Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006711.1 Corchorus capsularis cultivar CVL-1 contig06732, 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: 6842
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Found at i:66 original size:26 final size:26
Alignment explanation
Indices: 37--88 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
27 AACACTAAAG
37 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
63 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
89 CAAGCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.35, T:0.12
Consensus pattern (26 bp):
GAAACAAGGAACATGCAAGGGGCTGT
Found at i:96 original size:26 final size:26
Alignment explanation
Indices: 38--96 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
28 ACACTAAAGG
*
38 AAACAAGGAACATGCAAGGGGCTGTG
1 AAACAAGGAACATGCAAGGGGCTGTC
64 AAACAAGGAACATGCAAGGGGCTGTC
1 AAACAAGGAACATGCAAGGGGCTGTC
*
90 AAGCAAG
1 AAACAAG
97 CATGCATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.32, T:0.10
Consensus pattern (26 bp):
AAACAAGGAACATGCAAGGGGCTGTC
Found at i:3709 original size:16 final size:16
Alignment explanation
Indices: 3688--3749 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 16
3678 TAAGAGTAAA
3688 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
3704 AGTAAAA-TAGTAAT-
1 AGTAAAAGAAGTAATC
*
3718 --T--AAG-AGTAA-A
1 AGTAAAAGAAGTAATC
3728 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
3744 AGTAAA
1 AGTAAA
3750 TCGGTAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
10 7 0.19
12 2 0.06
14 3 0.08
15 11 0.31
16 13 0.36
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:3721 original size:40 final size:39
Alignment explanation
Indices: 3670--3749 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 39
3660 GGAAGTGATC
3670 AATAGAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
1 AATAGAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
3709 AATAGTAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
1 AATAG-AATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
3749 A
1 A
3750 TCGGTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.21
Consensus pattern (39 bp):
AATAGAATTAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
Found at i:3849 original size:32 final size:32
Alignment explanation
Indices: 3792--3899 Score: 182
Period size: 32 Copynumber: 3.3 Consensus size: 32
3782 AGTAATCAGT
3792 AAAGAGTAAAATGGTA-AAATGGTAATCAAATTC
1 AAAGAGTAAAAT-G-ACAAATGGTAATCAAATTC
3825 AAAGAGTAAAATGACAAATGGTAATCAAATTC
1 AAAGAGTAAAATGACAAATGGTAATCAAATTC
*
3857 AAAGAGTAAAATGACAAATGGTAATTAAATTC
1 AAAGAGTAAAATGACAAATGGTAATCAAATTC
3889 AAAGAGTAAAA
1 AAAGAGTAAAA
3900 ATAGTAGTTA
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
31 1 0.01
32 60 0.82
33 12 0.16
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.22
Consensus pattern (32 bp):
AAAGAGTAAAATGACAAATGGTAATCAAATTC
Found at i:3865 original size:17 final size:17
Alignment explanation
Indices: 3813--3865 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3803 TGGTAAAATG
