Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2602
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: 62617
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1848 original size:43 final size:41
Alignment explanation
Indices: 1794--2045 Score: 208
Period size: 43 Copynumber: 5.9 Consensus size: 41
1784 GCGCTTTTTC
*
1794 AAACGCCGCTAAAGCAACCCAGCATTAAGCGGCGCTTTTCCAG
1 AAACGCGGCTAAAGC-ACCCAGCATT-AGCGGCGCTTTTCCAG
* *
1837 AAACGCGGCTAAAGCACCCTAACTTTAGCCGAGCGCTTTTCCCAG
1 AAACGCGGCTAAAGCACCC-AGCATTAG-CG-GCGCTTTT-CCAG
* * *
1882 AAATTCCCGCCT-AAG-ACCCTAGCTTTAGCGGCGCTTTTTCCAG
1 AAA--CGCGGCTAAAGCACCC-AGCATTAGCGGCGC-TTTTCCAG
*
1925 AAACGCGGCTAAAAG-ACCTCAGCATTAGCGGCGCTTTTCCAA
1 AAACGCGGCT-AAAGCACC-CAGCATTAGCGGCGCTTTTCCAG
* * * *
1967 AAACGTCGTCTAAAGCCCCCAGCATTAGCGGCCGCTTTT-TAA
1 AAACG-CGGCTAAAGCACCCAGCATTAGCGG-CGCTTTTCCAG
* * *
2009 AAACGCCGCTAAA-CAACGCAGCATTAGCGGCGGTTTT
1 AAACGCGGCTAAAGC-ACCCAGCATTAGCGGCGCTTTT
2046 TTAAAAAAAT
Statistics
Matches: 177, Mismatches: 18, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
40 7 0.04
41 24 0.14
42 41 0.23
43 63 0.36
44 15 0.08
45 19 0.11
46 3 0.02
47 5 0.03
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (41 bp):
AAACGCGGCTAAAGCACCCAGCATTAGCGGCGCTTTTCCAG
Found at i:2716 original size:19 final size:18
Alignment explanation
Indices: 2694--2737 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
2684 AGAATAATAA
* *
2694 TAAAATAATAAATATCATT
1 TAAAATAAAAAATAAC-TT
*
2713 TAAAAAAAAAAATAACTT
1 TAAAATAAAAAATAACTT
2731 TAAAATA
1 TAAAATA
2738 TTATAAACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATAAAAAATAACTT
Found at i:8151 original size:24 final size:25
Alignment explanation
Indices: 8124--8173 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
8114 CATTTTGTCA
8124 GATATTTAATTTTTCTT-TTCTTCT
1 GATATTTAATTTTTCTTATTCTTCT
8148 GATATTTAATTTTTCTTATTCTTCT
1 GATATTTAATTTTTCTTATTCTTCT
8173 G
1 G
8174 TTGAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (25 bp):
GATATTTAATTTTTCTTATTCTTCT
Found at i:12329 original size:14 final size:14
Alignment explanation
Indices: 12310--12336 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12300 GTGGTCCAGT
12310 TGAACTGAACCGAG
1 TGAACTGAACCGAG
12324 TGAACTGAACCGA
1 TGAACTGAACCGA
12337 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:13351 original size:53 final size:53
Alignment explanation
Indices: 13290--13396 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
13280 AGTCTTTTAT
*
13290 GTGCTTATTAAATCGAGTTAATTGTTTGAATTGACATAGAGATATGTACAAGA
1 GTGCTTATTAAATCGAGTTAATTATTTGAATTGACATAGAGATATGTACAAGA
* *
13343 GTGCTTATTAAATTGAGTTAATTATTTGAATTGACATAGGGATATGTACAAGA
1 GTGCTTATTAAATCGAGTTAATTATTTGAATTGACATAGAGATATGTACAAGA
13396 G
1 G
13397 ATTATTTCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (53 bp):
GTGCTTATTAAATCGAGTTAATTATTTGAATTGACATAGAGATATGTACAAGA
Found at i:20147 original size:19 final size:19
Alignment explanation
Indices: 20095--20149 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
20085 ACGTGTGGAC
**
20095 TTAT-GTTGCTTCAACATA
1 TTATCGTTGCTTCAATTTA
* *
20113 TTTTCCTTGCTTCAATTTA
1 TTATCGTTGCTTCAATTTA
20132 TTATCGTTGCTTCAATTT
1 TTATCGTTGCTTCAATTT
20150 TTACCAGTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 3 0.10
19 27 0.90
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (19 bp):
TTATCGTTGCTTCAATTTA
Found at i:25331 original size:50 final size:50
Alignment explanation
Indices: 25242--25582 Score: 362
Period size: 50 Copynumber: 6.8 Consensus size: 50
25232 ATTTGGGTAA
* * * *
25242 AGAGATCCTATGTAAGACCATGTCTGGAACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
25292 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
25342 AGAGGTCCCATGTAAGACCATGTTTGGGACATGACATTGGCACAGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
25392 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
25442 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * * * * *
25492 AGAACTCTCATGTACGACCATATCTAGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** * * *
25541 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
25583 TGTTATATTC
Statistics
Matches: 243, Mismatches: 47, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
49 34 0.14
50 209 0.86
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:32715 original size:8 final size:9
Alignment explanation
Indices: 32683--32715 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
32673 TTGCCACCCT
32683 AGTGATTTC
1 AGTGATTTC
32692 AGTGATTTC
1 AGTGATTTC
*
32701 GGTGATTTC
1 AGTGATTTC
32710 -GTGATT
1 AGTGATT
32716 CAATTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 6 0.26
9 17 0.74
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45
Consensus pattern (9 bp):
AGTGATTTC
Found at i:37186 original size:14 final size:15
Alignment explanation
Indices: 37151--37188 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
37141 GTGGCTGGTT
*
37151 CGGTTC-ACTAGATT
1 CGGTTCAACTAGATG
37165 CGGTTCAACTA-ATG
1 CGGTTCAACTAGATG
37179 CGGTTCAACT
1 CGGTTCAACT
37189 GGCCCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (15 bp):
CGGTTCAACTAGATG
Found at i:43811 original size:27 final size:27
Alignment explanation
Indices: 43780--43957 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43770 TAAATTGTAC
43780 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43807 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43833 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43861 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
