Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold840
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: 44085
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:932 original size:11 final size:11
Alignment explanation
Indices: 916--940 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
906 ACATGACAGC
916 ATTATTTATTT
1 ATTATTTATTT
927 ATTATTTATTT
1 ATTATTTATTT
938 ATT
1 ATT
941 TATTCTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:4140 original size:151 final size:150
Alignment explanation
Indices: 3718--4140 Score: 560
Period size: 151 Copynumber: 2.8 Consensus size: 150
3708 CAATATTTCC
* * * * * *
3718 TAATATAAATTTCCAACTCTTCTGGCTAAATTGTTGTTTTGAAAGTATTGACAAATCATGATTTG
1 TAATATAAGTTTCAAACTCTTCTGGCTAAATTATTGTTTTGAAAATCTTGACAAATCATGAATTG
* * * * *
3783 TTTGAACATTCAAATGTGCTTGAAATGAAGACATTCTTATTTCTTCTTTACTTTTTCGTGGCTAA
66 TTTGAACATCCAAATGTGCTTGAAATGAAGACATTCTTATTACTTATTTAC-CTTTCATGGCTAA
*
3848 ATTATTTTTCCATCATATTCA
130 ATTATTTTTCCAGCATATTCA
* *
3869 TAATATAAGTTTCAAACTCTTCTGGCTAAATTATTGTTTTGAAAATCTTGAGAAATCATTAATTG
1 TAATATAAGTTTCAAACTCTTCTGGCTAAATTATTGTTTTGAAAATCTTGACAAATCATGAATTG
* * * * *
3934 TTGGAACAACCAAATGTGCTTGAAATGAAGACATTCATATTGCTTATTATCCCTTTCATGGCTAA
66 TTTGAACATCCAAATGTGCTTGAAATGAAGACATTCTTATTACTTATT-TACCTTTCATGGCTAA
*
3999 ATTATTTTTCCAGGGA-ATTCA
130 ATTATTTTTCCA-GCATATTCA
* * *
4020 TAATATAAGTTTTAAACTCTTCTGGCCAAATTATTGTTTTTGAAAATCTTGACAAATCGTGAATT
1 TAATATAAGTTTCAAACTCTTCTGGCTAAATTATTG-TTTTGAAAATCTTGACAAATCATGAATT
* * * *
4085 GTTTGAACATCCAAGTGCGCTTGAAATGAAGACGTTCTTATTACTTATTTTCCTTT
65 GTTTGAACATCCAAATGTGCTTGAAATGAAGACATTCTTATTACTTATTTACCTTT
4141 TACCTTTCAG
Statistics
Matches: 237, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
151 167 0.70
152 70 0.30
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (150 bp):
TAATATAAGTTTCAAACTCTTCTGGCTAAATTATTGTTTTGAAAATCTTGACAAATCATGAATTG
TTTGAACATCCAAATGTGCTTGAAATGAAGACATTCTTATTACTTATTTACCTTTCATGGCTAAA
TTATTTTTCCAGCATATTCA
Found at i:12781 original size:16 final size:16
Alignment explanation
Indices: 12745--12805 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
12735 TTATTTTCAG
* *
12745 ATTCGGATCATTTTAG
1 ATTCGGGTCATTTTAA
*
12761 GTTCGGGTCATTTTAA
1 ATTCGGGTCATTTTAA
* * * *
12777 ATTCGCGTTACTTTAT
1 ATTCGGGTCATTTTAA
*
12793 ATTCGGGTTATTT
1 ATTCGGGTCATTT
12806 CGGATTCGGA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.48
Consensus pattern (16 bp):
ATTCGGGTCATTTTAA
Found at i:13449 original size:17 final size:17
Alignment explanation
Indices: 13427--13459 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13417 AATAACAATT
*
13427 TAAAAAATTTAAATTAA
1 TAAAAAATTAAAATTAA
13444 TAAAAAATTAAAATTA
1 TAAAAAATTAAAATTA
13460 TTATAATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAATTAAAATTAA
Found at i:21502 original size:20 final size:21
Alignment explanation
Indices: 21457--21511 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
21447 CATTAATGAA
*
21457 TGTATCGATACATGCTTCTAAT
1 TGTATCGATACAT-CATCTAAT
*
21479 TGTATCGATACAT-ATCTCAT
1 TGTATCGATACATCATCTAAT
21499 TGTATCGATACAT
1 TGTATCGATACAT
21512 TTTGGGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 18 0.58
22 13 0.42
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCATCTAAT
Found at i:28837 original size:6 final size:6
Alignment explanation
Indices: 28826--28858 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
28816 AATTAATTTC
28826 GCTATT GCTATT GCTATT GCTATT GCTATT GCT
1 GCTATT GCTATT GCTATT GCTATT GCTATT GCT
28859 GGTACCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (6 bp):
GCTATT
Found at i:30142 original size:2 final size:2