3813 GTAATCAAATTCAAAGA
1 GTAATCAAATTCAAAGA
*
3830 GT-A--AAATGACAAATG-
1 GTAATCAAAT-TCAAA-GA
3845 GTAATCAAATTCAAAGA
1 GTAATCAAATTCAAAGA
3862 GTAA
1 GTAA
3866 AATGACAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 4 0.14
17 10 0.36
18 4 0.14
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (17 bp):
GTAATCAAATTCAAAGA
Found at i:3901 original size:26 final size:28
Alignment explanation
Indices: 3807--3936 Score: 106
Period size: 32 Copynumber: 4.5 Consensus size: 28
3797 GTAAAATGGT
3807 AAAATGGTAATCAAATTCAAAGAGTAAAATG
1 AAAATGGTAATCAAATTCAAAGAGT--AA-G
3838 ACAAATGGTAATCAAATTCAAAGAGTAAAATG
1 A-AAATGGTAATCAAATTCAAAGAGT--AA-G
*
3870 ACAAATGGTAATTAAATTCAAAGAGT-A-
1 A-AAATGGTAATCAAATTCAAAGAGTAAG
* * *
3897 AAAATAGTAGTTAAATTCAAGAGAGT-A-
1 AAAATGGTAATCAAATTCAA-AGAGTAAG
*
3924 AAAATAGTAATCA
1 AAAATGGTAATCA
3937 GTAAAGAGAA
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
26 17 0.18
27 18 0.20
29 1 0.01
31 1 0.01
32 55 0.60
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (28 bp):
AAAATGGTAATCAAATTCAAAGAGTAAG
Found at i:3929 original size:27 final size:26
Alignment explanation
Indices: 3872--3934 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
3862 GTAAAATGAC
*
3872 AAATGGTAATTAAATTCAAAGAGTAA
1 AAATAGTAATTAAATTCAAAGAGTAA
*
3898 AAATAGTAGTTAAATTCAAGAGAGTAA
1 AAATAGTAATTAAATTCAA-AGAGTAA
3925 AAATAGTAAT
1 AAATAGTAAT
3935 CAGTAAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 17 0.52
27 16 0.48
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATAGTAATTAAATTCAAAGAGTAA
Found at i:3974 original size:22 final size:22
Alignment explanation
Indices: 3939--4048 Score: 111
Period size: 22 Copynumber: 5.0 Consensus size: 22
3929 AGTAATCAGT
*
3939 AAAGAGAAAAGAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
3961 AAATG-GTAAAGAGTAAAGAGTA
1 AAA-GAGTAAAGAGTAAAGAGTA
* *
3983 AAAGAGAAAAGAGTAAGGAGT-
1 AAAGAGTAAAGAGTAAAGAGTA
* **
4004 TAAGAGTAATCAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
4026 AAATG-GTCAAA-AGTAAAGAGTA
1 AAA-GAGT-AAAGAGTAAAGAGTA
4048 A
1 A
4049 TCAGTAAAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
21 17 0.23
22 52 0.71
23 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.15
Consensus pattern (22 bp):
AAAGAGTAAAGAGTAAAGAGTA
Found at i:3998 original size:29 final size:31
Alignment explanation
Indices: 3936--4012 Score: 99
Period size: 29 Copynumber: 2.6 Consensus size: 31
3926 AATAGTAATC
*
3936 AGTAAAGAGAAAAGAGT-AAAGAGTAAAATG
1 AGTAAAGAGTAAAGAGTAAAAGAGTAAAATG
3966 -GTAAAGAGTAAAGAGTAAAAGAG-AAAA-G
1 AGTAAAGAGTAAAGAGTAAAAGAGTAAAATG
* *
3994 AGTAAGGAGTTAAGAGTAA
1 AGTAAAGAGTAAAGAGTAA
4013 TCAGTAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 35 0.83
30 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (31 bp):
AGTAAAGAGTAAAGAGTAAAAGAGTAAAATG
Found at i:4027 original size:7 final size:7
Alignment explanation
Indices: 3936--4154 Score: 112
Period size: 7 Copynumber: 30.7 Consensus size: 7
3926 AATAGTAATC
3936 AGTAAAG
1 AGTAAAG
