Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1621
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: 39382
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:13303 original size:20 final size:20
Alignment explanation
Indices: 13257--13303 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13247 AGCTCGTTTC
*
13257 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
13277 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
13297 CAGCTCA
1 CAGCTCA
13304 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:15787 original size:18 final size:18
Alignment explanation
Indices: 15766--15800 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15756 AGAAAAGAAA
15766 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
15784 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
15801 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:23439 original size:20 final size:20
Alignment explanation
Indices: 23393--23439 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23383 AGCTTGTTTC
*
23393 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
23413 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
23433 CAGCTCA
1 CAGCTCA
23440 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:24472 original size:29 final size:30
Alignment explanation
Indices: 24439--24511 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
24429 ACTTAAGCCA
24439 AGCTCAAACGAGCTAAAGTAAGCTAAT-TG
1 AGCTCAAACGAGCTAAAGTAAGCTAATGTG
* *
24468 AGCTCAAACGAGCTAAATTAAGCTCATGTG
1 AGCTCAAACGAGCTAAAGTAAGCTAATGTG
24498 AGCT-AAATCGAGCT
1 AGCTCAAA-CGAGCT
24512 GGGAAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (30 bp):
AGCTCAAACGAGCTAAAGTAAGCTAATGTG
Found at i:26324 original size:33 final size:33
Alignment explanation
Indices: 26286--26348 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
26276 GATTACTCAC
26286 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
26319 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
26349 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:26375 original size:21 final size:21
Alignment explanation
Indices: 26346--26401 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
26336 CAAGCTCTCT
*
26346 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
26367 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
26388 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
26402 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:26394 original size:14 final size:14
Alignment explanation
Indices: 26345--26401 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
26335 TCAAGCTCTC
26345 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
26358 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
26372 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
26386 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
26400 TT
1 TT
26402 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:26455 original size:18 final size:18
Alignment explanation
Indices: 26363--26465 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
26353 TCTTTTTTCG
26363 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
26382 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* ** *
26402 CTCTCACTTTTTGA-TTT
1 CTTTTTCTTTTTCATTTT
* *
26419 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
26437 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
26455 CTTTTTGTTTT
1 CTTTTTCTTTT
26466 CTTTCAATTT
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
17 12 0.19
18 33 0.52
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:26482 original size:6 final size:6
Alignment explanation
Indices: 26363--26469 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
26353 TCTTTTTTCG
* * * **
26363 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
26414 -GATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
26461 -GTTTT CTTT
1 CTTTTT CTTT
26470 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
5 7 0.10
6 53 0.74
7 9 0.12
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:30248 original size:18 final size:18
Alignment explanation
Indices: 30227--30261 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30217 AGAAAAGAAA
30227 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
30245 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
30262 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:38045 original size:9 final size:10
Alignment explanation
Indices: 38038--38100 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
38028 AAGAGAAAAT
38038 AAAGAAAAGA
1 AAAGAAAAGA
38048 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
38060 AAAGAAGA-A
1 AAAGAAAAGA
38069 AAAGAAAAAGA
1 AAAG-AAAAGA
38080 AAATGAAATA-A
1 AAA-GAAA-AGA
38091 AAAGAAAAGA
1 AAAGAAAAGA
38101 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 6 0.14
10 12 0.27
11 19 0.43
12 7 0.16
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:38062 original size:6 final size:5
Alignment explanation
Indices: 38038--38100 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
38028 AAGAGAAAAT
*
38038 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA
38086 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
38101 GAGGCAAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.08
5 25 0.51
6 19 0.39
7 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:38071 original size:21 final size:20
Alignment explanation
Indices: 38038--38098 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
38028 AAGAGAAAAT
38038 AAAGAAAAGAAAAGAAAAAGCA
1 AAAGAAAA-AAAAGAAAAAG-A
*
38060 AAAGAAGAAAAAGAAAAAGA
1 AAAGAAAAAAAAGAAAAAGA
38080 AAATGAAATAAAAAGAAAA
1 AAA-GAAA-AAAAAGAAAA
38099 GAGAGGCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 17 0.49
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAAAAGAAAAAGA
Found at i:38180 original size:11 final size:12
Alignment explanation
Indices: 38148--38178 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38138 TTGAGAGAAC
38148 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38160 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38172 TTGAAAA
1 TTGAAAA
38179 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38189 original size:12 final size:12
Alignment explanation
Indices: 38181--38205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38171 TTTGAAAAGC
38181 AAAAAGAAAATG
1 AAAAAGAAAATG
38193 AAAAAGAAAATG
1 AAAAAGAAAATG
38205 A
1 A
38206 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:38202 original size:18 final size:18
Alignment explanation
Indices: 38175--38230 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
38165 AAAGCCTTTG
*
38175 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
38194 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
*
38212 AAAAGAGAATGAAAA-GA
1 AAAAGAAAATGAAAATGA
38229 AA
1 AA
38231 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:38215 original size:30 final size:31
Alignment explanation
Indices: 38181--38262 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
38171 TTTGAAAAGC
*
38181 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* *
38211 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
38241 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
38263 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Done.