Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1998
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: 13138
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5685 original size:13 final size:12
Alignment explanation
Indices: 5667--5699 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
5657 TAATTTATGG
5667 GAACAAATAAATA
1 GAACAAATAAA-A
5680 GAACAAATAAAA
1 GAACAAATAAAA
5692 -AACAAATA
1 GAACAAATA
5700 GCGGTAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 1 0.05
13 11 0.55
ACGTcount: A:0.73, C:0.09, G:0.06, T:0.12
Consensus pattern (12 bp):
GAACAAATAAAA
Found at i:7740 original size:15 final size:15
Alignment explanation
Indices: 7720--7753 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
7710 TCCTATTACC
7720 TATTATTTAATTTAA
1 TATTATTTAATTTAA
7735 TATTATTTAATTTAA
1 TATTATTTAATTTAA
7750 TATT
1 TATT
7754 GATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTTAATTTAA
Found at i:12026 original size:19 final size:16
Alignment explanation
Indices: 11981--12039 Score: 61
Period size: 15 Copynumber: 3.7 Consensus size: 16
11971 TCAAATTCGA
11981 AATT-ATTAAATTAAT
1 AATTAATTAAATTAAT
11996 AATTAA-TAAATTAAT
1 AATTAATTAAATTAAT
12011 ATATTTAACTTAAATTAA-
1 A-A-TTAA-TTAAATTAAT
*
12029 AATTAAATAAA
1 AATTAATTAAA
12040 AATAAATAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 18 0.47
16 6 0.16
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTAATTAAATTAAT
Found at i:12052 original size:3 final size:3
Alignment explanation
Indices: 12034--12225 Score: 61
Period size: 3 Copynumber: 65.3 Consensus size: 3
12024 ATTAAAATTA
* * * * *
12034 AAT AAA AAT AAAT AAT AAT ATT TA- AAT AAT AAT AAT ATT TA- AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
12078 AAAT AAT AAT AAT ATT TA- AAT -AT AA- AAT AAT -TT AA- ATAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
12120 TA- AAT AAT AAT AAT ATT TA- AAT AAAT AAT AAT ATT TA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* *
12163 -AT AAAT AAT ATAT AAAT AAT -AT AAT AAT AAT -AT ATT ATAT ATT AAT
1 AAT -AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
12209 AAAT AAT -AT AAAT AAT A
1 -AAT AAT AAT -AAT AAT A
12226 TAGAAATATA
Statistics
Matches: 135, Mismatches: 30, Indels: 48
0.63 0.14 0.23
Matches are distributed among these distances:
2 20 0.15
3 91 0.67
4 23 0.17
5 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:12061 original size:11 final size:10
Alignment explanation
Indices: 12047--12226 Score: 97
Period size: 11 Copynumber: 18.8 Consensus size: 10
12037 AAAAATAAAT
12047 AATAATATTTA
1 AATAATA-TTA
*
12058 AATAATAAT-
1 AATAATATTA
12067 AAT-AT-TTA
1 AATAATATTA
*
12075 AATAA-ATAA
1 AATAATATTA
12084 TAATAATATTTA
1 -AATAATA-TTA
12096 AAT-ATA--A
1 AATAATATTA
12103 AATAAT-TTA
1 AATAATATTA
12112 AAT-ATAATTA
1 AATAAT-ATTA
*
12122 AATAATAAT-
1 AATAATATTA
12131 AAT-AT-TTA
1 AATAATATTA
12139 AATAA-A-T-
1 AATAATATTA
12146 AATAATATTTA
1 AATAATA-TTA
12157 AATAATA-TA
1 AATAATATTA
12166 AATAATATATA
1 AATAATAT-TA
*
12177 AATAATATAA
1 AATAATATTA
12187 TAATAATATATTA
1 -AAT-A-ATATTA
* * *
12200 TATATTAATA
1 AATAATATTA
12210 AATAATA-TA
1 AATAATATTA
12219 AATAATAT
1 AATAATAT
12227 AGAAATATAG
Statistics
Matches: 131, Mismatches: 13, Indels: 51
0.67 0.07 0.26
Matches are distributed among these distances:
7 11 0.08
8 16 0.12
9 32 0.24
10 28 0.21
11 34 0.26
12 5 0.04
13 5 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAATATTA
Found at i:12104 original size:64 final size:63
Alignment explanation
Indices: 12034--12225 Score: 197
Period size: 64 Copynumber: 3.1 Consensus size: 63
12024 ATTAAAATTA
12034 AATAAAAATAAATAATAATATTTAAATAATAATAATATTTAAATAAATAATAATAATATTTAAAT
1 AATAAAAATAAATAATAATA-TTAAATAATAATAATATTTAAAT-AATAATAATAATATTTAAAT
*
12099 -AT-AAAATAATTTAA-ATATAATTAAATAATAATAATATTTAAAT-A-AATAATAATATTTAAA
1 AATAAAAATAA-ATAATA-AT-ATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAA
12159 T
63 T
* * *
12160 AATATAAAT-AATATATAA-A-TAATATAATAATAATATATTATATATTAATAAATAATA--TAA
1 AATAAAAATAAATA-ATAATATTAA-ATAATAATAATAT-TTAAATAATAAT-AATAATATTTAA
12220 AT
62 AT
12222 AATA
1 AATA
12226 TAGAAATATA
Statistics
Matches: 110, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
59 3 0.03
60 14 0.13
61 24 0.22
62 15 0.14