*
3943 AGAAAAG
1 AGTAAAG
3950 AGTAAAG
1 AGTAAAG
3957 AGTAAA-
1 AGTAAAG
3963 ATGGTAAAG
1 A--GTAAAG
3972 AGTAAAG
1 AGTAAAG
3979 AGTAAAAG
1 AGT-AAAG
*
3987 AGAAAAG
1 AGTAAAG
*
3994 AGTAAGG
1 AGTAAAG
*
4001 AGTTAAG
1 AGTAAAG
**
4008 AGTAATC
1 AGTAAAG
4015 AGTAAAG
1 AGTAAAG
4022 AGTAAA-
1 AGTAAAG
4028 ATGGTCAAA-
1 A--GT-AAAG
4037 AGTAAAG
1 AGTAAAG
**
4044 AGTAATC
1 AGTAAAG
4051 AGTAAAAG
1 AGT-AAAG
*
4059 AAG-AATG
1 -AGTAAAG
*
4066 -GTAAAA
1 AGTAAAG
*
4072 AGTTAAG
1 AGTAAAG
**
4079 AGTAATC
1 AGTAAAG
4086 AGTAAAG
1 AGTAAAG
*
4093 AGTAAAAT
1 AGT-AAAG
4101 AGTCAAA-
1 AGT-AAAG
4108 AGTAAAG
1 AGTAAAG
**
4115 AGTAATC
1 AGTAAAG
4122 AGTAAAAG
1 AGT-AAAG
*
4130 AAG-AATG
1 -AGTAAAG
*
4137 -GTAAAA
1 AGTAAAG
4143 AGTAAAG
1 AGTAAAG
4150 AGTAA
1 AGTAA
4155 TCAGTAAAGG
Statistics
Matches: 158, Mismatches: 36, Indels: 36
0.69 0.16 0.16
Matches are distributed among these distances:
5 2 0.01
6 12 0.08
7 109 0.69
8 26 0.16
9 9 0.06
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:4073 original size:35 final size:35
Alignment explanation
Indices: 4005--4197 Score: 266
Period size: 35 Copynumber: 5.5 Consensus size: 35
3995 GTAAGGAGTT
*
4005 AAGAGTAATCAGTAAAGAGTAA-AATGGTCAAAAGTA
1 AAGAGTAATCAGTAAA-AG-AAGAATGGTAAAAAGTA
*
4041 AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTT
1 AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTA
* *
4076 AAGAGTAATCAGTAAAGAGTAA-AATAGTCAAAAGTA
1 AAGAGTAATCAGTAAA-AG-AAGAATGGTAAAAAGTA
4112 AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTA
1 AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTA
* *
4147 AAGAGTAATCAGTAAAGGAAGAATGGT-AAGAGTA
1 AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTA
*
4181 AAGGGTAATCAGTAAAA
1 AAGAGTAATCAGTAAAA
4198 AGATAATCAG
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
34 25 0.18
35 70 0.49
36 45 0.32
37 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (35 bp):
AAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTA
Found at i:4083 original size:14 final size:14
Alignment explanation
Indices: 4066--4376 Score: 68
Period size: 15 Copynumber: 21.8 Consensus size: 14
4056 AAGAAGAATG
*
4066 GTAAAAAGTTAAGA
1 GTAAAAAGTAAAGA
**
4080 GTAATCAGTAAAGA
1 GTAAAAAGTAAAGA
4094 GTAAAATAGTCAAA-A
1 GTAAAA-AGT-AAAGA
* **
4109 GTAAAGAGTAATCA
1 GTAAAAAGTAAAGA
*
4123 GTAAAAGAAG-AATG-
1 GT-AAA-AAGTAAAGA
4137 GTAAAAAGTAAAGA
1 GTAAAAAGTAAAGA
**
4151 GTAATCAGTAAAG-
1 GTAAAAAGTAAAGA
*
4164 G-AAGAATGGT-AAGA
1 GTAA-AA-AGTAAAGA
** **
4178 GTAAAGGGTAATCA
1 GTAAAAAGTAAAGA
**
4192 GTAAAAAGATAATCA
1 GTAAAAAG-TAAAGA
* *
4207 GTAAAGAGTAAAATA
1 GTAAAAAGT-AAAGA
* **
4222 GTAAAAGGTAATCA
1 GTAAAAAGTAAAGA
*
4236 GTAAAAAAGTAATGA
1 GT-AAAAAGTAAAGA
**
4251 -TAATCAGTAAA-A
1 GTAAAAAGTAAAGA
**
4263 GGTAAAATAGTAATCA
1 -GTAAAA-AGTAAAGA
*
4279 GT-AAGAGTAAA-A
1 GTAAAAAGTAAAGA
* *
4291 TGGAAATCAGTAAAGA
1 -GTAAA-AAGTAAAGA
**
4307 GTAAAATAGTAATCA
1 GTAAAA-AGTAAAGA
4322 GTAAAAAGT-AAGAA
1 GTAAAAAGTAAAG-A
**
4336 GGTAATCAGTAAAGA
1 -GTAAAAAGTAAAGA
**
4351 GTAAAATAGTAATCA
