Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1262
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: 28636
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:4195 original size:14 final size:13
Alignment explanation
Indices: 4173--4209 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
4163 GTCTTAAAAT
4173 AAAATAAAAGTAA
1 AAAATAAAAGTAA
4186 AAACATAAAA-TAA
1 AAA-ATAAAAGTAA
4199 AAAATAAAAGT
1 AAAATAAAAGT
4210 TTTTAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 6 0.27
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAATAAAAGTAA
Found at i:13697 original size:94 final size:92
Alignment explanation
Indices: 13457--13724 Score: 244
Period size: 94 Copynumber: 2.9 Consensus size: 92
13447 GGGCAAGTTA
* *
13457 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGTGTCGACGCCATGTCCC
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACA-AT-TG-GCCGATG-CATGT-CC
* * *
13522 AAACATGGTCTTACACT-G-ACACATTTCGTAG
61 AGACAT-GTCTTACACTAGCACACATCTCATAG
* * * * *
13553 CCGATG-CATGTCCTAGACAT-GTCTTACATTAGCTTACGTCCCAA--GACCGATGCTTGTCGCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC-T-C-TCACAATTGGCCGATGCATGTC-CA
* * *
13614 GACGTGTCTTACACTAGCACTCGTCTCAATA-
62 GACATGTCTTACACTAGCACACATCTC-ATAG
* *
13645 CTGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAATTTGGCCGATGCATGTCCAGAT
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAA-TTGGCCGATGCATGTCCAGAC
13710 ATGTCTTACACTAGC
65 ATGTCTTACACTAGC
13725 CCAAAATAGG
Statistics
Matches: 139, Mismatches: 21, Indels: 27
0.74 0.11 0.14
Matches are distributed among these distances:
90 11 0.08
91 15 0.11
92 16 0.12
93 35 0.25
94 36 0.26
95 14 0.10
96 8 0.06
97 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (92 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACAATTGGCCGATGCATGTCCAGACA
TGTCTTACACTAGCACACATCTCATAG
Found at i:14627 original size:26 final size:26
Alignment explanation
Indices: 14598--14647 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
14588 CTACAACTAG
14598 TCAAAATTGGTGACATACACTTTACC
1 TCAAAATTGGTGACATACACTTTACC
14624 TCAAAATTGGTGACATACACTTTA
1 TCAAAATTGGTGACATACACTTTA
14648 ACTAATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (26 bp):
TCAAAATTGGTGACATACACTTTACC
Found at i:17332 original size:49 final size:48
Alignment explanation
Indices: 17268--17533 Score: 203
Period size: 49 Copynumber: 5.6 Consensus size: 48
17258 ACACCAAAGT
17268 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATAT-GAGGC
* * *
17317 CGATGCCATGTCCCAGACAAGTCTTACACTGGA-TTTCATCTATTG-GTGT
1 CGATGCCATGTCCCAGACAAGTCTTACACT-AACTTTCATATA-TGAG-GC
* * * * *
17366 CGATGCCATGTCCCAGAC-AGTCTTACACTGAC--ACACA-AT-AAGT
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
* * * * * *
17409 TGACGCCATGTCCCAGATAGGTCTTACACTAGCTTGT-ATATCTCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTT-TCATATAT-GAGGC
* ** * *
17458 CGATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATA-ATGTGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
* * *
17504 CAATG-CTTGTCCCAGACATGTCTTACACTA
1 CGATGCCATGTCCCAGACAAGTCTTACACTA
17534 GCACACATAT
Statistics
Matches: 175, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
43 17 0.10
44 12 0.07
45 1 0.01
46 35 0.20
47 5 0.03
48 40 0.23
49 63 0.36
50 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
Found at i:19202 original size:49 final size:48
Alignment explanation
Indices: 19138--19403 Score: 203
Period size: 49 Copynumber: 5.6 Consensus size: 48
19128 ACACCAAAGT
19138 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATAT-GAGGC
* * *
19187 CGATGCCATGTCCCAGACAAGTCTTACACTGGA-TTTCATCTATTG-GTGT
1 CGATGCCATGTCCCAGACAAGTCTTACACT-AACTTTCATATA-TGAG-GC
* * * * *
19236 CGATGCCATGTCCCAGAC-AGTCTTACACTGAC--ACACA-AT-AAGT
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
* * * * * *
19279 TGACGCCATGTCCCAGATAGGTCTTACACTAGCTTGT-ATATCTCGAGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTT-TCATATAT-GAGGC
* ** * *
19328 CGATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATA-ATGTGGC
1 CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
* * *
19374 CAATG-CTTGTCCCAGACATGTCTTACACTA
1 CGATGCCATGTCCCAGACAAGTCTTACACTA
19404 GCACACATAT
Statistics
Matches: 175, Mismatches: 29, Indels: 29
0.75 0.12 0.12
Matches are distributed among these distances:
43 17 0.10
44 12 0.07
45 1 0.01
46 35 0.20
47 5 0.03
48 40 0.23
49 63 0.36
50 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACAAGTCTTACACTAACTTTCATATATGAGGC
Found at i:21800 original size:27 final size:27
Alignment explanation
Indices: 21690--21800 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 27
21680 AGCATGGCTG
* * *
21690 CCAGAACAGAT-AATGTGACAAAGTCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
* * *
21716 CCAAAATAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
* * *
21743 CCAGAACAGATATATATGGCAGAGCTA
1 CCAGAACAGATAAATGTGGCAGAGCCA
* *
21770 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
21797 CCAG
1 CCAG
21801 GACGCTTCCT
Statistics
Matches: 67, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
26 9 0.13
27 58 0.87
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAAATGTGGCAGAGCCA
Found at i:22237 original size:16 final size:15
Alignment explanation
Indices: 22216--22247 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
22206 CCAAAATACC
22216 GACTTTTCGGCATTTT
1 GACTTTTCGGC-TTTT
22232 GACTTTTCGGCTTTT
1 GACTTTTCGGCTTTT
22247 G
1 G
22248 CCGATCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.50
Consensus pattern (15 bp):
GACTTTTCGGCTTTT
Found at i:23267 original size:24 final size:24
Alignment explanation
Indices: 23232--23308 Score: 127
Period size: 24 Copynumber: 3.2 Consensus size: 24
23222 CCAACACCGT
*
23232 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
23256 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
23280 TCTCCCTTATCAGCTCCCAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
23304 TCTCC
1 TCTCC
23309 TGACAGCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.21, C:0.43, G:0.04, T:0.32
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Done.