Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3591
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, 429
Length: 715
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Found at i:87 original size:18 final size:19
Alignment explanation
Indices: 64--231 Score: 107
Period size: 21 Copynumber: 8.4 Consensus size: 19
54 TCTTCCCTCT
64 TCTTCTTC-TTCTTTTTTC
1 TCTTCTTCTTTCTTTTTTC
*
82 TCTTCTCCTTTCGTTTTCTT-
1 TCTTCTTCTTTC-TTTT-TTC
102 TCCTTCTTTCTTTCTTTTTTC
1 T-CTTC-TTCTTTCTTTTTTC
*
123 T-TCTCTT-TTCCTTTTCTTC
1 TCT-TCTTCTTTCTTTT-TTC
142 TTCTTCTTTCTTTCTTTTTTTC
1 -TCTTC-TTCTTTC-TTTTTTC
*
164 TCTTCTCCTTTCCTTTTCTT-
1 TCTTCTTCTTT-CTTTT-TTC
184 TCCTTCTT-TTTCTTTCTTTCC
1 T-CTTCTTCTTTCTTT-TTT-C
*
205 TCTCCTTTCTTTCTTTCTTTC
1 TCTTC-TTCTTTCTTT-TTTC
226 T-TTCTT
1 TCTTCTT
232 TCCCCCAACA
Statistics
Matches: 121, Mismatches: 8, Indels: 41
0.71 0.05 0.24
Matches are distributed among these distances:
18 14 0.12
19 17 0.14
20 31 0.26
21 32 0.26
22 23 0.19
23 4 0.03
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (19 bp):
TCTTCTTCTTTCTTTTTTC
Found at i:112 original size:4 final size:4
Alignment explanation
Indices: 96--233 Score: 101
Period size: 4 Copynumber: 34.0 Consensus size: 4
86 CTCCTTTCGT
*
96 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
* * *
142 -TTC -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
*
190 -TT- TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
234 CCCCAACAAC
Statistics
Matches: 110, Mismatches: 9, Indels: 30
0.74 0.06 0.20
Matches are distributed among these distances:
3 16 0.15
4 72 0.65
5 15 0.14
6 7 0.06
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:124 original size:48 final size:48
Alignment explanation
Indices: 42--202 Score: 134
Period size: 52 Copynumber: 3.5 Consensus size: 48
32 TACTTTTTTT
* *
42 CTTTTTTTTCCTTCTTCCCTCTTCTTCTTCTTCTTTTTTCTCTTCTCCTTTC
1 CTTTTCTTTCCTTCTT-TCT-TTCTT-TT-TTCTTTTTTCTCTTCTCCTTTC
*
94 GTTTTCTTTCCTTCTTTCTTTCTTTTTTC-----T-TC-TCT--TTTC
1 CTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTTTTTCTCTTCTCCTTTC
*
133 CTTTTC-TT-CTTC-TTCTTTCTTT-CT-TTTTTTCTCTTCTCCTTTC
1 CTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTTTTTCTCTTCTCCTTTC
176 CTTTTCTTTCCTTCTTTTTCTTTCTTT
1 CTTTTCTTTCCTTC--TTTCTTTCTTT
203 CCTCTCCTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 32
0.71 0.04 0.25
Matches are distributed among these distances:
35 1 0.01
36 10 0.11
37 4 0.04
38 2 0.02
39 10 0.11
40 2 0.02
41 6 0.07
42 2 0.02
43 11 0.12
44 2 0.02
45 4 0.04
48 13 0.14
49 2 0.02
50 5 0.06
51 2 0.02
52 14 0.16
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (48 bp):
CTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTTTTTCTCTTCTCCTTTC
Found at i:127 original size:44 final size:41
Alignment explanation
Indices: 75--233 Score: 190
Period size: 40 Copynumber: 4.0 Consensus size: 41
65 CTTCTTCTTC
75 TTTTTTCTCTTCTCCTTTCGTTTTCTTTCCTTCTTTCTTTC-
1 TTTTTTCTCTTCTCCTTTC-TTTTCTTTCCTTCTTTCTTTCT
* *
116 -TTTTT-TCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCT
1 TTTTTTCTCTTCTCCTTT-CTTTTCTT-TCCTTCTTTCTTTCT
157 TTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTC-TT-TTTCT
1 TTTTTTCTCTTCTCCTTT-CTTTTCTTTCCTTCTTTCTTTCT
* *
197 TTCTTTC-C-TCTCCTTTC-TTTCTTTCTTTCTTTCTTTC
1 TTTTTTCTCTTCTCCTTTCTTTTCTTTCCTTCTTTCTTTC
234 CCCCAACAAC
Statistics
Matches: 105, Mismatches: 6, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