1 GTAAAA-AGTAAAGA
*
4366 GTAAAAGGTAA
1 GTAAAAAGTAA
4377 TCAGTAAGAG
Statistics
Matches: 217, Mismatches: 52, Indels: 56
0.67 0.16 0.17
Matches are distributed among these distances:
12 7 0.03
13 29 0.13
14 72 0.33
15 99 0.46
16 10 0.05
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.20
Consensus pattern (14 bp):
GTAAAAAGTAAAGA
Found at i:4099 original size:71 final size:71
Alignment explanation
Indices: 3966--4197 Score: 328
Period size: 71 Copynumber: 3.3 Consensus size: 71
3956 GAGTAAAATG
** * **
3966 GTAAAGAGTAAAGAGTAAAAG-AGAAAAGAGTAAGGAGTTAAGAGTAATCAGTAAAGAGTAAAAT
1 GTAAAGAGTAATCAGTAAAAGAAG-AATG-GTAAAAAGTTAAGAGTAATCAGTAAAGAGTAAAAT
4030 GGTCAAAA
64 GGTCAAAA
*
4038 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTTAAGAGTAATCAGTAAAGAGTAAAATAG
1 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTTAAGAGTAATCAGTAAAGAGTAAAATGG
4103 TCAAAA
66 TCAAAA
*
4109 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAAGAGTAATCAGTAAAG-G-AAGAATG
1 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTTAAGAGTAATCAGTAAAGAGTAA-AATG
*
4172 GT-AAGA
65 GTCAAAA
*
4178 GTAAAGGGTAATCAGTAAAA
1 GTAAAGAGTAATCAGTAAAA
4198 AGATAATCAG
Statistics
Matches: 148, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
69 24 0.16
70 6 0.04
71 94 0.64
72 22 0.15
73 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.25, T:0.18
Consensus pattern (71 bp):
GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAAGTTAAGAGTAATCAGTAAAGAGTAAAATGG
TCAAAA
Found at i:4210 original size:22 final size:21
Alignment explanation
Indices: 4185--4371 Score: 114
Period size: 22 Copynumber: 8.6 Consensus size: 21
4175 AGAGTAAAGG
4185 GTAATCAGTAAAAAGATAATCA
1 GTAATCAGTAAAAAGATAAT-A
** *
4207 GTAAAGAGTAAAATAG-TAAAA
1 GTAATCAGTAAAA-AGATAATA
4228 GGTAATCAGTAAAAA-AGTAAT-
1 -GTAATCAGTAAAAAGA-TAATA
* *
4249 GATAATCAGTAAAAGGTAAAATA
1 G-TAATCAGTAAAAAG-ATAATA
* * *
4272 GTAATCAGT-AAGAGTAAAATG
1 GTAATCAGTAAAAAG-ATAATA
* * *
4293 GAAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAAAG-ATAATA
*
4315 GTAATCAGTAAAAAG-TAAGAA
1 GTAATCAGTAAAAAGATAA-TA
* *
4336 GGTAATCAGTAAAGAGTAAAATA
1 -GTAATCAGTAAAAAG-ATAATA
4359 GTAATCAGTAAAA
1 GTAATCAGTAAAA
4372 GGTAATCAGT
Statistics
Matches: 131, Mismatches: 21, Indels: 26
0.74 0.12 0.15
Matches are distributed among these distances:
20 3 0.02
21 32 0.24
22 89 0.68
23 5 0.04
24 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (21 bp):
GTAATCAGTAAAAAGATAATA
Found at i:4210 original size:29 final size:28
Alignment explanation
Indices: 4177--4240 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
4167 GAATGGTAAG
*
4177 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
4206 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
4235 AGTAAA
1 AGTAAA
4241 AAAGTAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:4232 original size:44 final size:44
Alignment explanation
Indices: 4185--4492 Score: 198
Period size: 43 Copynumber: 7.1 Consensus size: 44
4175 AGAGTAAAGG
4185 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAA-AA
