Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1450
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: 25460
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:62 original size:14 final size:16
Alignment explanation
Indices: 43--92 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
33 CAAAGATAAC
43 AAGAAAAT-C-GAATA
1 AAGAAAATCCAGAATA
57 AAG-AAATCCAGAATA
1 AAGAAAATCCAGAATA
* *
72 AAG-AGATCCAGGATA
1 AAGAAAATCCAGAATA
87 AAGAAA
1 AAGAAA
93 CCCAAGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 21 0.70
16 1 0.03
ACGTcount: A:0.60, C:0.10, G:0.18, T:0.12
Consensus pattern (16 bp):
AAGAAAATCCAGAATA
Found at i:72 original size:15 final size:15
Alignment explanation
Indices: 52--92 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
42 CAAGAAAATC
52 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
67 GAATAAAGAGATCCA
1 GAATAAAGAAATCCA
*
82 GGATAAAGAAA
1 GAATAAAGAAA
93 CCCAAGATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:101 original size:15 final size:15
Alignment explanation
Indices: 54--101 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
44 AGAAAATCGA
54 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
68 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
84 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
99 ATA
1 ATA
102 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:3070 original size:45 final size:45
Alignment explanation
Indices: 3006--3168 Score: 174
Period size: 45 Copynumber: 3.7 Consensus size: 45
2996 TGTAACCCGC
*
3006 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGACGTTAGCAT
* * * *
3051 CCATAAGTGAACTCGGACTCAACTCAACGAGCTGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGACG-TTAGCAT
* * * * * *
3096 ACATCACTCGAACTC-GACTC--CTCAACGAGTTC-ACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGACGTTAGCAT
3138 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
3169 TTCGGATGCC
Statistics
Matches: 94, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
41 8 0.09
42 12 0.13
43 10 0.11
44 9 0.10
45 47 0.50
46 8 0.09
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGACGTTAGCAT
Found at i:3138 original size:87 final size:91
Alignment explanation
Indices: 3014--3178 Score: 257
Period size: 87 Copynumber: 1.8 Consensus size: 91
3004 GCCCATAAGT
*
3014 GAACTCGGACTCAACTCAACGAGCTCGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTC-ACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
3079 GAGCT-GGATGCCTAGTTACATCACTC
65 GAGCTCGGATGCCTAGTTACATCACTC
* *
3105 GAACTC-GACTC-CTCAACGAGTTC-ACATTTGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
*
3167 AGTTCGGATGCC
66 AGCTCGGATGCC
3179 AAACATCCTA
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
87 40 0.58
88 18 0.26
90 5 0.07
91 6 0.09
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.22
Consensus pattern (91 bp):
GAACTCGGACTCACTCAACGAGCTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGCTCGGATGCCTAGTTACATCACTC
Found at i:7575 original size:44 final size:43
Alignment explanation
Indices: 7466--7582 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 43
7456 ATATGCGTTC
7466 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCGACTTATGATA
1 TCGTGTAAGACC-CTGTCTGGGACATTGGCATCGACTTATGATA
* * *
7509 T-GTGTAAGACCATGTTTGGGACATTGGCATC-A-TATATTTGATT
1 TCGTGTAAGACCCTGTCTGGGACATTGGCATCGACT-TA--TGATA
* *
7552 TCGTGTAAGACCCTGTCTAGGACAGTGGCAT
1 TCGTGTAAGACCCTGTCTGGGACATTGGCAT
7583 TGTAACAGCC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.02
41 3 0.05
42 27 0.44
43 6 0.10
44 25 0.40
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGTGTAAGACCCTGTCTGGGACATTGGCATCGACTTATGATA
Found at i:22826 original size:47 final size:47
Alignment explanation
Indices: 22658--23093 Score: 697
Period size: 47 Copynumber: 9.4 Consensus size: 47
22648 CAGCCAAGAC
22658 AGTGTATATATGTGATAA-G-CTAATGGCCGATGTGGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGT-GATGAATGTGAA
*
22704 AGTGTATATATGTGATAAGGCCTAATAGCCGATG-GATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
22750 AGTG--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
22795 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
22842 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
22889 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
22936 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTG-A
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
22982 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
23029 AGT-TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
23075 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
23094 TCCCGAAGGG
Statistics
Matches: 366, Mismatches: 17, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
44 28 0.08
45 16 0.04
46 118 0.32
47 192 0.52
48 12 0.03
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:22971 original size:38 final size:39
Alignment explanation
Indices: 22929--23018 Score: 101
Period size: 46 Copynumber: 2.2 Consensus size: 39
22919 GATGTGATGA
22929 ATGTGA-AAGTGTATATATGTAATAAGGCCTAATGGCCG
1 ATGTGAGAAGTGTATATATGTAATAAGGCCTAATGGCCG
*
22967 ATGTGATGAATGTGAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 A--TG-TG-A---GAAGTGTATATATGTAATAAGGCCTAATGGCCG
23013 ATGTGA
1 ATGTGA
23019 TGAATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
38 1 0.02
40 2 0.05
41 2 0.05
42 2 0.05
43 2 0.05
44 2 0.05
46 32 0.74
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (39 bp):
ATGTGAGAAGTGTATATATGTAATAAGGCCTAATGGCCG
Found at i:23257 original size:37 final size:37
Alignment explanation
Indices: 23201--23279 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
23191 CCGAGCTCTA
* *
23201 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
23238 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
23275 AAGAC
1 AAGAC
23280 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Done.