Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1931
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: 18702
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Found at i:10414 original size:141 final size:141
Alignment explanation
Indices: 10160--10439 Score: 429
Period size: 141 Copynumber: 2.0 Consensus size: 141
10150 ATTTGATACC
* * * *
10160 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAAAATTAGGCACGGCATAGCCAGCAAATC
1 TTAAGCAAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
** *
10225 AGTTCTTAACCTCTCATTTGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAT
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
10290 TTCAATTAACT
131 TTCAATTAACT
* *
10301 TTAAGCAAAGTTCAGTTAAAACT-GCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCAAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCC-AGCAAA
* *
10364 TCAGTTCTTAACCTCTCATCCGCCATGATTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCA
10429 ACTTCAATTAA
129 ACTTCAATTAA
10440 AACTAGCTTA
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 117 0.93
142 9 0.07
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (141 bp):
TTAAGCAAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCACTTCAAC
TTCAATTAACT
Found at i:11201 original size:1 final size:1
Alignment explanation
Indices: 10974--11181 Score: 398
Period size: 1 Copynumber: 208.0 Consensus size: 1
10964 CCGGAAAGAT
*
10974 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
11039 AAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11169 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
11182 TTAATACCCC
Statistics
Matches: 203, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
1 203 1.00
ACGTcount: A:0.99, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11212 original size:14 final size:14
Alignment explanation
Indices: 11193--11290 Score: 65
Period size: 14 Copynumber: 6.9 Consensus size: 14
11183 TAATACCCCT
11193 AAAAAAAAAAAATA
1 AAAAAAAAAAAATA
* **
11207 AAAAAACAACCAT-
1 AAAAAAAAAAAATA
* *
11220 -AAAAATAAAATTA
1 AAAAAAAAAAAATA
**
11233 AAAAAAACCACTAATA
1 AAAAAAA--AAAAATA
* *
11249 AAAAAAATAAATTA
1 AAAAAAAAAAAATA
11263 AAAAAAAAAAAATA
1 AAAAAAAAAAAATA
11277 ACAATAAAAAAAAA
1 A-AA-AAAAAAAAA
11291 ACTATACAGA
Statistics
Matches: 61, Mismatches: 17, Indels: 10
0.69 0.19 0.11
Matches are distributed among these distances:
12 8 0.13
14 31 0.51
15 2 0.03
16 20 0.33
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAAAAAAATA
Found at i:11223 original size:25 final size:26
Alignment explanation
Indices: 11197--11259 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
11187 ACCCCTAAAA
11197 AAAAAAAATAAAAAAACAACCA-TAA-
1 AAAAAAAATAAAAAAA-AACCACTAAT
* *
11222 AAATAAAATTAAAAAAAACCACTAAT
1 AAAAAAAATAAAAAAAAACCACTAAT
11248 AAAAAAAATAAA
1 AAAAAAAATAAA
11260 TTAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 5 0.16
25 17 0.53
26 10 0.31
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.13
Consensus pattern (26 bp):
AAAAAAAATAAAAAAAAACCACTAAT
Found at i:11265 original size:26 final size:25
Alignment explanation
Indices: 11168--11266 Score: 76
Period size: 27 Copynumber: 3.8 Consensus size: 25
11158 AAAAAAAAAA
* * * *
11168 AAAAAAAAAAAAAATTAATACCCCT
1 AAAAAAAAAATAAATAAAAACCACT
*
11193 AAAAAAAAAAAATAAAAAAACAACCA-T
1 --AAAAAAAAAATAAATAAA-AACCACT
*
11220 AAAAATAAAATTAAA-AAAAACCACT
1 AAAAA-AAAAATAAATAAAAACCACT
11245 AATAAAAAAAATAAATTAAAAA
1 AA-AAAAAAAATAAA-TAAAAA
11267 AAAAAAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
24 5 0.08
25 19 0.32
26 11 0.19
27 21 0.36
28 3 0.05
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAATAAATAAAAACCACT
Found at i:11270 original size:19 final size:20
Alignment explanation
Indices: 11248--11291 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
11238 AACCACTAAT
*
11248 AAAAAAAATAA-ATTAAAAA
1 AAAAAAAATAACAATAAAAA
11267 AAAAAAAATAACAATAAAAA
1 AAAAAAAATAACAATAAAAA
11287 AAAAA
1 AAAAA
11292 CTATACAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAAATAACAATAAAAA
Found at i:12355 original size:20 final size:18
Alignment explanation
Indices: 12303--12373 Score: 56
Period size: 20 Copynumber: 3.7 Consensus size: 18
12293 GAACTTAGGT
12303 AATAAATATATTAAATAAAA
1 AATAAA-AT-TTAAATAAAA
*
12323 AATTAAA-TT-AATAAAA
1 AATAAAATTTAAATAAAA
12339 ATATAAAAATTTAAATAGATAA
1 A-AT-AAAATTTAAATA-A-AA
*
12361 GATAAAATTTAAA
1 AATAAAATTTAAA
12374 ATTATGAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 8 0.19
17 4 0.10
18 3 0.07
19 3 0.07
20 19 0.45
21 3 0.07
22 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AATAAAATTTAAATAAAA
Found at i:13238 original size:1 final size:1
Alignment explanation
Indices: 13232--13266 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
13222 GTACGTAAAT
*
13232 AAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13267 GAGTGACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:13989 original size:1 final size:1
Alignment explanation
Indices: 13983--14224 Score: 394
Period size: 1 Copynumber: 242.0 Consensus size: 1
13973 ATCAAAGAAG
* *
13983 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
14048 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGTAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
14113 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
14178 AAAAAAAAAAAAAAAAAATAAGAAAAAAAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14225 CAATGAAAGA
Statistics
Matches: 222, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 222 1.00
ACGTcount: A:0.96, C:0.01, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:18136 original size:6 final size:6
Alignment explanation
Indices: 18099--18160 Score: 58
Period size: 6 Copynumber: 10.2 Consensus size: 6
18089 TATTTACACC
*
18099 TATACA CTATACA TTGATACA TTATA-A TATACA TATAC- -ATGCA TATACA
1 TATACA -TATACA -T-ATACA -TATACA TATACA TATACA TATACA TATACA
18148 TATACA TATACA T
1 TATACA TATACA T
18161 GAAGGTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.06
5 4 0.08
6 24 0.50
7 10 0.21
8 7 0.15
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:18152 original size:22 final size:21
Alignment explanation
Indices: 18121--18161 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
18111 ATTGATACAT
18121 TATAATATACATATACATGCA
1 TATAATATACATATACATGCA
18142 TATACATATACATATACATG
1 TATA-ATATACATATACATG
18162 AAGGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (21 bp):
TATAATATACATATACATGCA
Done.