Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1801
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: 20796
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Found at i:3258 original size:20 final size:19
Alignment explanation
Indices: 3211--3285 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
3201 AAAAAGATAT
*
3211 AATGTATCGATACATTGAA
1 AATGTATCGATACATTCAA
*
3230 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCA-A
* *
3251 CATGTATCGATATA-TCGAAA
1 AATGTATCGATACATTC--AA
3271 AATGTATCGATACAT
1 AATGTATCGATACAT
3286 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 40 0.91
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTCAA
Found at i:9560 original size:31 final size:31
Alignment explanation
Indices: 9522--9631 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
9512 CACTATAATC
9522 ATATTTTGTTTTGAAAAATTCTTTGTTGACT
1 ATATTTTGTTTTGAAAAATTCTTTGTTGACT
* * * *
9553 ATATTTTGTAATTAAAAGTACATT-TTTGTCACTATAAT
1 ATATTTTGT-TTTGAAA--A-ATTCTTTGT---T-GACT
9591 CATATTTTGTTTTGAAAAATTCTTTGTTGACT
1 -ATATTTTGTTTTGAAAAATTCTTTGTTGACT
9623 ATATTTTGT
1 ATATTTTGT
9632 AATTAAAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
31 18 0.30
32 7 0.11
33 1 0.02
34 6 0.10
35 6 0.10
36 6 0.10
37 1 0.02
38 7 0.11
39 9 0.15
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (31 bp):
ATATTTTGTTTTGAAAAATTCTTTGTTGACT
Found at i:9599 original size:70 final size:70
Alignment explanation
Indices: 9505--9649 Score: 290
Period size: 70 Copynumber: 2.1 Consensus size: 70
9495 GTGATCACAT
9505 TTTTTGTCACTATAATCATATTTTGTTTTGAAAAATTCTTTGTTGACTATATTTTGTAATTAAAA
1 TTTTTGTCACTATAATCATATTTTGTTTTGAAAAATTCTTTGTTGACTATATTTTGTAATTAAAA
9570 GTACA
66 GTACA
9575 TTTTTGTCACTATAATCATATTTTGTTTTGAAAAATTCTTTGTTGACTATATTTTGTAATTAAAA
1 TTTTTGTCACTATAATCATATTTTGTTTTGAAAAATTCTTTGTTGACTATATTTTGTAATTAAAA
9640 GTACA
66 GTACA
9645 TTTTT
1 TTTTT
9650 TGTGACAATG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (70 bp):
TTTTTGTCACTATAATCATATTTTGTTTTGAAAAATTCTTTGTTGACTATATTTTGTAATTAAAA
GTACA
Found at i:12652 original size:25 final size:26
Alignment explanation
Indices: 12605--12654 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12595 AAGAATTATA
12605 AAAAAAAAAAAAAAACTACATGCTTCT
1 AAAAAAAAAAAAAAACTA-ATGCTTCT
* *
12632 AAAAACAAAAAAAATCT-ATGCTT
1 AAAAAAAAAAAAAAACTAATGCTT
12655 ACAACTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
27 15 0.71
ACGTcount: A:0.62, C:0.14, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAAAAAAAAAAAAACTAATGCTTCT
Found at i:13215 original size:2 final size:2
Alignment explanation
Indices: 13202--13234 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13192 AAATCAACCC
*
13202 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13235 GTATCCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13928 original size:2 final size:2
Alignment explanation
Indices: 13921--13946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13911 GATTAACATA
13921 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13947 TTATTAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14110 original size:43 final size:43
Alignment explanation
Indices: 14045--14130 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
14035 TTATGTCTTC
* *
14045 GTTGTCTGCTTATACAACGCATTTAGTTTCCTTACATTTTCTA
1 GTTGTCTGCTTATACAAAGCATTTAGTTTACTTACATTTTCTA
14088 GTTGTCTGCTTATACAAAGCATTTAGTTTACTTACATTTTCTA
1 GTTGTCTGCTTATACAAAGCATTTAGTTTACTTACATTTTCTA
14131 CCAGACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (43 bp):
GTTGTCTGCTTATACAAAGCATTTAGTTTACTTACATTTTCTA
Found at i:16672 original size:13 final size:13
Alignment explanation
Indices: 16654--16681 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16644 TAAATTAAGC
16654 TTCAACCTCAATT
1 TTCAACCTCAATT
16667 TTCAACCTCAATT
1 TTCAACCTCAATT
16680 TT
1 TT
16682 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (13 bp):
TTCAACCTCAATT
Found at i:18496 original size:2 final size:2
Alignment explanation
Indices: 18489--18523 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18479 GTTATGGAAG
18489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18524 TCAAATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19486 original size:23 final size:23
Alignment explanation
Indices: 19442--19486 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19432 TTTATTATCG
19442 ATATTTAAAAAATTAAATTTAAAT
1 ATATTTAAAAAA-TAAATTTAAAT
19466 ATATTTAAATAAA-AAATTTAA
1 ATATTTAAA-AAATAAATTTAA
19487 TTTAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 9 0.45
25 3 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTTAAAAAATAAATTTAAAT
Done.