1 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATAA
*
4228 GGTAATCAGTAAAAAAGTAATGATAATCAGTAAA-AGGTAAAATAGTAATCA
1 -GTAATCAGT---AAA--AA-GATAATCAGTAAAGA-GTAAAATAGTAATAA
* * *
4279 GTAA-GAGTAAAATGGA-AATCAGTAAAGAGTAAAATAGTAATCA
1 GTAATCAGTAAAA-AGATAATCAGTAAAGAGTAAAATAGTAATAA
** * *
4322 GTAAAAAGTAAGAAGGTAATCAGTAAAGAGT---A-A--AAT-A
1 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATAA
* **
4359 GTAATCAGT-AAAAGGTAATCAGT-AAGAGTAAAATAGTAATCG
1 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATAA
* ** * * * *
4401 GCAAAAAGTAAAGAG-TAATCAGT-AAGAAGTCAAATTGTAATCA
1 GTAATCAGTAAAAAGATAATCAGTAAAG-AGTAAAATAGTAATAA
* * * * *
4444 GTAA-AATGTGAAAAGACAATCAGTAAAGAGTAAAATGGTAAAAA
1 GTAATCA-GTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATAA
4488 GTAAT
1 GTAAT
4493 GGTGATCAGT
Statistics
Matches: 213, Mismatches: 26, Indels: 49
0.74 0.09 0.17
Matches are distributed among these distances:
35 6 0.03
36 13 0.06
37 8 0.04
38 4 0.02
39 1 0.00
40 1 0.00
41 4 0.02
42 19 0.09
43 56 0.26
44 56 0.26
45 3 0.01
46 3 0.01
47 3 0.01
49 6 0.03
50 29 0.14
51 1 0.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (44 bp):
GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAATAA
Found at i:4247 original size:15 final size:14
Alignment explanation
Indices: 4185--4383 Score: 93
Period size: 15 Copynumber: 13.8 Consensus size: 14
4175 AGAGTAAAGG
4185 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
*
4199 GATAATCAGTAAAGA
1 G-TAATCAGTAAAAA
*
4214 GTAAAAT-AGTAAAAG
1 GT--AATCAGTAAAAA
4229 GTAATCAGTAAAAAA
1 GTAATCAGT-AAAAA
* **
4244 GTAATGA-TAATCA
1 GTAATCAGTAAAAA
*
4257 GTAA-AAGGTAAAATA
1 GTAATCA-GTAAAA-A
*
4272 GTAATCAGT-AAGA
1 GTAATCAGTAAAAA
* * *
4285 GTAA-AATGGAAATCA
1 GTAATCA-GTAAA-AA
**
4300 GTAAAGAGTAAAATA
1 GTAATCAGTAAAA-A
4315 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
** **
4329 GTAAGAAGGTAATCA
1 GTAATCA-GTAAAAA
**
4344 GTAAAGAGTAAAATA
1 GTAATCAGTAAAA-A
*
4359 GTAATCAGTAAAAG
1 GTAATCAGTAAAAA
4373 GTAATCAGTAA
1 GTAATCAGTAA
4384 GAGTAAAATA
Statistics
Matches: 138, Mismatches: 31, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
12 2 0.01
13 16 0.12
14 34 0.25
15 81 0.59
16 5 0.04
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22
Consensus pattern (14 bp):
GTAATCAGTAAAAA
Found at i:4276 original size:43 final size:43
Alignment explanation
Indices: 4185--4449 Score: 211
Period size: 43 Copynumber: 6.3 Consensus size: 43
4175 AGAGTAAAGG
* ** * *
4185 GTAATCAGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAAAA-G
1 GTAATCAGTAAAAAG-TAATGAGTAATCAGTAAAA-GGTAAAATA
4229 GTAATCAGTAAAAAAGTAATGA-TAATCAGTAAAAGGTAAAATA
1 GTAATCAGT-AAAAAGTAATGAGTAATCAGTAAAAGGTAAAATA
* *
4272 GTAATCAGT-AAGAGTAAAATG-GAAATCAGT-AAAGAGTAAAATA
1 GTAATCAGTAAAAAGT--AATGAGTAATCAGTAAAAG-GTAAAATA
4315 GTAATCAGTAAAAAGTAA-GAAGGTAATCAGT-AAAGAGTAAAATA
1 GTAATCAGTAAAAAGTAATG-A-GTAATCAGTAAAAG-GTAAAATA
*
4359 GTAATCAGT---AA--AA-G-GTAATCAGTAAGA-GTAAAATA
1 GTAATCAGTAAAAAGTAATGAGTAATCAGTAAAAGGTAAAATA
* * * * *
