Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2120
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: 36535
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:7309 original size:11 final size:11
Alignment explanation
Indices: 7293--7322 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7283 TGATCGATTC
7293 AAATTTAATTA
1 AAATTTAATTA
*
7304 AAATTTTATTA
1 AAATTTAATTA
7315 AAATTTAA
1 AAATTTAA
7323 AAAGTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATTTAATTA
Found at i:8497 original size:15 final size:16
Alignment explanation
Indices: 8477--8510 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8467 GGATTTATTG
8477 AAAGAAAA-AAAAAGA
1 AAAGAAAAGAAAAAGA
*
8492 AAAGAAAAGAAAAGGA
1 AAAGAAAAGAAAAAGA
8508 AAA
1 AAA
8511 AAGAAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAAGA
Found at i:8509 original size:6 final size:5
Alignment explanation
Indices: 8477--8510 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
8467 GGATTTATTG
*
8477 AAAGA AAAAA AAAGA AAAGA AAAGA AAAGGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA-GA AAA
8511 AAGAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:10057 original size:29 final size:30
Alignment explanation
Indices: 9989--10069 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
9979 TTTCACCAAT
9989 ACTTTTAAAAATTACATTTTATTTATCTATA
1 ACTTTTAAAAATTACA-TTTATTTATCTATA
*
10020 A-TCTTTAAAAATTATATTTATTGT-T-TATA
1 ACT-TTTAAAAATTACATTTATT-TATCTATA
*
10049 ACTTTTAAAAATTAGATTTAT
1 ACTTTTAAAAATTACATTTAT
10070 CATTCATAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 22 0.49
30 9 0.20
31 14 0.31
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
ACTTTTAAAAATTACATTTATTTATCTATA
Found at i:10078 original size:29 final size:28
Alignment explanation
Indices: 9989--10079 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 28
9979 TTTCACCAAT
*
9989 ACTTTTAAAAATTACATTTTATTTATCTATA
1 ACTTTTAAAAATTACA-TTTATAT-TC-ATA
* * *
10020 A-TCTTTAAAAATTATATTTATTGTTTATA
1 ACT-TTTAAAAATTACATTTA-TATTCATA
*
10049 ACTTTTAAAAATTAGATTTATCATTCATA
1 ACTTTTAAAAATTACATTTAT-ATTCATA
10078 AC
1 AC
10080 CTGTGAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.02
29 27 0.54
30 7 0.14
31 15 0.30
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (28 bp):
ACTTTTAAAAATTACATTTATATTCATA
Found at i:13749 original size:2 final size:2
Alignment explanation
Indices: 13742--13776 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13732 ATTTATATTT
13742 TA TA TA TA TA 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 TA T
13777 TTGAACTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17780 original size:16 final size:16
Alignment explanation
Indices: 17759--17793 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17749 ATAAATAAAA
17759 ATATATATGTATATAT
1 ATATATATGTATATAT
17775 ATATATATGTATATAT
1 ATATATATGTATATAT
17791 ATA
1 ATA
17794 CACACACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
ATATATATGTATATAT
Found at i:17807 original size:2 final size:2
Alignment explanation
Indices: 17759--17793 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17749 ATAAATAAAA
* *
17759 AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17794 CACACACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19831 original size:12 final size:12
Alignment explanation
Indices: 19814--19849 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19804 TATCATCATC
19814 ATCATTATTATT
1 ATCATTATTATT
*
19826 ATCATTATCATT
1 ATCATTATTATT
*
19838 ATTATTATTATT
1 ATCATTATTATT
19850 TGCTAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
ATCATTATTATT
Found at i:19835 original size:18 final size:18
Alignment explanation
Indices: 19797--19845 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
19787 AAAAATTTAA
*
19797 ATCATTA-TATCATCATC
1 ATCATTATTATTATCATC
*
19814 ATCATTATTATTATCATT
1 ATCATTATTATTATCATC
19832 ATCATTATTATTAT
1 ATCATTATTATTAT
19846 TATTTGCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
ATCATTATTATTATCATC
Found at i:21117 original size:15 final size:16
Alignment explanation
Indices: 21078--21119 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
21068 AAATATTCAT
21078 ATTTAATAATATAATAA
1 ATTTAA-AATATAATAA
21095 ACTTTAAAATATAAT-A
1 A-TTTAAAATATAATAA
21111 ATTTAAAAT
1 ATTTAAAAT
21120 TTCATTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.33
16 2 0.08
17 9 0.38
18 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTAAAATATAATAA
Found at i:21246 original size:3 final size:3
Alignment explanation
Indices: 21240--21268 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21230 TAATTACAGA
21240 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
21269 CAACAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21885 original size:2 final size:2
Alignment explanation
Indices: 21880--21914 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
21870 TTTTAAACCT
21880 TA TA TA TA T- TA TA T- 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 TA TA T
21915 GTACTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:24472 original size:12 final size:12
Alignment explanation
Indices: 24450--24479 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24440 GCAAAAATAA
24450 ATAAT-TAAAAT
1 ATAATATAAAAT
24461 ATAATATAAAAT
1 ATAATATAAAAT
24473 ATAATAT
1 ATAATAT
24480 TATCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:24541 original size:31 final size:32
Alignment explanation
Indices: 24484--24543 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
24474 TAATATTATC
* *
24484 AAAAATATATAAATATATTAAAATTTATACAT
1 AAAAATATATAAACATATCAAAATTTATACAT
*
24516 AAAAA-ATATTAACATATCAAAATTTATA
1 AAAAATATATAAACATATCAAAATTTATA
24544 TAAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAAATATATAAACATATCAAAATTTATACAT
Found at i:25276 original size:3 final size:3
Alignment explanation
Indices: 25250--25298 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
25240 ATTTACTTTC
25250 ATT ATT -TT ATT ATT -TT -TT AGTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
25293 ATT ATT
1 ATT ATT
25299 TACTGAGGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:27304 original size:4 final size:4
Alignment explanation
Indices: 27297--27321 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27287 TATATATATA
27297 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
27322 GTGTGTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:28287 original size:80 final size:81
Alignment explanation
Indices: 28097--28297 Score: 228
Period size: 80 Copynumber: 2.5 Consensus size: 81
28087 CAAAGCAAAC
* * *
28097 AGCTCCTTCAGCAAATTTTCGGGAAAAACGAACTCCACAAGGAATTGATGGGTACAATTCATACC
1 AGCTCCTTCAGCAAATTTTCAGGAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATACC
**
28162 AAAGTTCGTCTTCGGT
66 AAAGTTCGTCTTCACT
* * * * * * *
28178 AGCTCATCCAGC-AATTTTCTGAAAAAGCGAACTCCACAAGGAATCGGTGGGTGCAATTCATATC
1 AGCTCCTTCAGCAAATTTTCAGGAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATACC
*
28242 AAAGTT-TTCTTCCACT
66 AAAGTTCGTCTT-CACT
** *
28258 -GCTCCTTCAGCAAAAGTTCAGGAAGAGCGAACTCCACAAG
1 AGCTCCTTCAGCAAATTTTCAGGAAAAGCGAACTCCACAAG
28298 TATGGCTGTG
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
79 13 0.13
80 76 0.77
81 10 0.10
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (81 bp):
AGCTCCTTCAGCAAATTTTCAGGAAAAGCGAACTCCACAAGGAATCGATGGGTACAATTCATACC
AAAGTTCGTCTTCACT
Done.