Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2660
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: 18410
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:5031 original size:36 final size:35
Alignment explanation
Indices: 4976--5053 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
4966 ATTAGATCTA
*
4976 ATAATTTATGTAATCATATTGTGTATTTATTATATT
1 ATAATTTATGTAATCATATTGTATATTTA-TATATT
* * *
5012 ATAATTTTATTTAAT-ATATTTTATATTTATATATG
1 ATAA-TTTATGTAATCATATTGTATATTTATATATT
5047 AT-ATTTA
1 ATAATTTA
5054 AATAATTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 1 0.03
35 7 0.19
36 16 0.43
37 9 0.24
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (35 bp):
ATAATTTATGTAATCATATTGTATATTTATATATT
Found at i:5035 original size:27 final size:28
Alignment explanation
Indices: 5005--5131 Score: 98
Period size: 27 Copynumber: 4.4 Consensus size: 28
4995 TGTGTATTTA
5005 TTATATTATA-ATTTTATTTAATATATT
1 TTATATTATATATTTTATTTAATATATT
** *
5032 TTATATTTATATATGATATTTAA-ATAAT
1 TTATA-TTATATATTTTATTTAATATATT
** *
5060 TTATATTATATAAATT-TTTAAAATATT
1 TTATATTATATATTTTATTTAATATATT
* *
5087 TATATATTTATATTATTTTGTATTATCATTTATT
1 T-TATA-TTATA-TA-TTT-TATT-TAATATATT
5121 TTATATTATAT
1 TTATATTATAT
5132 TTTAATTATT
Statistics
Matches: 78, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
26 5 0.06
27 18 0.23
28 18 0.23
29 14 0.18
30 2 0.03
31 2 0.03
32 6 0.08
33 6 0.08
34 7 0.09
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATATTATATATTTTATTTAATATATT
Found at i:5132 original size:22 final size:22
Alignment explanation
Indices: 5092--5175 Score: 56
Period size: 22 Copynumber: 4.0 Consensus size: 22
5082 ATATTTATAT
* * *
5092 ATTTATATTATTTTGTATTATC
1 ATTTATTTTATATTATATTATC
*
5114 ATTTATTTTATATTATATT-TT
1 ATTTATTTTATATTATATTATC
*
5135 AATTATTTT-T-TTATA-TA--
1 ATTTATTTTATATTATATTATC
5152 A-TTATTTTATATTTAATATTATC
1 ATTTATTTTATA-TT-ATATTATC
5175 A
1 A
5176 AATCTAGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
16 7 0.14
17 2 0.04
18 1 0.02
19 7 0.14
20 4 0.08
21 11 0.22
22 16 0.33
23 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.64
Consensus pattern (22 bp):
ATTTATTTTATATTATATTATC
Found at i:5140 original size:38 final size:38
Alignment explanation
Indices: 5086--5164 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
5076 TTTAAAATAT
5086 TTATATATTTATATTATTTTGTATTATCAT-TTATTTTATA
1 TTATATATTTATATTATTTT-T-TTAT-ATATTATTTTATA
5126 TTATAT-TTTA-ATTATTTTTTTATATAATTATTTTATA
1 TTATATATTTATATTATTTTTTTATAT-ATTATTTTATA
5163 TT
1 TT
5165 TAATATTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
35 2 0.05
36 4 0.11
37 13 0.35
38 8 0.22
39 4 0.11
40 6 0.16
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (38 bp):
TTATATATTTATATTATTTTTTTATATATTATTTTATA
Found at i:5142 original size:21 final size:18
Alignment explanation
Indices: 5083--5164 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 18
5073 ATTTTTAAAA
5083 TATTTATATATT-TAT-AT
1 TATTT-TATATTATATAAT
*
5100 TATTTTGTATTATCAT--T
1 TATTTTATATTAT-ATAAT
5117 TATTTTATATTATATTTTAAT
1 TATTTTATATTATA---TAAT
5138 TATTTT-T-TTATATAAT
1 TATTTTATATTATATAAT
5154 TATTTTATATT
1 TATTTTATATT
5165 TAATATTATC
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 16 0.30
17 20 0.37
18 4 0.07
19 6 0.11
20 1 0.02
21 7 0.13
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
TATTTTATATTATATAAT
Found at i:5145 original size:11 final size:12
Alignment explanation
Indices: 5086--5164 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 12
5076 TTTAAAATAT
5086 TTATATATTTATA
1 TTATAT-TTTATA
5099 TTAT-TTTGTATTA
1 TTATATTT-TA-TA
*
5112 TCATTTATTTTATA
1 T--TATATTTTATA
5126 TTATATTTTA-A
1 TTATATTTTATA
*
5137 TTATTTTTTTATA
1 TTA-TATTTTATA
*
5150 TAATTATTTTATA
1 TTA-TATTTTATA
5163 TT
1 TT
5165 TAATATTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
11 6 0.11
12 17 0.32
13 20 0.38
14 3 0.06
15 4 0.08
16 3 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:6623 original size:2 final size:2
Alignment explanation
Indices: 6616--6640 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6606 TAACAAATCA
6616 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6641 AATTAATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11361 original size:40 final size:40
