Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold812
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: 51560
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6468 original size:16 final size:15
Alignment explanation
Indices: 6447--6494 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
6437 GATGTGAATA
6447 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
6463 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
6478 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
6494 A
1 A
6495 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:6470 original size:24 final size:24
Alignment explanation
Indices: 6443--6498 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
6433 TAATGATGTG
*
6443 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
6467 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
6491 AATAATAA
1 AATAATAA
6499 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:6477 original size:8 final size:8
Alignment explanation
Indices: 6443--6494 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
6433 TAATGATGTG
*
6443 AATAATAA
1 AATATTAA
6451 AATATATAA
1 AATAT-TAA
6460 AATA-TAA
1 AATATTAA
6467 AATATTAA
1 AATATTAA
*
6475 AATATCAA
1 AATATTAA
*
6483 AATATTAG
1 AATATTAA
6491 AATA
1 AATA
6495 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:6765 original size:25 final size:25
Alignment explanation
Indices: 6641--6856 Score: 119
Period size: 25 Copynumber: 8.7 Consensus size: 25
6631 TAAATACGTG
*
6641 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAAATATATACATAAT
* * *
6666 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAAATATATACATAAT
* * *
6691 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAAATATATACATAAT
* * *
6713 ATAACATGTAGAAAAACAATATATATAAT
1 ATAATAT-T--AAAAA-TATATACATAAT
* *
6742 ATAATATTAAATATATATACATAAA
1 ATAATATTAAAAATATATACATAAT
* * *
6767 ATAGTATAAAATATATATATACGTAAT
1 ATAATATTAAA-A-ATATATACATAAT
* *
6794 ATAGA-ATT-TAAA-ATATACCT-A-
1 ATA-ATATTAAAAATATATACATAAT
*
6815 AT-ATATTAAAAGA-ATATATATAAT
1 ATAATATTAAAA-ATATATACATAAT
6839 ATAATATTAAGAAATATA
1 ATAATATTAA-AAATATA
6857 ATAATAACAA
Statistics
Matches: 143, Mismatches: 30, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 4 0.03
22 23 0.16
23 12 0.08
24 4 0.03
25 51 0.36
26 10 0.07
27 16 0.11
28 4 0.03
29 15 0.10
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.34
Consensus pattern (25 bp):
ATAATATTAAAAATATATACATAAT
Found at i:6809 original size:27 final size:26
Alignment explanation
Indices: 6750--6810 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
6740 ATATAATATT
*
6750 AAATATATATACATAAAATAGTATAA
1 AAATATATATACATAAAATAGAATAA
* * *
6776 AATATATATATACGTAATATAGAATTTA
1 AA-ATATATATACATAAAATAGAA-TAA
6804 AAATATA
1 AAATATA
6811 CCTAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 23 0.79
28 4 0.14
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (26 bp):
AAATATATATACATAAAATAGAATAA
Found at i:7429 original size:30 final size:30
Alignment explanation
Indices: 7395--7455 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
7385 AATGGAGCAA
* *
7395 GTGTGGCTAGTGGATTTGGTGGTGGAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGAAAAAG
7425 GTGTGGCTAGTGGAGTTGGTGGTGAAAAAG
1 GTGTGGCTAGTGGAGTTGGTGGTGAAAAAG
7455 G
1 G
7456 CTAAGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.03, G:0.48, T:0.28
Consensus pattern (30 bp):
GTGTGGCTAGTGGAGTTGGTGGTGAAAAAG
Found at i:10412 original size:31 final size:31
Alignment explanation
Indices: 10371--10443 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
10361 TTAAAAAAAA
* **
10371 AATTCAGTGACTTAAATAAAAACTTTTGAAT
1 AATTTAGTGACTTAAATAAAAACTTTCAAAT
* *
10402 AGTTTAGTGACTTAAATGAAAACTTTCAAAT
1 AATTTAGTGACTTAAATAAAAACTTTCAAAT
10433 AATTTAGTGAC
1 AATTTAGTGAC
10444 CAAATTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
AATTTAGTGACTTAAATAAAAACTTTCAAAT
Found at i:11020 original size:20 final size:20
Alignment explanation
Indices: 10992--11037 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
10982 AAACAATAGC
*
10992 AAAATAGCAACAAAACAGGA
1 AAAAAAGCAACAAAACAGGA
* * *
11012 AAAAAAGCAATAAAATAGTA
1 AAAAAAGCAACAAAACAGGA
11032 AAAAAA
1 AAAAAA
11038 TAACAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.72, C:0.09, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAAAAGCAACAAAACAGGA
Found at i:12071 original size:9 final size:8
Alignment explanation
Indices: 12054--12083 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12044 TTTACACTAT
*
12054 AAAACAAA
1 AAAATAAA
12062 AAAATAAA
1 AAAATAAA
12070 AAAATAAA
1 AAAATAAA
12078 AAAATA
1 AAAATA
12084 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAATAAA
Found at i:18739 original size:20 final size:20
Alignment explanation
Indices: 18714--18763 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
18704 TGGCTTAAAA
18714 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
18734 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
18751 GTGGTAGTGGATT
1 TTGGTAGTGGATT
18764 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:23369 original size:20 final size:20
Alignment explanation
Indices: 23344--23393 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
23334 TGGCTTAAAA
23344 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
23364 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
23381 GTGGTAGTGGATT
1 TTGGTAGTGGATT
23394 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:24351 original size:18 final size:18
Alignment explanation
Indices: 24324--24362 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
24314 TATATCTCTT
*
24324 ATATATATATATTATAAA
1 ATATAAATATATTATAAA
* *
24342 ATATAAATATTTTTTAAA
1 ATATAAATATATTATAAA
24360 ATA
1 ATA
24363 ATATAAATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAAATATATTATAAA
Found at i:44393 original size:103 final size:104
Alignment explanation
Indices: 44164--44429 Score: 410
Period size: 103 Copynumber: 2.6 Consensus size: 104
44154 GTTGTACATA
** * *
44164 AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
44229 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
44268 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
44332 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
44371 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
44430 AATAACGGTT
Statistics
Matches: 148, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 65 0.44
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Done.