Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1618
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: 43698
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7175 original size:27 final size:28
Alignment explanation
Indices: 7091--7188 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
7081 CATGAGATTG
* * * *
7091 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
7120 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
7148 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
7175 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
7189 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:7199 original size:27 final size:27
Alignment explanation
Indices: 7119--7201 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
7109 TAAATTGTAC
* *
7119 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
7147 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
7174 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
7201 A
1 A
7202 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:7202 original size:29 final size:27
Alignment explanation
Indices: 7091--7202 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
7081 CATGAGATTG
** * *
7091 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
7120 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
7148 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
7175 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
7203 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:15253 original size:27 final size:28
Alignment explanation
Indices: 15169--15266 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
15159 CATGAGATTG
* * * *
15169 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
15198 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
15226 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
15253 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
15267 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:15277 original size:27 final size:27
Alignment explanation
Indices: 15197--15279 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
15187 TAAATTGTAC
* *
15197 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
15225 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
15252 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
15279 A
1 A
15280 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:15280 original size:29 final size:27
Alignment explanation
Indices: 15169--15280 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
15159 CATGAGATTG
** * *
15169 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
15198 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
15226 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
15253 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
15281 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:20527 original size:47 final size:47
Alignment explanation
Indices: 20472--20663 Score: 276
Period size: 47 Copynumber: 4.1 Consensus size: 47
20462 TTAGGATTTT
* * *
20472 AATGTGATGAATGTGAATATGCGTATGTGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* *
20519 AATGTGATGAATGTGAACATGCATATGTGCGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* *
20566 AATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAAGGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* * * * *
20613 GATGTGATGAATGTGAACATGTATATATCTGGTAAGGCCGAATGGCT
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
20660 AATG
1 AATG
20664 CGAAATGTGT
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:20773 original size:46 final size:46
Alignment explanation
Indices: 20637--20773 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
20627 GAACATGTAT
* * *
20637 ATATCTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
20683 ATATGAGATAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
20729 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
20774 TGTATATATA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:25957 original size:28 final size:29
Alignment explanation
Indices: 25904--26031 Score: 122
Period size: 28 Copynumber: 4.5 Consensus size: 29
25894 TTCTCGAAGT
* * *
25904 TTCGCACACTCAGTACCTTCAC-GGATGTA
1 TTCGCACACTAAGTGCCATC-CTGGATGTA
25933 TT-GCACACTAAGTGCCATCCTGGATGT-
1 TTCGCACACTAAGTGCCATCCTGGATGTA
* * *
25960 CTCGCACACTAAGTGCCATCCTCGAT-AA
1 TTCGCACACTAAGTGCCATCCTGGATGTA
* * *
25988 TTCGCTCACTAAGAGCCATTTCTGGATGT-
1 TTCGCACACTAAGTGCCA-TCCTGGATGTA
26017 TTCGCACACTAAGTG
1 TTCGCACACTAAGTG
26032 TTGTCCTCAG
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
27 2 0.03
28 57 0.71
29 21 0.26
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (29 bp):
TTCGCACACTAAGTGCCATCCTGGATGTA
Found at i:26039 original size:57 final size:57
Alignment explanation
Indices: 25935--26065 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 57
25925 CGGATGTATT
* *
25935 GCACACTAAGTGCCA-TCCTGGATGTCTCGCACACTAAGTGCCATCCTC-GATAATTC
1 GCACACTAAGTGCCATTTCTGGATGTCTCGCACACTAAGTGCCATCCTCAG-TAACTC
* * * ***
25991 GCTCACTAAGAGCCATTTCTGGATGTTTCGCACACTAAGTGTTGTCCTCAGTAACTC
1 GCACACTAAGTGCCATTTCTGGATGTCTCGCACACTAAGTGCCATCCTCAGTAACTC
26048 GCACACTAAGTGCCATTT
1 GCACACTAAGTGCCATTT
26066 TCAAAATCGA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
56 13 0.21
57 49 0.78
58 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (57 bp):
GCACACTAAGTGCCATTTCTGGATGTCTCGCACACTAAGTGCCATCCTCAGTAACTC
Found at i:32812 original size:3 final size:3
Alignment explanation
Indices: 32804--32836 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
32794 GGATGTTTTG
*
32804 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32837 TAGTATGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:36732 original size:40 final size:40
Alignment explanation
Indices: 36702--36926 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
36692 GCTACTCGTT
* *
36702 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
36742 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
36782 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGAA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
36822 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * *
36862 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
*
36902 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
36927 CATCATTCAA
Statistics
Matches: 170, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 19 0.11
40 149 0.88
41 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Done.