Alignment explanation
Indices: 11308--11419 Score: 124
Period size: 39 Copynumber: 2.9 Consensus size: 40
11298 TTTTATATTA
* *
11308 AAAATTAAG-TTTTAAAGATTATTTTTACACTTTCACATC
1 AAAATAAAGCTTTTAAAGATTATTTTTACATTTTCACATC
* * * *
11347 AAAATCAAGCTTTTAAA-ATTATTTTAATATTTTTACATC
1 AAAATAAAGCTTTTAAAGATTATTTTTACATTTTCACATC
* *
11386 AAAATAAAACTTTT-AAGATT-TATTTACATTTTCA
1 AAAATAAAGCTTTTAAAGATTATTTTTACATTTTCA
11420 TCAAAACTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
38 12 0.20
39 41 0.68
40 7 0.12
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (40 bp):
AAAATAAAGCTTTTAAAGATTATTTTTACATTTTCACATC
Found at i:11399 original size:39 final size:38
Alignment explanation
Indices: 11276--11425 Score: 110
Period size: 39 Copynumber: 3.9 Consensus size: 38
11266 GACGAAAATG
* * * * *
11276 AACTTTTAAAGTCATTTTAATATTTTATATTAAAA-ATT
1 AACTTTTAAAATTATTTTAATATTTTACATCAAAATA-A
* * * * *
11314 AAGTTTTAAAGATTATTTTTACACTTTCACATCAAAATCA
1 AACTTTTAAA-ATTATTTTAATA-TTTTACATCAAAATAA
*
11354 AGCTTTTAAAATTATTTTAATATTTTTACATCAAAATAA
1 AACTTTTAAAATTATTTTAATA-TTTTACATCAAAATAA
* *
11393 AACTTTTAAGATT-TATTT-ACATTTT-CATCAAAA
1 AACTTTTAAAATTAT-TTTAATATTTTACATCAAAA
11426 CTAAGTCTTT
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
36 8 0.09
37 4 0.05
38 12 0.14
39 46 0.52
40 18 0.20
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (38 bp):
AACTTTTAAAATTATTTTAATATTTTACATCAAAATAA
Found at i:13009 original size:21 final size:23
Alignment explanation
Indices: 12980--13035 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
12970 TAGAAAAAAG
12980 AAATAATTATATAATATA-AATT
1 AAATAATTATATAATATATAATT
*
13002 AAAT-ATTATATCATATATAATT
1 AAATAATTATATAATATATAATT
13024 -AATAATTA-ATAA
1 AAATAATTATATAA
13036 AAATATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAATTATATAATATATAATT
Found at i:13176 original size:19 final size:20
Alignment explanation
Indices: 13152--13201 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
13142 TTATTTATTT
13152 TTTTAAATATTAAAT-AA-AA
1 TTTTAAAT-TTAAATAAATAA
13171 TTTTAAATTTAAATAAATAA
1 TTTTAAATTTAAATAAATAA
13191 TTTTAAATTTA
1 TTTTAAATTTA
13202 TAGATCTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTAAATTTAAATAAATAA
Found at i:13410 original size:22 final size:21
Alignment explanation
Indices: 13385--13435 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
13375 TCATTTTATT
13385 TATATTTAAATTAATTATAAAA
1 TATATTTAAATTAA-TATAAAA
** *
13407 TATAAAATATATTAATATAAAA
1 TAT-ATTTAAATTAATATAAAA
13429 TATATTT
1 TATATTT
13436 TTTAATATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 2 0.09
22 13 0.57
23 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATTTAAATTAATATAAAA
Found at i:13425 original size:15 final size:15
Alignment explanation
Indices: 13405--13434 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
13395 TTAATTATAA
13405 AATATAAAATATATT
1 AATATAAAATATATT
13420 AATATAAAATATATT
1 AATATAAAATATATT
13435 TTTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAAAATATATT
Found at i:13640 original size:94 final size:96
Alignment explanation
Indices: 13529--13717 Score: 301
Period size: 96 Copynumber: 2.0 Consensus size: 96
13519 ACATGATATA
* * * *
13529 AATATATAAATTATTTTTTTAATTTA-TTTTTTTGTCAATTTTTTTATTTATC-AAAAAGCTAAG
1 AATACATAAATTATTTTTTTAATTTACTTATTTTGTCAAATATTTTATTTATCAAAAAAGCTAAG
*
13592 TATTATTAAGAAATATCCAAATGTTGATGTG
66 TACTATTAAGAAATATCCAAATGTTGATGTG
* *
13623 AATACATAAATTTTTTTTTTAATTTACTTATTTTGTTAAATATTTTATTTATCAAAAAAGCTAAG
1 AATACATAAATTATTTTTTTAATTTACTTATTTTGTCAAATATTTTATTTATCAAAAAAGCTAAG
13688 TACTATTAAGAAATATCCAAATGTTGATGT
66 TACTATTAAGAAATATCCAAATGTTGATGT
13718 CAAAAGACCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 24 0.28
95 22 0.26
96 40 0.47
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (96 bp):
AATACATAAATTATTTTTTTAATTTACTTATTTTGTCAAATATTTTATTTATCAAAAAAGCTAAG
TACTATTAAGAAATATCCAAATGTTGATGTG
Found at i:18006 original size:2 final size:2
Alignment explanation
Indices: 17999--18046 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
17989 AAGTATTCGA
*
17999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18040 AT AT AT A
1 AT AT AT A
18047 CACATCAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.