Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6034.1
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: 14607
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1167 original size:10 final size:12
Alignment explanation
Indices: 1152--1206 Score: 71
Period size: 11 Copynumber: 4.7 Consensus size: 12
1142 ACAGTATTGT
1152 AAAAAAAA-T-A
1 AAAAAAAATTCA
1162 AAAAAAAATTCAAA
1 AAAAAAAATTC--A
1176 AAAAAAAATTC-
1 AAAAAAAATTCA
1187 AAAAAAAATTCA
1 AAAAAAAATTCA
1199 AAAAAAAA
1 AAAAAAAA
1207 GTTTGTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.20
11 12 0.30
12 8 0.20
14 12 0.30
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:1168 original size:11 final size:12
Alignment explanation
Indices: 1152--1206 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
1142 ACAGTATTGT
1152 AAAAAAAAT-AA
1 AAAAAAAATCAA
*
1163 AAAAAAATTCAAA
1 AAAAAAAATC-AA
1176 AAAAAAAATTC-A
1 AAAAAAAA-TCAA
*
1188 AAAAAAATTCAA
1 AAAAAAAATCAA
1200 AAAAAAA
1 AAAAAAA
1207 GTTTGTATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.27
12 16 0.43
13 9 0.24
14 2 0.05
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:1178 original size:14 final size:14
Alignment explanation
Indices: 1161--1206 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
1151 TAAAAAAAAT
1161 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
1175 AAAAAAAAATTC--
1 AAAAAAAAATTCAA
1187 -AAAAAAAATTCAA
1 AAAAAAAAATTCAA
1200 AAAAAAA
1 AAAAAAA
1207 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.38
14 18 0.62
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:1190 original size:25 final size:24
Alignment explanation
Indices: 1152--1206 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
1142 ACAGTATTGT
1152 AAAAAAAATAAAAAAAAATTCAAA
1 AAAAAAAATAAAAAAAAATTCAAA
*
1176 AAAAAAAATTCAAAAAAAATTCAAA
1 AAAAAAAA-TAAAAAAAAATTCAAA
1201 AAAAAA
1 AAAAAA
1207 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAAAAATAAAAAAAAATTCAAA
Found at i:1306 original size:26 final size:28
Alignment explanation
Indices: 1253--1316 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
1243 TATTGAAGAA
* *
1253 AAAAAAAGAAGAAAAAATATTCGGAATT-
1 AAAAAAA-AAGAAAAAATAATCGAAATTG
1281 AAAAAAAAAGAAAAAA-AATCGAAATTG
1 AAAAAAAAAGAAAAAATAATCGAAATTG
1308 AAAAAAAAA
1 AAAAAAAAA
1317 AGAGTGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 8 0.24
27 18 0.55
28 7 0.21
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.12
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAATAATCGAAATTG
Found at i:1317 original size:28 final size:28
Alignment explanation
Indices: 1252--1319 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
1242 GTATTGAAGA
* *
1252 AAAAAAAAGAAGAAAAAATATTCGGAATT
1 AAAAAAAA-AAGAAAAAATAATCGAAATT
1281 -AAAAAAAAAGAAAAAA-AATCGAAATT
1 AAAAAAAAAAGAAAAAATAATCGAAATT
1307 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
1320 GTGATTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 8 0.23
27 9 0.26
28 18 0.51
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.12
Consensus pattern (28 bp):
AAAAAAAAAAGAAAAAATAATCGAAATT
Found at i:2184 original size:17 final size:15
Alignment explanation
Indices: 2164--2202 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
2154 GCGAGCGAGA
2164 AAATGAACATGAAAAAG
1 AAATGAA-A-GAAAAAG
2181 AAATGAAAGAAAAAG
1 AAATGAAAGAAAAAG
2196 AAGATGA
1 AA-ATGA
2203 GTGGGAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10
Consensus pattern (15 bp):
AAATGAAAGAAAAAG
Found at i:3712 original size:20 final size:20
Alignment explanation
Indices: 3687--3741 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
3677 TGTGGTTCAA
*
3687 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
3707 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
3727 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
3742 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:6384 original size:22 final size:22
Alignment explanation
Indices: 6354--6397 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6344 TTTGGTATTT
6354 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
6376 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
6398 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:12012 original size:12 final size:12
Alignment explanation
Indices: 11995--12045 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
11985 GATGAGAAAG
11995 AGAAAAAAAAAT
1 AGAAAAAAAAAT
12007 AGAAAAACAAAA-
1 AGAAAAA-AAAAT
12019 AGAAACAAAAAAATT
1 AG-AA-AAAAAAA-T
*
12034 ATAAAAAAAAAT
1 AGAAAAAAAAAT
12046 GAGAGTGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
12 10 0.30
13 17 0.52
14 5 0.15
15 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.06, T:0.10
Consensus pattern (12 bp):
AGAAAAAAAAAT
Done.