAGGATTTGATAAGAAGCCTAAAC
196 AAATAAGGATTTGATAAGAAACATAAAC
4055 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
1 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
4120 AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGAAT
66 AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGAA-
* * ** * * * *
4185 TTTGATAAGAAACCTAAACAG-GAATCTTGAA-TAAGGTTTTGAT-GAGACACCTAAATAGGGAC
130 TTTGATAAGAAACCTAAACAGTG-ATCTTAAACAAAAATTTTG-TCAAGAAACCTAAACAGGCAC
*
4247 CTTAAATAAGGATTTGATAAGAAATATAAAC
193 CTTAAATAAGGATTTGATAAGAAACATAAAC
* ** * * * * *
4278 AGGAATCTTGGACAAGGTTTTGGTGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGT
1 AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
** * *
4343 AACCTAATTAGAAATCTTGAACAAGGTTTTGATGAGAC
66 AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGAC
4381 TGAATTTTGT
Statistics
Matches: 298, Mismatches: 25, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
223 269 0.90
224 29 0.10
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (223 bp):
AGGGATCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTAATGAGA
AACCTAAACAGGAATCTTGAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGAAT
TTGATAAGAAACCTAAACAGTGATCTTAAACAAAAATTTTGTCAAGAAACCTAAACAGGCACCTT
AAATAAGGATTTGATAAGAAACATAAAC
Found at i:5307 original size:87 final size:87
Alignment explanation
Indices: 5164--5326 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 87
5154 TGCCCCAAGC
* * * *
5164 CTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAACTGATGGTTCTAGATCAGCTTCCCA
1 CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTAGATCAACTTCCCA
5229 CCTTAAGAAATATTTCCCAAAT
66 CCTTAAGAAATATTTCCCAAAT
* * * * *
5251 CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCAATTTCTCA
1 CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTAGATCAACTTCCCA
*
5316 TCTTAAGAAAT
66 CCTTAAGAAAT
5327 GTTCAAACAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (87 bp):
CTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAACTGATGGTTCTAGATCAACTTCCCA
CCTTAAGAAATATTTCCCAAAT
Found at i:5479 original size:4 final size:4
Alignment explanation
Indices: 5459--5536 Score: 54
Period size: 4 Copynumber: 19.8 Consensus size: 4
5449 TCCTTTTGAT
* * **
5459 TTTC -TTC TTTA TTTC TTTC TTTC TTT- TTTT TTTC TCAC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* * *
5504 TTTGC TTTC TCTC TTTTT TTTC TTTT TTTC TTT
1 TTT-C TTTC TTTC -TTTC TTTC TTTC TTTC TTT
5537 AGATTGCTTC
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
3 9 0.16
4 41 0.73
5 6 0.11
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:5492 original size:30 final size:30
Alignment explanation
Indices: 5458--5536 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
5448 TTCCTTTTGA
* *
5458 TTTTCTTCTTTATTTCTTT-CTTTCTTTTTT
1 TTTTCTTCTTT-TTTCTTTGCTTTCTCTCTT
*
5488 TTTTCTCACTTTTTTCTTTGCTTTCTCTCTT
1 TTTTCT-TCTTTTTTCTTTGCTTTCTCTCTT
5519 TTTT-TTCTTTTTTTCTTT
1 TTTTCTTC-TTTTTTCTTT
5537 AGATTGCTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 24 0.57
31 17 0.40
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (30 bp):
TTTTCTTCTTTTTTCTTTGCTTTCTCTCTT
Found at i:5506 original size:22 final size:22
Alignment explanation
Indices: 5473--5532 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5463 TTCTTTATTT
*
5473 CTTTCTTTCTTTTTTTTTTCTCA
1 CTTT-TTTCTTTTTTTTCTCTCA
** *
5496 CTTTTTTCTTTGCTTTCTCTCT
1 CTTTTTTCTTTTTTTTCTCTCA
*
5518 TTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
5533 CTTTAGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (22 bp):
CTTTTTTCTTTTTTTTCTCTCA
Found at i:6237 original size:14 final size:13
Alignment explanation
Indices: 6171--6234 Score: 85
Period size: 14 Copynumber: 4.7 Consensus size: 13
6161 ACTCAAAACC
6171 TTTTGAAAACTCAT
1 TTTTGAAAA-TCAT
6185 TTTTGAAAATCAT
1 TTTTGAAAATCAT
6198 TTCTTGAAAA-CAGT
1 TT-TTGAAAATCA-T
6212 TTCTTGAAAATCAT
1 TT-TTGAAAATCAT
6226 TTTTGAAAA
1 TTTTGAAAA
6235 ATCCTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.32
14 30 0.64
15 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (13 bp):
TTTTGAAAATCAT
Done.