Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold944
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: 39454
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:11800 original size:11 final size:11
Alignment explanation
Indices: 11784--11809 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11774 GTCACACATG
11784 AAAGTTATTTT
1 AAAGTTATTTT
11795 AAAGTTATTTT
1 AAAGTTATTTT
11806 AAAG
1 AAAG
11810 CAATTATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (11 bp):
AAAGTTATTTT
Found at i:13998 original size:6 final size:6
Alignment explanation
Indices: 13989--14017 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13979 AAATGTCATG
13989 GCAATA GCAATA GCAATA GCAATA GCAAT
1 GCAATA GCAATA GCAATA GCAATA GCAAT
14018 GGGTAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GCAATA
Found at i:15937 original size:5 final size:5
Alignment explanation
Indices: 15927--15951 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15917 AAACGCCCAT
15927 CTTGC CTTGC CTTGC CTTGC CTTGC
1 CTTGC CTTGC CTTGC CTTGC CTTGC
15952 TCTAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.20, T:0.40
Consensus pattern (5 bp):
CTTGC
Found at i:25321 original size:23 final size:22
Alignment explanation
Indices: 25289--25338 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
25279 AATGAAAGGA
* *
25289 AAAAGGCATGTAATATTGGCTAT
1 AAAAGCCATG-AATATTGACTAT
* *
25312 AAAAGCCATGATTATTGACTGT
1 AAAAGCCATGAATATTGACTAT
25334 AAAAG
1 AAAAG
25339 GGGTTCGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (22 bp):
AAAAGCCATGAATATTGACTAT
Found at i:38853 original size:86 final size:86
Alignment explanation
Indices: 38707--38948 Score: 269
Period size: 86 Copynumber: 2.8 Consensus size: 86
38697 GACAGATCAA
* * * *
38707 TGAAGACAAAGGATCTTGCCTT-CTGCATTGACAGCGAAGCAGATCGAAGACAAAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAAC-AAAGCCTTGCCT
** * * *
38771 TTTCGGTTG-TGATAGAGCTGGT
65 CATCGATTGCAG-TAGAGCTAGT
* *
38793 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCATC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
*
38858 ATCGATTGCAGTGGAGCTAGT
66 ATCGATTGCAGTAGAGCTAGT
* *
38879 TAAAGA-AGTAGAGATCTTGCCTTCCTGCA-TAACAGCGAAGCAGATC-AAAGACAAAGCCTTGC
1 TGAAGACA--AAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGC
38941 CTCCATCG
63 CT-CATCG
38949 GTGCATTGGA
Statistics
Matches: 134, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
85 4 0.03
86 80 0.60
87 50 0.37
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (86 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTC
ATCGATTGCAGTAGAGCTAGT
Found at i:38894 original size:87 final size:85
Alignment explanation
Indices: 38803--38965 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 85
38793 TGAAGACAAA
*
38803 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCAT-CATCGATTG
1 AGATCTTGCCTTCCTACA-TAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCATCCATCG-GTG
38866 CAGTGGAGCTAGTTAAAGAAGTAG
63 CAGTGGAGC-AGTTAAAGAAGTAG
* * *
38890 AGATCTTGCCTTCCTGCATAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTGCAT
1 AGATCTTGCCTTCCTACATAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGGTGCAG
38955 TGGAGCAGTTA
66 TGGAGCAGTTA
38966 GCCAGAGTCT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
85 8 0.11
86 40 0.57
87 22 0.31
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (85 bp):
AGATCTTGCCTTCCTACATAACAGCGAAGCAGATCAAAGACAAAGCCTTGCATCCATCGGTGCAG
TGGAGCAGTTAAAGAAGTAG
Found at i:39096 original size:39 final size:39
Alignment explanation
Indices: 39053--39281 Score: 126
Period size: 39 Copynumber: 5.5 Consensus size: 39
39043 GATATAATCC
39053 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCT
* * ** * *
39092 TATCTCTCTGAAGTTACAGTAGAGAAGATCATCAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTA-AAGGATCT
*
39131 TATCTCCCTG-AGATTACA-TGGAACAGACCGAAGAATT-CA-GATCT
1 TATCTCCCTGAAG-TTACAGTGG---AG--CG--G-ATTAAAGGATCT
* * * * * *
39175 TATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATATAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAG----GATCT
39218 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAAAGGAATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATT----AAAGG-ATCT
*
39262 TATCTCTCTGAAGTTACAGT
1 TATCTCCCTGAAGTTACAGT
39282 AGAGTAGATC
Statistics
Matches: 141, Mismatches: 25, Indels: 43
0.67 0.12 0.21
Matches are distributed among these distances:
37 2 0.01
38 6 0.04
39 43 0.30
40 4 0.03
41 2 0.01
42 2 0.01
43 30 0.21
44 42 0.30
45 4 0.03
46 2 0.01
47 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (39 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCT
Found at i:39234 original size:43 final size:43
Alignment explanation
Indices: 39171--39454 Score: 195
