Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1212
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: 10278
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Found at i:736 original size:9 final size:9
Alignment explanation
Indices: 722--748 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
712 TTCTAATATG
722 TATATATAA
1 TATATATAA
731 TATATATAA
1 TATATATAA
740 TATATATAA
1 TATATATAA
749 AAGAGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATATAA
Found at i:893 original size:2 final size:2
Alignment explanation
Indices: 886--914 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
876 TATTGTAACC
886 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
915 ATAAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:918 original size:10 final size:11
Alignment explanation
Indices: 886--918 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
876 TATTGTAACC
886 TATATATATATA
1 TATATATATA-A
898 TATATATATAA
1 TATATATATAA
909 TATATA-ATAA
1 TATATATATAA
919 AAGAGACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 7 0.33
12 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATATATATAA
Found at i:1009 original size:169 final size:170
Alignment explanation
Indices: 722--1267 Score: 866
Period size: 169 Copynumber: 3.1 Consensus size: 170
712 TTCTAATATG
*
722 TATATATA-ATATATATA-ATATAT-ATAAAAGAGACAAAAGATTGCATCATTTGTGCACAGTTT
1 TATATATATATATATATATATATATAATAAAAGAGAC-GAAGATTGCATCATTTGTGCACAGTTT
*
784 AACTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAG
65 AGCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAG
849 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATA
130 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATA
890 TATATATATATATATATA-ATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTTA
1 TATATATATATATATATATATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTTA
* *
954 GCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAACATGTTGGAATTGTAGT
66 GCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGT
1019 TTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATATA
131 TTTTATAATTGAAATTCTATCTCTTGTATTGTAACC------------TATA
1071 TATATATATATATATATATATATATATTATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTT
1 TATATATATATATATATATATATATA--ATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTT
* *
1136 TAGCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGTA
64 TAGCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTA
*
1201 GTTTTTATAATTGAAATTCTATCTCTTGTATTGTAATCTATA
129 GTTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATA
1243 TATATATATATATATATATATATAT
1 TATATATATATATATATATATATAT
1268 GAAATGAAAG
Statistics
Matches: 352, Mismatches: 9, Indels: 30
0.90 0.02 0.08
Matches are distributed among these distances:
168 8 0.02
169 140 0.40
170 11 0.03
172 29 0.08
181 22 0.06
182 7 0.02
184 135 0.38
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (170 bp):
TATATATATATATATATATATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTTA
GCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGT
TTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATA
Found at i:1062 original size:2 final size:2
Alignment explanation
Indices: 1055--1101 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1045 TATTGTAACC
1055 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1097 T- TA TA
1 TA TA TA
1102 AAAGAGACGA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1200 original size:184 final size:183
Alignment explanation
Indices: 886--1267 Score: 701
Period size: 184 Copynumber: 2.1 Consensus size: 183
876 TATTGTAACC
886 TATATATATATATATATATATAATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGT
1 TATATATATATATATATATATAATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGT
* * *
951 TTAGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAACATGTTGGAATTGT
66 TTAGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGT
1016 AGTTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATA
131 AGTTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATA
*
1069 TATATATATATATATATATATATATATATTATAAAAGAGACGAAGATTGCATCATTTGTGCACAG
1 TATATATATATATATATATATA-ATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAG
*
1134 TTTAGCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTG
65 TTTAGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTG
*
1199 TAGTTTTTATAATTGAAATTCTATCTCTTGTATTGTAATCTATATATATATATA
130 TAGTTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATA
1253 TATATATATATATAT
1 TATATATATATATAT
1268 GAAATGAAAG
Statistics
Matches: 192, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
183 22 0.11
184 170 0.89
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (183 bp):
TATATATATATATATATATATAATATATAATAAAAGAGACGAAGATTGCATCATTTGTGCACAGT
TTAGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGT
AGTTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATA
Found at i:1246 original size:2 final size:2
Alignment explanation
Indices: 1239--1267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1229 TATTGTAATC
1239 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 T
1268 GAAATGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4127 original size:2 final size:2
Alignment explanation
Indices: 4120--4147 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4110 ATTTCATGTG
4120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4148 TGCATTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5565 original size:2 final size:2
Alignment explanation
Indices: 5558--5595 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5548 GGAAAGTATT
5558 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5596 TGAAAGAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6560 original size:2 final size:2
Alignment explanation
Indices: 6553--6589 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6543 GGCTAATACT
6553 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6590 ATGCTCAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6578 original size:17 final size:17
Alignment explanation
Indices: 6556--6591 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
6546 TAATACTTAT
6556 ATATATATATATATATA
1 ATATATATATATATATA
6573 ATATATATATATATATA
1 ATATATATATATATATA
6590 AT
1 AT
6592 GCTCAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:7917 original size:16 final size:16
Alignment explanation
Indices: 7898--8000 Score: 91
Period size: 16 Copynumber: 6.4 Consensus size: 16
7888 TTTTTAAAAT
*
7898 TTTAAATTATTTAAAA
1 TTTAAATTATTTTAAA
* * *
7914 TTTAAGTTATTTTGAT
1 TTTAAATTATTTTAAA
* *
7930 TTTAGATTATTTCAAA
1 TTTAAATTATTTTAAA
** * *
7946 TTTATGTCACTTT-AA
1 TTTAAATTATTTTAAA
7961 TTTAATATTATTTTAAA
1 TTTAA-ATTATTTTAAA
*
7978 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAA
7994 TTTAAAT
1 TTTAAAT
8001 CAATTAAGTT
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
15 6 0.09
16 53 0.80
17 7 0.11
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:7932 original size:32 final size:31
Alignment explanation
Indices: 7896--8000 Score: 111
Period size: 32 Copynumber: 3.3 Consensus size: 31
7886 AATTTTTAAA
7896 ATTTTAAATTATTTAAAATTTAAGTTATTTT
1 ATTTTAAATTATTTAAAATTTAAGTTATTTT
* * * * *
7927 GATTTTAGATTATTTCAAATTTATGTCACTTT
1 -ATTTTAAATTATTTAAAATTTAAGTTATTTT
* * *
7959 AATTTAATATTATTTTAAATTTAAATTATTTT
1 ATTTTAA-ATTATTTAAAATTTAAGTTATTTT
7991 AATTTTAAAT
1 -ATTTTAAAT
8001 CAATTAAGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
31 5 0.09
32 47 0.81
33 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (31 bp):
ATTTTAAATTATTTAAAATTTAAGTTATTTT
Found at i:7981 original size:22 final size:22
Alignment explanation
Indices: 7956--8000 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
7946 TTTATGTCAC
*
7956 TTTAATTTAATATT-ATTTTAAA
1 TTTAAATT-ATATTAATTTTAAA
*
7978 TTTAAATTATTTTAATTTTAAA
1 TTTAAATTATATTAATTTTAAA
8000 T
1 T
8001 CAATTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTATATTAATTTTAAA
Found at i:8087 original size:23 final size:23
Alignment explanation
Indices: 8050--8099 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
8040 TTTTATTCAG
*
8050 ATTATTTTTAGATTAATTATT-AAA
1 ATTATTTTTAAATT-ATT-TTCAAA
8074 ATTA-TTTTAAATTATTTTCAAA
1 ATTATTTTTAAATTATTTTCAAA
8096 ATTA
1 ATTA
8100 ATTGATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 10 0.42
23 8 0.33
24 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTTTTAAATTATTTTCAAA
Found at i:9613 original size:2 final size:2
Alignment explanation
Indices: 9606--9632 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9596 TGAAAAGTGC
9606 AT 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 AT A
9633 GAAAATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.