63 16 0.15
64 37 0.34
65 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (63 bp):
AATAAAAATAAATAATAATATTAAATAATAATAATATTTAAATAATAATAATAATATTTAAAT
Found at i:12134 original size:43 final size:44
Alignment explanation
Indices: 12024--12225 Score: 179
Period size: 43 Copynumber: 4.5 Consensus size: 44
12014 TTTAACTTAA
*
12024 ATTAAAATTAAATAAAAATAAATAATAATATTTAAAT-AATAATAAT
1 ATTAAAA-T-AATATAAAT-AATAATAATATTTAAATAAATAATAAT
12070 ATT----TAA-ATAAATAATAATAATATTTAAATATAA-AATAAT
1 ATTAAAATAATATAAATAATAATAATATTTAAATA-AATAATAAT
12109 -TTAAATATAAT-TAAATAATAATAATATTTAAATAAATAATAAT
1 ATTAAA-ATAATATAAATAATAATAATATTTAAATAAATAATAAT
* * *
12152 ATTTAAATAATATAAATAATATATAAATAATATAATAATAATATATTATAT
1 ATTAAAATAATATAAATAATA-AT-AAT-AT-TTA-AATAA-ATAATA-AT
12203 ATTAATAAATAATATAAATAATA
1 ATT-A-AAATAATATAAATAATA
12226 TAGAAATATA
Statistics
Matches: 131, Mismatches: 5, Indels: 33
0.78 0.03 0.20
Matches are distributed among these distances:
38 19 0.15
39 11 0.08
40 4 0.03
41 1 0.01
42 2 0.02
43 37 0.28
44 13 0.10
45 2 0.02
46 6 0.05
47 2 0.02
48 2 0.02
49 5 0.04
50 5 0.04
51 5 0.04
53 17 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (44 bp):
ATTAAAATAATATAAATAATAATAATATTTAAATAAATAATAAT
Found at i:12245 original size:21 final size:20
Alignment explanation
Indices: 12219--12257 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
12209 AAATAATATA
12219 AATAATATAGAAATATAGATT
1 AATAATATAGAAAT-TAGATT
12240 AATAATATAGAAATTAGA
1 AATAATATAGAAATTAGA
12258 AATATAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (20 bp):
AATAATATAGAAATTAGATT
Found at i:12248 original size:13 final size:13
Alignment explanation
Indices: 12230--12278 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
12220 ATAATATAGA
12230 AATATAGATTAAT
1 AATATAGATTAAT
12243 AATATAGAAATTAGA-
1 AATATAG--ATTA-AT
12258 AATATAGATTAAT
1 AATATAGATTAAT
12271 AATATAGA
1 AATATAGA
12279 AATATAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (13 bp):
AATATAGATTAAT
Found at i:12262 original size:28 final size:29
Alignment explanation
Indices: 12210--12286 Score: 129
Period size: 28 Copynumber: 2.7 Consensus size: 29
12200 TATATTAATA
*
12210 AATAATATAAATAATATAGAAATATAGATT
1 AATAATATAGA-AATATAGAAATATAGATT
12240 AATAATATAGAAAT-TAGAAATATAGATT
1 AATAATATAGAAATATAGAAATATAGATT
12268 AATAATATAGAAATATAGA
1 AATAATATAGAAATATAGA
12287 TTTCGAAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 28 0.62
29 7 0.16
30 10 0.22
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (29 bp):
AATAATATAGAAATATAGAAATATAGATT
Found at i:12342 original size:23 final size:22
Alignment explanation
Indices: 12316--12377 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
12306 TAATTTTATA
12316 TTAATATAAATATTAATAATTAC
1 TTAA-ATAAATATTAATAATTAC
*
12339 TT-AA-AATTATTAATAATTAC
1 TTAAATAAATATTAATAATTAC
*
12359 TTAAAATTAATATTAATAA
1 TT-AAATAAATATTAATAA
12378 CATTAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 17 0.52
21 1 0.03
22 3 0.09
23 12 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAAATAAATATTAATAATTAC
Found at i:12346 original size:10 final size:11
Alignment explanation
Indices: 12328--12367 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
12318 AATATAAATA
12328 TTAATAATTAC
1 TTAATAATTAC
12339 TTAA-AATTA-
1 TTAATAATTAC
12348 TTAATAATTAC
1 TTAATAATTAC
12359 TTAA-AATTA
1 TTAATAATTA
12368 ATATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 15 0.56
11 8 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAATAATTAC
Found at i:12351 original size:20 final size:20
Alignment explanation
Indices: 12326--12367 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12316 TTAATATAAA
12326 TATTAATAATTACTTAAAAT
1 TATTAATAATTACTTAAAAT
12346 TATTAATAATTACTTAAAAT
1 TATTAATAATTACTTAAAAT
12366 TA
1 TA
12368 ATATTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAATAATTACTTAAAAT
Found at i:12375 original size:20 final size:20
Alignment explanation
Indices: 12329--12375 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
12319 ATATAAATAT
*
12329 TAATAATTACTTAAAATTAT
1 TAATAATTACTTAAAATTAA
12349 TAATAATTACTTAAAATTAA
1 TAATAATTACTTAAAATTAA
*
12369 TATTAAT
1 TAATAAT
12376 AACATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAATTACTTAAAATTAA
Done.