Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold969
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: 34370
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:11130 original size:20 final size:20
Alignment explanation
Indices: 11091--11130 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11081 GAAATAATTG
* *
11091 CAGTATAAAAATATTTAAAA
1 CAGTATAAAAATAGTGAAAA
*
11111 CAGTATATAAATAGTGAAAA
1 CAGTATAAAAATAGTGAAAA
11131 GAGATTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (20 bp):
CAGTATAAAAATAGTGAAAA
Found at i:11389 original size:22 final size:22
Alignment explanation
Indices: 11352--11401 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
11342 AACAACATAG
11352 TAAAT-AATATATGATAAAATA
1 TAAATAAATATATGATAAAATA
*
11373 TAAATAAATA-ATAGATAATATA
1 TAAATAAATATAT-GATAAAATA
11395 TATAATA
1 TA-AATA
11402 GACAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 14 0.56
23 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
TAAATAAATATATGATAAAATA
Found at i:11509 original size:9 final size:9
Alignment explanation
Indices: 11491--11544 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
11481 TGAAATAAAT
11491 AATATATAA
1 AATATATAA
*
11500 AATATTTAA
1 AATATATAA
*
11509 AATAAAT-A
1 AATATATAA
*
11517 AATAAATAA
1 AATATATAA
11526 AAT-T-TAGA
1 AATATATA-A
11534 AATATATAA
1 AATATATAA
11543 AA
1 AA
11545 AAGGATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 2 0.05
8 12 0.32
9 21 0.57
10 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (9 bp):
AATATATAA
Found at i:11536 original size:25 final size:25
Alignment explanation
Indices: 11482--11543 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
11472 TGTTTATAGT
*
11482 GAAATAAATAATATATAAAATATTTA
1 GAAATAAATAA-ATATAAAAAATTTA
11508 -AAATAAATAAATA-AATAAAATTTA
1 GAAATAAATAAATATAA-AAAATTTA
*
11532 GAAATATATAAA
1 GAAATAAATAAA
11544 AAAGGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 10 0.31
25 20 0.62
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (25 bp):
GAAATAAATAAATATAAAAAATTTA
Found at i:12204 original size:17 final size:18
Alignment explanation
Indices: 12182--12219 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12172 GTATGTGTTG
12182 AAAAAAAAAC-AGAAACA
1 AAAAAAAAACAAGAAACA
* *
12199 AAAAAATAACAATAAACA
1 AAAAAAAAACAAGAAACA
12217 AAA
1 AAA
12220 TATCACCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.82, C:0.11, G:0.03, T:0.05
Consensus pattern (18 bp):
AAAAAAAAACAAGAAACA
Found at i:12822 original size:17 final size:16
Alignment explanation
Indices: 12799--12841 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
12789 TTAAATGGAC
12799 TGTTTAATTTTATTTT
1 TGTTTAATTTTATTTT
*
12815 TCGTTTAATTTCATTTT
1 T-GTTTAATTTTATTTT
12832 T-TTTAATTTT
1 TGTTTAATTTT
12842 TGTAAGCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 1 0.04
17 15 0.62
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (16 bp):
TGTTTAATTTTATTTT
Found at i:19061 original size:22 final size:22
Alignment explanation
Indices: 19031--19091 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
19021 ATTGAACATG
19031 TGCA-TGTGCGAACCTCTTCCA
1 TGCATTGTGCGAACCTCTTCCA
* * *
19052 TGCATTGTGCAAACCTCATCTA
1 TGCATTGTGCGAACCTCTTCCA
*
19074 TGCGTTGTGCGAA-CTCTT
1 TGCATTGTGCGAACCTCTT
19092 AGCATGAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 8 0.24
22 25 0.76
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
TGCATTGTGCGAACCTCTTCCA
Found at i:27131 original size:11 final size:11
Alignment explanation
Indices: 27115--27142 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
27105 TTTTAAAATA
27115 ATTTATGAATT
1 ATTTATGAATT
27126 ATTTATGAATT
1 ATTTATGAATT
27137 ATTTAT
1 ATTTAT
27143 TATTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
ATTTATGAATT
Found at i:27175 original size:17 final size:19
Alignment explanation
Indices: 27139--27188 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
27129 TATGAATTAT
27139 TTATTATTTTATTATTTAAA
1 TTATTATTTTATTA-TTAAA
27159 TTATTATTTT-TTA-TAAA
1 TTATTATTTTATTATTAAA
27176 -TATT-TTTGTATTA
1 TTATTATTT-TATTA
27189 GTGGCAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 7 0.25
19 3 0.11
20 10 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTATTATTTTATTATTAAA
Found at i:33150 original size:22 final size:22
Alignment explanation
Indices: 33125--33175 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
33115 TGCATGTGTG
33125 AACCTCTTCCATGCATTGTGCA
1 AACCTCTTCCATGCATTGTGCA
* * * *
33147 AACCTCATCTATGCGTTGTGCG
1 AACCTCTTCCATGCATTGTGCA
33169 AA-CTCTT
1 AACCTCTT
33176 AGCATGAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (22 bp):
AACCTCTTCCATGCATTGTGCA
Done.