4394 GTAATCGGCAAAAAGTAAAGAGTAATCAGTAAGAA-GTCAAATT
1 GTAATCAGTAAAAAGTAATGAGTAATCAGTAA-AAGGTAAAATA
4437 GTAATCAGTAAAA
1 GTAATCAGTAAAA
4450 TGTGAAAAGA
Statistics
Matches: 185, Mismatches: 17, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
35 15 0.08
36 9 0.05
37 2 0.01
38 2 0.01
39 3 0.02
40 2 0.01
41 9 0.05
42 23 0.12
43 65 0.35
44 49 0.26
45 6 0.03
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.22
Consensus pattern (43 bp):
GTAATCAGTAAAAAGTAATGAGTAATCAGTAAAAGGTAAAATA
Found at i:4376 original size:22 final size:22
Alignment explanation
Indices: 4251--4376 Score: 152
Period size: 22 Copynumber: 5.8 Consensus size: 22
4241 AAAGTAATGA
4251 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* *
4273 TAATCAGTAAGA-GTAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
*
4294 AAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* *
4316 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
4338 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
4360 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
4377 TCAGTAAGAG
Statistics
Matches: 87, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.02
21 20 0.23
22 56 0.64
23 9 0.10
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:4408 original size:36 final size:36
Alignment explanation
Indices: 4334--4408 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
4324 AAAAAGTAAG
*
4334 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAA
1 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGAAA
*
4370 AAGGTAATCAGT-AAGAGTAAAATAGTAATCGGCAAA
1 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAG-AAA
4406 AAG
1 AAG
4409 TAAAGAGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (36 bp):
AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGAAA
Found at i:4418 original size:35 final size:35
Alignment explanation
Indices: 4337--4418 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
4327 AAGTAAGAAG
* * *
4337 GTAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAG
1 GTAAACAGT-AAGAGTAAAATAGTAATCAGCAAAAA
* *
4373 GTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAA
1 GTAAACAGTAAGAGTAAAATAGTAATCAGCAAAAA
*
4408 GTAAAGAGTAA
1 GTAAACAGTAA
4419 TCAGTAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 32 0.78
36 9 0.22
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (35 bp):
GTAAACAGTAAGAGTAAAATAGTAATCAGCAAAAA
Found at i:4441 original size:22 final size:21
Alignment explanation
Indices: 4365--4447 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
4355 AATAGTAATC
4365 AGTAAA-AGGTAATCAGTAAG-
1 AGTAAATA-GTAATCAGTAAGA
* * *
4385 AGTAAAATAGTAATCGGCAAAA
1 AGT-AAATAGTAATCAGTAAGA
*
4407 AGTAAAGAGTAATCAGTAAGA
1 AGTAAATAGTAATCAGTAAGA
*
4428 AGTCAAATTGTAATCAGTAA
1 AGT-AAATAGTAATCAGTAA
4448 AATGTGAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.06
21 29 0.58
22 18 0.36
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTAAATAGTAATCAGTAAGA
Found at i:4441 original size:122 final size:120
Alignment explanation
