Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3006
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: 36209
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:3265 original size:93 final size:93
Alignment explanation
Indices: 3152--3323 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3142 CGCCCATAAG
* *
3152 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3217 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
3245 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3310 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3324 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3320 original size:46 final size:46
Alignment explanation
Indices: 3145--3320 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
3135 TGTAACCCGC
* * *
3145 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3191 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3241 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3284 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3321 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:10768 original size:47 final size:49
Alignment explanation
Indices: 10692--10824 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 49
10682 TGTAACCCGC
10692 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
10742 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
10785 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
10825 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 29 0.40
47 30 0.42
48 2 0.03
49 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:10840 original size:46 final size:44
Alignment explanation
Indices: 10700--10840 Score: 135
Period size: 46 Copynumber: 3.0 Consensus size: 44
10690 GCCCATAAGC
*
10700 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGT
* * *
10747 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGT
10793 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGT
10839 GA
1 GA
10841 CATGTCACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.42
47 31 0.39
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGT
Found at i:12920 original size:40 final size:40
Alignment explanation
Indices: 12865--13051 Score: 304
Period size: 40 Copynumber: 4.7 Consensus size: 40
12855 ATTTGAATGA
*
12865 TATCCGAGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
12905 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
12945 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
* * * *
12985 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTT
*
13025 TATCCGGGCTAAGACCCGAAGGCATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTT
13052 GTACGAGTTG
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
40 138 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
Found at i:13052 original size:40 final size:40
Alignment explanation
Indices: 12864--13115 Score: 294
Period size: 40 Copynumber: 6.3 Consensus size: 40
12854 CATTTGAATG
* *
12864 ATATCCGAGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
12904 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* *
12944 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
* * *
12984 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * *
13024 ATATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * * * *
13064 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
13104 ATATCC-GGCTAA
1 ATATCCGGGCTAA
13116 ATTTCGAAGA
Statistics
Matches: 193, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
39 7 0.04
40 183 0.95
41 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
Found at i:15894 original size:40 final size:40
Alignment explanation
Indices: 15837--16054 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
15827 TGGATGATAA
* * *
15837 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTA-TAT
* *
15877 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
*
15917 CCGGGCTAAGTCCCGAAGGCATTCGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
15957 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* * *
15997 CCGGGCTATGTCCCGGAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATAT
* *
16037 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
16055 TACTTGGCTT
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 15 0.09
40 147 0.91
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:24048 original size:40 final size:40
Alignment explanation
Indices: 23973--24078 Score: 171
Period size: 40 Copynumber: 2.6 Consensus size: 40
23963 CTAGTTTAGG
*
23973 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC-GGC
1 TAAGTCCCGAAGGCATCTGTGCGAGTTACTATATCCGGGC
24012 TAAGTCCCGAAGGCATCTGTCGCGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATCTGT-GCGAGTTACTATATCCGGGC
24053 TAAGTCCCGAAGGCAT-TCGTGCGAGT
1 TAAGTCCCGAAGGCATCT-GTGCGAGT
24079 CAATCGGCTA
Statistics
Matches: 63, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
39 19 0.30
40 23 0.37
41 21 0.33
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATCTGTGCGAGTTACTATATCCGGGC
Found at i:28594 original size:23 final size:23
Alignment explanation
Indices: 28574--28619 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
28564 CCACACTATG
28574 TAACTGAATGATAACAGACTAAC
1 TAACTGAATGATAACAGACTAAC
*
28597 TAACTGAATGATAATAGACTAAC
1 TAACTGAATGATAACAGACTAAC
28620 AGTCTCTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (23 bp):
TAACTGAATGATAACAGACTAAC
Done.