Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3737
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: 46240
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Found at i:1975 original size:16 final size:16
Alignment explanation
Indices: 1951--2050 Score: 139
Period size: 16 Copynumber: 6.2 Consensus size: 16
1941 TGGTTCACTA
*
1951 TAATGGAATAGGGTTG
1 TAATGGAATAGAGTTG
*
1967 TAATTGAATAGA-TGTG
1 TAATGGAATAGAGT-TG
1983 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
* *
1999 TAATTGAATAGAGGTG
1 TAATGGAATAGAGTTG
*
2015 TAATGTAATAGAGTTG
1 TAATGGAATAGAGTTG
2031 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
2047 TAAT
1 TAAT
2051 CAGTAATTCT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.01
16 71 0.97
17 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:2109 original size:40 final size:40
Alignment explanation
Indices: 2060--2142 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
2050 TCAGTAATTC
* *
2060 TATTGTTGTGGTTTAATGGAATGGAATAGA-GCTGTAATAG
1 TATTCTTGT-GTTTAATGGAATGGAATAGATGCTATAATAG
** * *
2100 TATTCTTGTGTTTCGTTGAATGGAATAGATGTTATAATAG
1 TATTCTTGTGTTTAATGGAATGGAATAGATGCTATAATAG
2140 TAT
1 TAT
2143 AAAGAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.29, C:0.04, G:0.25, T:0.42
Consensus pattern (40 bp):
TATTCTTGTGTTTAATGGAATGGAATAGATGCTATAATAG
Found at i:2306 original size:61 final size:56
Alignment explanation
Indices: 2215--2356 Score: 158
Period size: 61 Copynumber: 2.4 Consensus size: 56
2205 TTATTGTTAT
* * * * *
2215 TTTATTAAATTTTAATAAAATTATTGTTAAATATATTTTAATAAAAATAAAAATAAATAA
1 TTTAATAAATTTTAATATAATTATTATTAAATACAATTTAAT-AAAAT---AATAAATAA
* *
2275 TTTAATCAAATTTTAATATAATTCTTATTAAATACAATTTAATAAAATAATATATAA
1 TTTAAT-AAATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAA
2332 TTTAATAACATTCTTAATATAATTA
1 TTTAATAA-ATT-TTAATATAATTA
2357 CTATATGAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
56 2 0.03
57 17 0.24
58 11 0.15
60 10 0.14
61 31 0.44
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (56 bp):
TTTAATAAATTTTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAA
Found at i:5142 original size:43 final size:43
Alignment explanation
Indices: 4993--5151 Score: 182
Period size: 43 Copynumber: 3.7 Consensus size: 43
4983 TATGTGTTCT
* * *
4993 CGTGTAAGACCATGTCTGGGACTTTGGCATCGACT-TATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTA
* *
5037 CGTGCAAGACCACGTCTGGGACGTTGGCATCG-TATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
*
5079 CGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTA
* *
5122 CATGTAAGACCACATCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
5152 TGTACATGTT
Statistics
Matches: 98, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.31
43 37 0.38
44 30 0.31
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTA
Found at i:10599 original size:48 final size:48
Alignment explanation
Indices: 10498--10764 Score: 180
Period size: 48 Copynumber: 5.6 Consensus size: 48
10488 ATTGTGCGCT
* *
10498 AGTGTAAGA-CATGTCTAGGACAT-GCATC--CGC-TATGAGATGTGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTAT-AGAGGTGTC
* *
10542 AGTGCAAGACCATGTCTATGACATGGCATCGGCACGTATAGAGGTGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTC
* * * * * * *
10590 AGTGTAAGACCATGTTTGGGACATGGCATTGTCACGGTATGTGAGATCT-
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-GTAT-AGAGGTGTC
* * * *
10639 AGTGTAAGACCAT-TCT-GAGACATGCCATCGGCCTCGATTTCGA--TAGTC
1 AGTGTAAGACCATGTCTAG-GACATGGCATCGG-CACG-TATAGAGGT-GTC
* * * * * *
10687 AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTAATGGATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGT-ATAGAGGTGTC
*
10734 AGTGTAAGACCATGTCTAGGACGTGGCATCG
1 AGTGTAAGACCATGTCTAGGACATGGCATCG
10765 ATATTACACC
Statistics
Matches: 175, Mismatches: 30, Indels: 32
0.74 0.13 0.14
Matches are distributed among these distances:
44 8 0.05
45 14 0.08
46 10 0.06
47 32 0.18
48 68 0.39
49 37 0.21
50 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTC
Found at i:11792 original size:28 final size:28
Alignment explanation
Indices: 11751--11862 Score: 152
Period size: 28 Copynumber: 4.0 Consensus size: 28
11741 ACACGGGCTA
* *
11751 GGACACGGGTGTGTCATGGCCGTATGAG
1 GGACACGGGCGTGTCATGGCCGTGTGAG
* *
11779 GGACACGGGCGTGTCATGGTCGTGTAAG
1 GGACACGGGCGTGTCATGGCCGTGTGAG
11807 GGACACGGGCGTGTCATGGCCGTGTGAG
1 GGACACGGGCGTGTCATGGCCGTGTGAG