Indices: 4239--4512 Score: 302
Period size: 122 Copynumber: 2.2 Consensus size: 120
4229 GTAATCAGTA
* * * * *
4239 AAAAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAGAGTAAAATGGAAATCAGTAA
1 AAAAAGTAAAGGTAATCAGTAAGA-GTAAAATAGTAATCAGAAAAAGTAAAA-GGAAATCAGTAA
**
4304 AGAGTAAAATAGTAATCAGTAAAAAGT-AAGAAGGTAATCAGTAAAGAGTAAAATAGT
64 AGAGTAAAATAGTAATCAGTAAAAAGTGAA-AAGACAATCAGTAAAGAGTAAAATAGT
** * *
4361 AATCAGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGT-AAAGAGTAATCAGT-
1 AAAAAGT-AAAGGTAATCAGTAAGAGTAAAATAGTAATCAG-AAAAAGTAAAAG-GAAATCAGTA
* * * *
4424 AAGAAGTCAAATTGTAATCAGTAAAATGTGAAAAGACAATCAGTAAAGAGTAAAATGGT
63 AAG-AGTAAAATAGTAATCAGTAAAAAGTGAAAAGACAATCAGTAAAGAGTAAAATAGT
* *
4483 AAAAAGTAATGGTGATCAGTAAAGAGTAAA
1 AAAAAGTAAAGGTAATCAGT-AAGAGTAAA
4513 GAGCAATCAG
Statistics
Matches: 127, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
121 15 0.12
122 91 0.72
123 21 0.17
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.21
Consensus pattern (120 bp):
AAAAAGTAAAGGTAATCAGTAAGAGTAAAATAGTAATCAGAAAAAGTAAAAGGAAATCAGTAAAG
AGTAAAATAGTAATCAGTAAAAAGTGAAAAGACAATCAGTAAAGAGTAAAATAGT
Found at i:4529 original size:122 final size:122
Alignment explanation
Indices: 4295--4540 Score: 284
Period size: 122 Copynumber: 2.0 Consensus size: 122
4285 GTAAAATGGA
**
4295 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAG
1 AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGACAATCAGTAAAGAGTAAAATAG
** * * * *
4360 TAATCAGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAGTAAAGAGT
66 TAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAGAGCAATCGGAAAAAAGGAAAGAGT
* * *
4417 AATCAGT-AAGAAGTCAAATTGTAATCAGTAAAATGTGAA-AAGACAATCAGTAAAGAGTAAAAT
1 AATCAGTAAAG-AGTAAAATAGTAATCAGTAAAAAGT-AAGAAGACAATCAGTAAAGAGTAAAAT
* * * * *
4480 GGTAAAAAGT-AATGGTGATCAGTAAAGAGT-AAAGAGCAATCAGTAAAAAAGGGAAGAGT
64 AGTAAAAAGTAAAAGGTAATCAGT-AAGAGTAAAAGAGCAATC-GGAAAAAAGGAAAGAGT
4539 AA
1 AA
4541 AGAAGGGTAC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
121 23 0.22
122 79 0.76
123 2 0.02
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (122 bp):
AATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGACAATCAGTAAAGAGTAAAATAG
TAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAGAGCAATCGGAAAAAAGGAAAGAGT
Found at i:5789 original size:65 final size:66
Alignment explanation
Indices: 5684--5816 Score: 232
Period size: 65 Copynumber: 2.0 Consensus size: 66
5674 CTAGCTCCAA
* * *
5684 AAGCAAGTCTTGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAAGTCAATTGAGAAATGAC
1 AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
5749 C
66 C
5750 AAGCAAGCCTTGATAGGGAT-TTTTAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
1 AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
5814 C
66 C
5815 AA
1 AA
5817 AAAGTCTAGT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 46 0.72
66 18 0.28
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (66 bp):
AAGCAAGCCTTGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAAATCAATTGAGAAATGAC
C
Done.