36 11 0.10
37 3 0.03
38 12 0.11
39 18 0.17
40 30 0.29
41 2 0.02
42 10 0.10
43 19 0.18
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (41 bp):
TTTTTTCTCTTCTCCTTTCTTTTCTTTCCTTCTTTCTTTCT
Found at i:132 original size:29 final size:28
Alignment explanation
Indices: 39--233 Score: 95
Period size: 28 Copynumber: 7.3 Consensus size: 28
29 AATTACTTTT
* *
39 TTTCTTTTTTTTCCTTCTTCCCTCTTCTTC
1 TTTCTTTCTTTTCCTTC-T-CTTCTTCTTC
69 -TTC-TTCTTTT--TTCTCTTC-TC--C
1 TTTCTTTCTTTTCCTTCTCTTCTTCTTC
*
90 TTTCGTTT-TCTTTCCTTCT-TTCTTTCTTT
1 TTTC-TTTCT-TTTCCTTCTCTTC-TTCTTC
*
119 TTTCTTCTCTTTTCCTTTTCTTCTTCTTC
1 TTTCTT-TCTTTTCCTTCTCTTCTTCTTC
*
148 TTTCTTTCTTTT--TT-TC-TCTTCTCC
1 TTTCTTTCTTTTCCTTCTCTTCTTCTTC
172 TTTCCTTT-TCTTTCCTTCT-TT-TTCTTTC
1 TTT-CTTTCT-TTTCCTTCTCTTCTTC-TTC
* * *
200 TTTCCTCTCCTTTCTTTCT-TTC-T-TTC
1 TTT-CTTTCTTTTCCTTCTCTTCTTCTTC
226 TTTCTTTC
1 TTTCTTTC
234 CCCCAACAAC
Statistics
Matches: 132, Mismatches: 11, Indels: 49
0.69 0.06 0.26
Matches are distributed among these distances:
21 1 0.01
22 3 0.02
23 3 0.02
24 19 0.14
25 17 0.13
26 15 0.11
27 7 0.05
28 36 0.27
29 27 0.20
30 4 0.03
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (28 bp):
TTTCTTTCTTTTCCTTCTCTTCTTCTTC
Found at i:170 original size:82 final size:78
Alignment explanation
Indices: 36--233 Score: 237
Period size: 82 Copynumber: 2.5 Consensus size: 78
26 TAAAATTACT
* *
36 TTTTTTCTT-TTTTTTCCTTCTTCCCTCTTCTTC-TTC-TTCTTTTTTCTCTTCTCCTTTCGTTT
1 TTTTTTCTTCTCTTTTCCTT-TT--CTCTTCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTT
98 TCTTTCCTTCTTTCTTTC
63 TCTTTCCTTC-TT-TTTC
116 TTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTT
1 TTTTTTCTTCTCTTTTCCTTTTC-TCTTCTTCTTTCTTTC-TTTTTTCTCTTCTCCTTTCCTTTT
181 CTTTCCTTCTTTTTC
64 CTTTCCTTCTTTTTC
* *
196 TTTCTTTCCTCTCCTTT-C-TTTCT-TTCTTTCTTTCTTTC
1 TTT-TTTCTTCTCTTTTCCTTTTCTCTTC-TTCTTTCTTTC
234 CCCCAACAAC
Statistics
Matches: 107, Mismatches: 4, Indels: 16
0.84 0.03 0.13
Matches are distributed among these distances:
77 3 0.03
78 13 0.12
79 12 0.11
80 22 0.21
81 25 0.23
82 32 0.30
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (78 bp):
TTTTTTCTTCTCTTTTCCTTTTCTCTTCTTCTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTTTCT
TTCCTTCTTTTTC
Found at i:182 original size:70 final size:70
Alignment explanation
Indices: 34--233 Score: 182
Period size: 73 Copynumber: 2.8 Consensus size: 70
24 AATAAAATTA
*
34 CTTTT-TTTCTTTTTT-TTC-CTTCTTCCCTCTTCTTCTTCTTCTTT-TTTCTCTTCTCCTTTCG
1 CTTTTCTTTCTTTTTTCTTCTCTT-TT-CCTCTTCTTCTTCTTCTTTCTTTCT-TTCT-CTTTCC
*
95 TTTTCTTTC
62 TTTCCTTTC
*
104 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCTTCTTCTTCTTTCTTTCTTT-T-TTTCTCT
1 C-T-TTTCTTTCTTTTTTCTTCTCTTTTCCTCTTCTTCTTCTTCTTTCTTTCTTTCTCTTTC-CT
167 TCTCCTTTC
63 T-TCCTTTC
*
176 CTTTTCTTTCCTTCTTTTTCTT-TC-TTTCCTCTCCTTTCTTTCTTTCTTTCTTTCTTTC
1 CTTTTCTTT-C-T-TTTTTCTTCTCTTTTCCTCTTC-TTC-TTC-TTCTTTCTTTCTTTC
234 CCCCAACAAC
Statistics
Matches: 110, Mismatches: 5, Indels: 25
0.79 0.04 0.18
Matches are distributed among these distances:
70 12 0.11
71 13 0.12
72 17 0.15
73 41 0.37
74 24 0.22
75 3 0.03
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (70 bp):
CTTTTCTTTCTTTTTTCTTCTCTTTTCCTCTTCTTCTTCTTCTTTCTTTCTTTCTCTTTCCTTTC
CTTTC
Found at i:203 original size:48 final size:45
Alignment explanation
Indices: 97--233 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 45
87 TCCTTTCGTT
* * *
