Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3352
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: 24754
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:2738 original size:99 final size:98
Alignment explanation
Indices: 2584--2772 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 98
2574 CCTTTGAGTC
* * *
2584 AGTTTGTTGATATAACCTTGTGTGATTATTGCATTTCCTTTTTCTCTTGATAGTATGCTGTTTGT
1 AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
2649 GCATTAAACAAACAAAGTTAAAATTTGAAGTGTG
66 GCATTAAACAAAC-AAGTTAAAATTTGAAGTGTG
* * *
2683 AGTTTGTTGATGTAACATCTG-GTGATTATTGCAATT-CTTTGTTGTCTTTAAAGTATGCTGTTT
1 AGTTTGTTGATATAACAT-TGTGTGATTATTGCAATTCCTTT-TTCTCTTGAAAGTATGCTGTTT
* *
2746 GTGCATTAAAGAAACAAGTTGAAATTT
64 GTGCATTAAACAAACAAGTTAAAATTT
2773 AAATTTTTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 15 0.19
99 63 0.79
100 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (98 bp):
AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
GCATTAAACAAACAAGTTAAAATTTGAAGTGTG
Found at i:14167 original size:18 final size:18
Alignment explanation
Indices: 14135--14199 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
14125 TTATAACTAT
*
14135 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
14154 TTATTATATATTTATATC
1 TTATTATATATTTATATC
14172 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
14192 TTTTTATA
1 TTATTATA
14200 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:14378 original size:30 final size:30
Alignment explanation
Indices: 14306--14378 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
14296 TACGTCTATT
* *
14306 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
14336 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
14366 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
14379 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Found at i:14434 original size:10 final size:10
Alignment explanation
Indices: 14416--14499 Score: 57
Period size: 10 Copynumber: 8.5 Consensus size: 10
14406 CCCATTTTTT
*
14416 ATATATATAC
1 ATATTTATAC
14426 ATATTTATAC
1 ATATTTATAC
14436 -T-TTTATA-
1 ATATTTATAC
*
14443 ATATATATAC
1 ATATTTATAC
14453 ATATGTATATAC
1 ATAT-T-TATAC
* * *
14465 GTGTTTATAT
1 ATATTTATAC
* *
14475 ATATATACAC
1 ATATTTATAC
*
14485 ATACTTATAC
1 ATATTTATAC
14495 ATATT
1 ATATT
14500 ATTTATATTT
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
8 7 0.13
9 6 0.11
10 33 0.61
11 1 0.02
12 7 0.13
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (10 bp):
ATATTTATAC
Found at i:18892 original size:7 final size:8
Alignment explanation
Indices: 18871--18900 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
18861 TCTCATGAAT
18871 TCAAAAAA
1 TCAAAAAA
18879 TCAAAAAA
1 TCAAAAAA
18887 TCAAAAAAA
1 TC-AAAAAA
18896 TCAAA
1 TCAAA
18901 GTCAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (8 bp):
TCAAAAAA
Found at i:21174 original size:88 final size:88
Alignment explanation
Indices: 21030--21625 Score: 839
Period size: 88 Copynumber: 6.9 Consensus size: 88
21020 CAATGAAGTT
21030 AAAGATCTTGCC-TTCTGCATT----GCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
21090 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
21113 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
21178 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
21201 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
21266 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
21289 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
21354 TGTGATGGAGCTGGTTGAAGACA
66 TGTGATGGAGCTGGTTGAAGACA
* * * *
21377 AAAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
*
21442 TGT-AGTGGAGCTGGTTAAAGA-A
66 TGTGA-TGGAGCTGGTTGAAGACA
** * * **
21464 GCAGATCTT-CCTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCCATC-G
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGG
* *
21525 TTGAG-TGGAGCT-GTTAAAGA-A
65 TTGTGATGGAGCTGGTTGAAGACA
** * * * * **
21546 GCAGATCTTGCCTTCCTGCATTAACAGCAAAGCAGATC-AA-AAACAAAGCCTTGCCTCCATCGG
1 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTTTCGG
*
21609 TTG-CATTGGAGCTGGTT
65 TTGTGA-TGGAGCTGGTT
21626 AAAGGTTACA
Statistics
Matches: 484, Mismatches: 15, Indels: 25
0.92 0.03 0.05
Matches are distributed among these distances:
82 21 0.04
83 65 0.13
84 22 0.05
85 19 0.04
86 31 0.06
87 9 0.02
88 317 0.65
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
TGTGATGGAGCTGGTTGAAGACA
Found at i:23266 original size:18 final size:18
Alignment explanation
Indices: 23234--23298 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
23224 TTATAACTAT
*
23234 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
23253 TTATTATATATTTATATC
1 TTATTATATATTTATATC
23271 TTATTATATATCTATATATC
1 TTATTATATAT-T-TATATC
*
23291 TTTTTATA
1 TTATTATA
23299 AACATATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
18 24 0.57
19 5 0.12
20 13 0.31
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:23475 original size:30 final size:30
Alignment explanation
Indices: 23403--23475 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
23393 TACGTCTATT
* *
23403 TTCTTTTATATATACATATACATACTTACA
1 TTCTTTTATTTTTACATATACATACTTACA
* *
23433 TTGTTTTA-TTTTACGATATACATACTTATA
1 TTCTTTTATTTTTAC-ATATACATACTTACA
23463 -TCTTTTATTTTTA
1 TTCTTTTATTTTTA
23476 TGTAATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (30 bp):
TTCTTTTATTTTTACATATACATACTTACA
Done.