Period size: 44 Copynumber: 6.5 Consensus size: 43
39161 AAGAATTCAG
*
39171 ATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCAAAGATATA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAGATATA
* * * * * * *
39214 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAAAGGA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAGATA-TA
* ** * *
39258 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCATCA-G
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAG-AT-ATA
* * * *
39299 GTCTTATCTCCCTG-AGTTACAGCGGAACAGACCGAAGA-ATTGCA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAGATA-T--A
* * *
39343 GATCTTATCTCCCTGAGGATTACAGCGGAGCAGATCGAAGACATA
1 -ATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATCAAAGATATA
* * * * *
39388 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA-ATAAA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAGATATA
*
39430 GGATCTTATCTCTCTGAAGTTACAG
1 --ATCTTATCTCCCTGAAGTTACAG
Statistics
Matches: 186, Mismatches: 39, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
40 15 0.08
41 12 0.06
42 5 0.03
43 52 0.28
44 65 0.35
45 14 0.08
46 1 0.01
47 21 0.11
48 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATCAAAGATATA
Found at i:39263 original size:87 final size:86
Alignment explanation
Indices: 39025--39454 Score: 318
Period size: 87 Copynumber: 5.1 Consensus size: 86
39015 TATCTCCTGA
39025 TTACAGCGGAGCA-ATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT----AA
1 TTACAGCGGAGCAGATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
*
39085 AGG-ATCTTATCTCTCTGAAG
66 AGGAATCTTATCTCCCTGAAG
** * ** * * * *** *
39105 TTACAGTAGAGAAGATC---ATCA-GGTCTTATCTCCCTG-AGATTACA-TGGAACAGACCGAAG
1 TTACAGCGGAGCAGATCAAGAT-ATAATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAA
*** *
39164 AATTCAGATCTTATCTCCCTGAGG
64 AAAGGA-ATCTTATCTCCCTGAAG
39188 TTACAGCGGAGCAGATCAAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAA
1 TTACAGCGGAGCAGATC-AAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAA
*
39253 AAGGAATCTTATCTCTCTGAAG
65 AAGGAATCTTATCTCCCTGAAG
** * ** * * * * ** *
39275 TTACAGTAGAGTAGATC--GCATCA-GGTCTTATCTCCCTG-AGTTACAGCGGAACAGACCGAAG
1 TTACAGCGGAGCAGATCAAG-AT-ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAAA
** * *
39336 AATTGCAGATCTTATCTCCCTGAGG
63 AAAAGGA-ATCTTATCTCCCTGAAG
*
39361 ATTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA
1 -TTACAGCGGAGCAGATC-AAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA
*
39426 TAAAGG-ATCTTATCTCTCTGAAG
64 -AAAGGAATCTTATCTCCCTGAAG
39449 TTACAG
1 TTACAG
Statistics
Matches: 256, Mismatches: 67, Indels: 47
0.69 0.18 0.13
Matches are distributed among these distances:
77 9 0.04
78 19 0.07
79 1 0.00
80 10 0.04
81 5 0.02
83 29 0.11
84 15 0.06
85 20 0.08
86 17 0.07
87 68 0.27
88 30 0.12
89 16 0.06
90 17 0.07
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (86 bp):
TTACAGCGGAGCAGATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
AGGAATCTTATCTCCCTGAAG
Found at i:39412 original size:174 final size:169
Alignment explanation
Indices: 39023--39454 Score: 716
Period size: 174 Copynumber: 2.6 Consensus size: 169
39013 TCTATCTCCT
39023 GATTACAGCGGAGCA-ATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT----
1 GATTACAGCGGAGCAGATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA
39083 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCATCAGGTCTTATCTCCCTGAGATTAC
66 AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCATCAGGTCTTATCTCCCTGAGATTAC
*
39148 ATGGAACAGACCGAAGAATTCAGATCTTATCTCCCTGAG
131 ACGGAACAGACCGAAGAATTCAGATCTTATCTCCCTGAG
39187 G-TTACAGCGGAGCAGATCAAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
1 GATTACAGCGGAGCAGATC-AAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
*
39251 AAAAGGAATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAG-
65 AAAAGG-ATCTTATCTCTCTGAAGTTACAGTAGAGAAGAT--CATCAGGTCTTATCTCCCTGAGA
39315 TTACAGCGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAG
127 TTACA-CGGAACAGACCGAAGAATT-CAGATCTTATCTCCCTGAG
*
39360 GATTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
1 GATTACAGCGGAGCAGATC-AAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
39425 ATAAAGGATCTTATCTCTCTGAAGTTACAG
65 A-AAAGGATCTTATCTCTCTGAAGTTACAG
Statistics
Matches: 251, Mismatches: 4, Indels: 16
0.93 0.01 0.06
Matches are distributed among these distances:
163 13 0.05
164 4 0.02
165 42 0.17
169 5 0.02
170 32 0.13
171 5 0.02
172 40 0.16
173 20 0.08
174 85 0.34
175 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (169 bp):
GATTACAGCGGAGCAGATCAAGATATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA
AAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCATCAGGTCTTATCTCCCTGAGATTAC
ACGGAACAGACCGAAGAATTCAGATCTTATCTCCCTGAG
Done.