Alignment explanation
Indices: 30135--30172 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30125 GGAGGCAAAG
30135 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30173 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:30177 original size:2 final size:2
Alignment explanation
Indices: 30172--30199 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30162 TCTCTCTCTC
30172 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
30200 AATTAGAGAA
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):
TA
Found at i:33055 original size:2 final size:2
Alignment explanation
Indices: 33042--33072 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
33032 ACATTCATAC
*
33042 AT AT AC 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 AT AT A
33073 CCGGCTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:36194 original size:13 final size:13
Alignment explanation
Indices: 36176--36201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36166 TATTCTTTGC
36176 AAAAAAAGGAAAA
1 AAAAAAAGGAAAA
36189 AAAAAAAGGAAAA
1 AAAAAAAGGAAAA
36202 TGGAGAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGAAAA
Found at i:36915 original size:124 final size:122
Alignment explanation
Indices: 36729--36974 Score: 359
Period size: 124 Copynumber: 2.0 Consensus size: 122
36719 CAAATTGCAG
* * * * *
36729 GTTCTTCACTGTGTACTAGAGAGACATGGGTCCAAAAATTTCATTTATCTTCCGAAACGAGAATA
1 GTTCTTCACTGTGTACTAGAGAAACATAGGTCCAAAAATTTCATTGATCTTCAGAAACGAGAAGA
*
36794 CATGCAGCAAAAACAAATTAATTTGCAACCAAAAGTTTGCATCTTTTAAGATGTAACAA
66 CATGCAGCAAAAACAAACTAATTTGCAACCAAAAGTTT-CATCTTTT-AGATGTAACAA
* * * *
36853 GTTCTTCACTGTGTA-TCGGATAAACATAGGTCCAAACATTTCATTGATCTTCAGAAATGAGAAG
1 GTTCTTCACTGTGTACT-AGAGAAACATAGGTCCAAAAATTTCATTGATCTTCAGAAACGAGAAG
*
36917 ACATGCAGCAAAAACAAACTAATTTGCAACCAAAAGTTTCTTCTTTTAGATGTAACAA
65 ACATGCAGCAAAAACAAACTAATTTGCAACCAAAAGTTTCATCTTTTAGATGTAACAA
36975 ACTTCAAGAG
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 11 0.10
123 8 0.07
124 91 0.83
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (122 bp):
GTTCTTCACTGTGTACTAGAGAAACATAGGTCCAAAAATTTCATTGATCTTCAGAAACGAGAAGA
CATGCAGCAAAAACAAACTAATTTGCAACCAAAAGTTTCATCTTTTAGATGTAACAA
Found at i:40382 original size:2 final size:2
Alignment explanation
Indices: 40375--40399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40365 TTAATTTAGC
40375 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
40400 GAAAAAATAA
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:42153 original size:2 final size:2
Alignment explanation
Indices: 42146--42178 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42136 TGCTTTTTAT
42146 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 T
42179 TATTCTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42251 original size:92 final size:92
Alignment explanation
Indices: 42086--42266 Score: 303
Period size: 92 Copynumber: 2.0 Consensus size: 92
42076 CAATTACTAC
* *
42086 TTATTCTTTGAAAAATTAAATTTACAATTTTGGTGCTAAAATTATTGTTTTGCTTTTTATTATAT
1 TTATTCTTTGAAAAATTAAATTTACAATTTTGGTGCTAAAATGATGGTTTTGCTTTTTATTATAT
*
42151 ATATATATATATATATATATATATATA
66 ATAGATATATATATATATATATATATA
42178 TTATTCTTTGAAAAATT-AATTTACAATTTTGGTGCTAAAATGAGTGGTTTTGCTTTTTATTATG
1 TTATTCTTTGAAAAATTAAATTTACAATTTTGGTGCTAAAATGA-TGGTTTTGCTTTTTATTAT-
42242 ATAT-GATATATATATATATATATAT
64 ATATAGATATATATATATATATATAT
42267 GGCCATTCTT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
91 25 0.30
92 55 0.65
93 4 0.05
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.51
Consensus pattern (92 bp):
TTATTCTTTGAAAAATTAAATTTACAATTTTGGTGCTAAAATGATGGTTTTGCTTTTTATTATAT
ATAGATATATATATATATATATATATA
Done.