97 TTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTTTCTTC
1 TTCTTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTC
142 TTC-TTCTTTCTTTCTTT-TTTTCTCTTCTCCTTTCCTTTTC-T-
1 TTCTTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTC
*
183 TTCCTTC-TT-TTTCTTTC-TTTC-C-TCTCCTTT-C-TTTC-T-
1 TTCTTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTC
219 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
234 CCCCAACAAC
Statistics
Matches: 84, Mismatches: 4, Indels: 15
0.82 0.04 0.15
Matches are distributed among these distances:
36 11 0.13
37 3 0.04
38 12 0.14
39 1 0.01
40 11 0.13
41 5 0.06
42 4 0.05
43 21 0.25
44 13 0.15
45 3 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (45 bp):
TTCTTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCTTTTCTTC
Found at i:232 original size:40 final size:39
Alignment explanation
Indices: 66--232 Score: 121
Period size: 38 Copynumber: 4.2 Consensus size: 39
56 TTCCCTCTTC
* *
66 TTCTTCTTCTTT-TTTCTCTTCTCCTTTCGTTTTCTTTCCTTCT
1 TTCTTTTTCTTTCTTTC-C-TCTCCTTTC---TTCTTTCTTTCT
* * *
109 TTCTTTCTTTTTTCTTCTCTTTTCCTTTTCTTC-TTC-TTCT
1 TTCTTT-TTCTTTCTT-TCCTCTCC-TTTCTTCTTTCTTTCT
* * *
149 TTCTTTCTT-TTT-TTCTCTTCTCCTTTCCT-TTTCTTTCC
1 TTCTTT-TTCTTTCTT-TCCTCTCCTTTCTTCTTTCTTTCT
187 TTCTTTTTCTTTCTTTCCTCTCCTTTCTTTCTTTCTTTCT
1 TTCTTTTTCTTTCTTTCCTCTCCTTTC-TTCTTTCTTTCT
227 TTCTTT
1 TTCTTT
233 CCCCCAACAA
Statistics
Matches: 104, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
37 10 0.10
38 33 0.32
39 6 0.06
40 27 0.26
41 3 0.03
42 3 0.03
43 5 0.05
44 9 0.09
45 6 0.06
46 2 0.02
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (39 bp):
TTCTTTTTCTTTCTTTCCTCTCCTTTCTTCTTTCTTTCT
Found at i:234 original size:48 final size:47
Alignment explanation
Indices: 95--234 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 47
85 TCTCCTTTCG
95 TTTTCTTTCCTT-CTTTCTTTCTTT-TTTCTTCTCTTTTCCTTTTCTTC
1 TTTTCTTTCCTTCCTTTCTTTCTTTCTTTCTT-TC-TTTCCTTTTCTTC
* * * *
142 TTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-TTCTTTCCTTCCTTTCTT-TCTT-T-CTTT-C-TTTCTTTCCTT-TTCTTC
196 -TTTCTTTCCTCTCCTTTCTTTCTTTCTTTCTTTCTTTCC
1 TTTTCTTTCCT-TCCTTTCTTTCTTTCTTTCTTTCTTTCC
235 CCCAACAACT
Statistics
Matches: 76, Mismatches: 7, Indels: 19
0.75 0.07 0.19
Matches are distributed among these distances:
47 2 0.03
48 18 0.24
49 6 0.08
50 8 0.11
51 2 0.03
52 12 0.16
53 18 0.24
54 8 0.11
55 2 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (47 bp):
TTTTCTTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCCTTTTCTTC
Found at i:302 original size:27 final size:27
Alignment explanation
Indices: 264--342 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
254 TATTATAACA
*
264 TTGGTGCCGCCAATGTCTTTGGCACCT
1 TTGGTGCCGCCAATGACTTTGGCACCT
291 TTGGTGCCGCCAATGACTTTGGCACCT
1 TTGGTGCCGCCAATGACTTTGGCACCT
* *
318 TTGGTGCCGCCAATCACCTTGGCAC
1 TTGGTGCCGCCAATGACTTTGGCAC
343 GACCAGTGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.14, C:0.32, G:0.25, T:0.29
Consensus pattern (27 bp):
TTGGTGCCGCCAATGACTTTGGCACCT
Found at i:430 original size:27 final size:27
Alignment explanation
Indices: 399--459 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
389 TGTTTCTGGT
399 ATATTTTGGTAAATAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
* *
426 TTATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAATTATA
453 ATATTTT
1 ATATTTT
460 AGTTATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAATTATA
Done.