Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2444
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: 36846
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:776 original size:56 final size:52
Alignment explanation
Indices: 641--782 Score: 157
Period size: 49 Copynumber: 2.7 Consensus size: 52
631 TCTTATATCG
* * *
641 ATGCCTATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCACCTCAAT
** *
693 A--CCAACACCATGT-CCAAACATGGTCTTACATGGGACCTCTCCTAACCTCAAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT-C--ACCTCAAT
745 AATGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
1 -ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGG
783 GTCTCATCCC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
48 1 0.01
49 24 0.33
50 10 0.14
52 7 0.10
53 1 0.01
55 10 0.14
56 20 0.27
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (52 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCACCTCAAT
Found at i:3958 original size:40 final size:40
Alignment explanation
Indices: 3912--3988 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3902 CAAGACCTAA
3912 TGATACGAGTCATAAAGGCCCAACCCAAGTTCAAGAAAGT
1 TGATACGAGTCATAAAGGCCCAACCCAAGTTCAAGAAAGT
*
3952 TGATACGAGTCATAAAGGCCCAATCCAAGTTCAAGAA
1 TGATACGAGTCATAAAGGCCCAACCCAAGTTCAAGAA
3989 CGTGATGGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (40 bp):
TGATACGAGTCATAAAGGCCCAACCCAAGTTCAAGAAAGT
Found at i:12179 original size:75 final size:75
Alignment explanation
Indices: 12030--12179 Score: 248
Period size: 75 Copynumber: 2.0 Consensus size: 75
12020 TTTCAGATCT
* *
12030 GTTCGTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCGTGCGT
1 GTTCGTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCATGCGA
**
12095 CCCTTTATCA
66 CCCCGTATCA
12105 GTTCGTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCATGC-A
1 GTTCGTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCATGCGA
12169 CCTCCGTATCA
66 CC-CCGTATCA
12180 AAAGTGATGG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 2 0.03
75 68 0.97
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.35
Consensus pattern (75 bp):
GTTCGTCTAGGATCTTTCGTAGGAGTTTCTCGTGACTTGGCAACTCGATCTTGGTCCGCATGCGA
CCCCGTATCA
Found at i:17687 original size:37 final size:37
Alignment explanation
Indices: 17637--17715 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
17627 TTATTACGAA
* *
17637 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
17674 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
17711 GTCTT
1 GTCTT
17716 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:17911 original size:47 final size:47
Alignment explanation
Indices: 17833--18243 Score: 651
Period size: 47 Copynumber: 8.6 Consensus size: 47
17823 CCCTTCGGGA
* * * * * *
17833 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17880 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17927 CTTATCACATATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17974 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18025 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18072 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
18119 CTTATCACATATATACACTCTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18166 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18217 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
18244 TATTCAAATA
Statistics
Matches: 340, Mismatches: 16, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
47 248 0.73
51 92 0.27
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18107 original size:145 final size:141
Alignment explanation
Indices: 17833--18243 Score: 651
Period size: 145 Copynumber: 2.9 Consensus size: 141
17823 CCCTTCGGGA
* * * * * * * *
17833 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
17898 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
17963 GGCCATTAGGC
131 GGCCATTAGGC
17974 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
*
18039 ACGCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
62 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
18104 CATCGGCCATTAGGC
127 CATCGGCCATTAGGC
*
18119 CTTATCACATATATACACTCTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC----ATATAT
18184 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
62 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATT
18244 TATTCAAATA
Statistics
Matches: 250, Mismatches: 12, Indels: 12
0.91 0.04 0.04
Matches are distributed among these distances:
141 54 0.22
145 196 0.78
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:18160 original size:192 final size:192
Alignment explanation
Indices: 17833--18243 Score: 741
Period size: 192 Copynumber: 2.1 Consensus size: 192
17823 CCCTTCGGGA
* * * * * *
17833 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
17898 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
17963 GGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
18025 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
18090 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
18155 GGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
18217 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
18244 TATTCAAATA
Statistics
Matches: 209, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
192 209 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (192 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTCTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:22957 original size:23 final size:23
Alignment explanation
Indices: 22931--23029 Score: 155
Period size: 23 Copynumber: 4.3 Consensus size: 23
22921 ATAAGTGCCA
*
22931 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
22954 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
22977 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
23000 CACTGA-ATTGTAGCTGAGGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
23023 CACTGAT
1 CACTGAT
23030 CAATAACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
22 1 0.01
23 70 0.99
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:23333 original size:20 final size:20
Alignment explanation
Indices: 23294--23334 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
23284 TATAACTTAG
* *
23294 TCGATAACTTTCTCTTTTCC
1 TCGATAACTTTCACTATTCC
*
23314 TCGATCACTTTCACTATTCC
1 TCGATAACTTTCACTATTCC
23334 T
1 T
23335 TCTTTCTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.32, G:0.05, T:0.46
Consensus pattern (20 bp):
TCGATAACTTTCACTATTCC
Found at i:31502 original size:20 final size:20
Alignment explanation
Indices: 31456--31502 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31446 AGCTCGTTTC
*
31456 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
31476 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
31496 CAGCTCA
1 CAGCTCA
31503 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35537 original size:24 final size:24
Alignment explanation
Indices: 35505--35556 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
35495 AAAGGCACGA
*
35505 GCACCGACTAGGGCTTATGTATTC
1 GCACCGACTAGAGCTTATGTATTC
35529 GCACCGACTAGAGCTTATGTATTC
1 GCACCGACTAGAGCTTATGTATTC
35553 GCAC
1 GCAC
35557 ACTTTCTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (24 bp):
GCACCGACTAGAGCTTATGTATTC
Found at i:35978 original size:40 final size:41
Alignment explanation
Indices: 35875--36000 Score: 209
Period size: 41 Copynumber: 3.1 Consensus size: 41
35865 TTTAATTAGG
*
35875 TGTTTTAAATATGCCTGGACGAATTTAATGCTGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
* *
35916 TGTTATAAATATGCCTGGACGAATCTAATGTTGCCACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
*
35957 TGTTAT-AATATGCCTGGACGAATTTAATGCTGCTACTACA
1 TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
35997 TGTT
1 TGTT
36001 TGGCCGAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 35 0.44
41 44 0.56
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
TGTTATAAATATGCCTGGACGAATTTAATGCTGCCACTACA
Done.