* **
11835 GGACACGGACGTGTGTTAGGCCGTGTGA
1 GGACACGGGCGTGTCAT-GGCCGTGTGA
11863 AAACCCTTGT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 64 0.86
29 10 0.14
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.21
Consensus pattern (28 bp):
GGACACGGGCGTGTCATGGCCGTGTGAG
Found at i:18182 original size:48 final size:47
Alignment explanation
Indices: 18077--18298 Score: 175
Period size: 48 Copynumber: 4.7 Consensus size: 47
18067 AATTGTGCGC
* *
18077 TAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-C-TATGAGATGTGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGACGTAT-AGAGGTGT
* * *
18121 CAGTGTAATACCATGTTTGGGACATGGCATCGGTACGTATAGAGGTGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG-ACGTATAGAGGTGT
* * * * * * *
18169 TAGTGTAAGACCATATTTGGGACATGGCATCGGCATGGATATGTGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG-ACGTATA-GAG-GTGT
* * * * * *
18219 TAGTGTAAGACCATGTCTGGGACATGGCAT-TGACTTAATGGATGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGACGT-ATAGAGGTGT
* *
18266 CAGTGTAAGACCATGTCTAGGACATGGCATCGG
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG
18299 CATTACACCT
Statistics
Matches: 143, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
44 8 0.06
45 13 0.09
46 6 0.04
47 32 0.22
48 46 0.32
49 8 0.06
50 30 0.21
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (47 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGGACGTATAGAGGTGT
Found at i:18282 original size:47 final size:50
Alignment explanation
Indices: 18170--18297 Score: 156
Period size: 47 Copynumber: 2.6 Consensus size: 50
18160 TAGAGGTGTT
* * * *
18170 AGTGTAAGACCATATTTGGGACATGGCATCGGCATGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATGGATATGTGAGAGCC
* *
18220 AGTGTAAGACCATGTCTGGGACATGGCATTGAC-T-TA-ATG-GATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACATGGATATGTGA-GAGCC
*
18267 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
18298 GCATTACACC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 2 0.03
47 36 0.52
48 1 0.01
49 1 0.01
50 29 0.42
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACATGGATATGTGAGAGCC
Found at i:19163 original size:30 final size:30
Alignment explanation
Indices: 19127--19192 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
19117 CACGGGCAGA
19127 GACACGG-CTGTGTGTCTCAGCCATGTGGAG
1 GACACGGTC-GTGTGTCTCAGCCATGTGGAG
* *
19157 GACACGGTCGTGTGTCTTAGCCGTGTGGAG
1 GACACGGTCGTGTGTCTCAGCCATGTGGAG
19187 GACACG
1 GACACG
19193 ACCTCTGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (30 bp):
GACACGGTCGTGTGTCTCAGCCATGTGGAG
Found at i:23197 original size:42 final size:43
Alignment explanation
Indices: 23139--23244 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 43
23129 TATGATTTAC
*
23139 GTGTAAGACCACATCTGGGACATTAGCATCG-TATTTGATTTT
1 GTGTAAGACCACATCTGGGACAGTAGCATCGATATTTGATTTT
* * **
23181 GTGTAAGACC-CTATCTGGGACAGTGGCATTGATATTTGATTAC
1 GTGTAAGACCAC-ATCTGGGACAGTAGCATCGATATTTGATTTT
* *
23224 ATGTAAGACCACGTCTGGGAC
1 GTGTAAGACCACATCTGGGAC
23245 GTTTGCATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 26 0.48
43 26 0.48
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCACATCTGGGACAGTAGCATCGATATTTGATTTT
Found at i:23254 original size:43 final size:42
Alignment explanation
Indices: 23094--23252 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 42
23084 TATGTGTTCT
** * *
23094 CGTGTAAGACCATGTTTGGGACGTTGTCATCGACT-TATGATTTA
1 CGTGTAAGACCACATCTGGGACGTTG-CATCGA-TATTTGA-TTA
* *
23138 CGTGTAAGACCACATCTGGGACATTAGCATCG-TATTTGATTT
1 CGTGTAAGACCACATCTGGGACGTT-GCATCGATATTTGATTA
* * *
23180 TGTGTAAGACC-CTATCTGGGACAGTGGCATTGATATTTGATTA
1 CGTGTAAGACCAC-ATCTGGGAC-GTTGCATCGATATTTGATTA
* *
23223 CATGTAAGACCACGTCTGGGACGTTTGCAT
1 CGTGTAAGACCACATCTGGGACG-TTGCAT
23253 TGTATGAGTT
Statistics
Matches: 93, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 28 0.30
43 36 0.39
44 27 0.29
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
CGTGTAAGACCACATCTGGGACGTTGCATCGATATTTGATTA
Found at i:27600 original size:30 final size:30
Alignment explanation
Indices: 27566--27626 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27556 TCCTTAACTC
*
27566 AAACTTTGGTAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
27596 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
27626 A
1 A
27627 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Done.