43889 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43916 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43943 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43958 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43894 original size:82 final size:81
Alignment explanation
Indices: 43781--43936 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43771 AAATTGTACA
* *
43781 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
43845 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43862 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
43927 TGCGAGTTGA
65 TGCGAATTGA
43937 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43948 original size:82 final size:81
Alignment explanation
Indices: 43777--43957 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
43767 GATTAAATTG
* *
43777 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
43842 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43858 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
43922 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43940 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43958 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:51990 original size:27 final size:27
Alignment explanation
Indices: 51959--52135 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
51949 TAAATTGTAC
51959 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
51986 TGCACTAAGTGTGCGAAATGAAT-TG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52011 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
52039 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
52067 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52094 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
52121 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52136 GACTCAATAT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 21 0.17
27 83 0.65
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:52099 original size:55 final size:54
Alignment explanation
Indices: 51959--52135 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 54
51949 TAAATTGTAC
* **
51959 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAAT-TG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
* * ** *
52011 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATGT
* * * *
52067 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
*
52121 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52136 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
52 1 0.01
53 38 0.36
54 26 0.25
55 39 0.37
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
Found at i:60197 original size:27 final size:27
Alignment explanation
Indices: 60110--60288 Score: 130
Period size: 27 Copynumber: 6.5 Consensus size: 27
60100 TAAATGTACA
* *
60110 GCACTAAGGTGTGGCGATTTGACTATGTT
1 GCACTAA-GTGT-GCGAATTGACTATGTG
*
60139 GCACTAAGTGGTGCGAAATGA--ATGTG
1 GCACTAAGT-GTGCGAATTGACTATGTG
* *
60165 ATGCACTAAGTGTGCGAATTGACCATGCG
1 --GCACTAAGTGTGCGAATTGACTATGTG
* * *
60194 GCACTAAGTGTGAGAGTTGACTA-GTA
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
60220 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
60247 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-ATTGACTATGTG
*
60275 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
60289 GATCAATATG
Statistics
Matches: 127, Mismatches: 16, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
26 25 0.20
27 48 0.38
28 41 0.32
29 13 0.10
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:60276 original size:28 final size:27
Alignment explanation
Indices: 60194--60288 Score: 122
Period size: 28 Copynumber: 3.5 Consensus size: 27
60184 TGACCATGCG
* *
60194 GCACTAAGTGTGAGAG-TTGACTAGTA
1 GCACTAAGTGTGCGAGTTTGATTAGTA
60220 GCACTAAGTGTGCGA-TTTGATTACGTA
1 GCACTAAGTGTGCGAGTTTGATTA-GTA
*
60247 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTA-GTA
*
60275 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
60289 GATCAATATG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 20 0.33
27 18 0.30
28 23 0.38
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTTGATTAGTA
Found at i:62513 original size:18 final size:17
Alignment explanation
Indices: 62490--62563 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 17
62480 TACTATAAAG
* *
62490 AAACAAAAAAAAGACACT
1 AAACAAAAAAAAAACA-A
62508 AAACAAAAAAAAAACAA
1 AAACAAAAAAAAAACAA
62525 AAACAAAAACAAAAA-AA
1 AAACAAAAA-AAAAACAA
*
62542 ATACAATAAAAATAAACAA
1 AAACAA-AAAAA-AAACAA
62561 AAA
1 AAA
62564 TCAATTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
17 18 0.38
18 26 0.54
19 4 0.08
ACGTcount: A:0.81, C:0.12, G:0.01, T:0.05
Consensus pattern (17 bp):
AAACAAAAAAAAAACAA
Found at i:62524 original size:11 final size:11
Alignment explanation
Indices: 62508--62563 Score: 76
Period size: 12 Copynumber: 4.8 Consensus size: 11
62498 AAAAGACACT
62508 AAACAAAAAAA
1 AAACAAAAAAA
62519 AAACAAAAACAA
1 AAACAAAAA-AA
62531 AAACAAAAAAA
1 AAACAAAAAAA
*
62542 ATACAATAAAAA
1 AAACAA-AAAAA
62554 TAAACAAAAA
1 -AAACAAAAA
62564 TCAATTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
11 16 0.40
12 19 0.47
13 5 0.12
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (11 bp):
AAACAAAAAAA
Found at i:62584 original size:20 final size:20
Alignment explanation
Indices: 62529--62601 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 20
62519 AAACAAAAAC
*
62529 AAAAACAAAAAAAATACAAT
1 AAAAATAAAAAAAATACAAT
62549 AAAAATAAACAAAAAT-CAATT
1 AAAAATAAA-AAAAATACAA-T
62570 AATAAAT-AAAAAAATA-ACAT
1 AA-AAATAAAAAAAATACA-AT
62590 AAAAATACAAAA
1 AAAAATA-AAAA
62602 GATAACAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
19 4 0.09
20 21 0.47
21 16 0.36
22 4 0.09
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAATAAAAAAAATACAAT
Done.