Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1405
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: 32059
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Found at i:1335 original size:40 final size:40
Alignment explanation
Indices: 1278--1498 Score: 283
Period size: 40 Copynumber: 5.5 Consensus size: 40
1268 ACCCAAGTAT
* *
1278 CTTC-GGATTTAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
1316 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
1356 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
1396 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGC
* *
1439 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
1479 CTTC-GGAC-TAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
1499 CATCCGAATA
Statistics
Matches: 164, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
38 16 0.10
39 11 0.07
40 99 0.60
41 1 0.01
43 37 0.23
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:1473 original size:83 final size:80
Alignment explanation
Indices: 1278--1498 Score: 290
Period size: 83 Copynumber: 2.8 Consensus size: 80
1268 ACCCAAGTAT
* * * *
1278 CTTC-GGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
1341 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
1356 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1420 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
1439 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTC-GGAC-TAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1499 CATCCGAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
78 4 0.03
79 8 0.06
80 49 0.39
81 11 0.09
82 4 0.03
83 50 0.40
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:9279 original size:104 final size:104
Alignment explanation
Indices: 9157--9380 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
9147 AATGGATATC
9157 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
9222 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
9261 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
9326 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
9365 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
9381 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:16188 original size:26 final size:26
Alignment explanation
Indices: 16158--16208 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
16148 ACCAATGAAC
*
16158 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
16184 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
16209 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:16248 original size:103 final size:103
Alignment explanation
Indices: 16064--16285 Score: 367
Period size: 103 Copynumber: 2.2 Consensus size: 103
16054 AATGGATATC
16064 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
16129 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATATCGCACATAGCACCACC-ATAAACCGGGGAATCA
16168 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
*
16232 GGATCA-CGCACATAGCACCACCATAAATCGGGGAATCA
66 GGAT-ATCGCACATAGCACCACCATAAACCGGGGAATCA
**
16270 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
16286 TTTATATACA
Statistics
Matches: 112, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 28 0.25
103 66 0.59
104 18 0.16
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATATCGCACATAGCACCACCATAAACCGGGGAATCA
Found at i:17658 original size:40 final size:40
Alignment explanation
Indices: 17510--17701 Score: 217
Period size: 40 Copynumber: 4.8 Consensus size: 40
17500 CATTTGAATG
* * *
17510 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* * * * *
17550 TTATCCGGGCTAAGTCCCGAAGGAATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* *
17590 TTATCCGGCCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
*
17630 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * *
17670 ATACCCGGGTTAAGACCCAAAGGCAATTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC
17702 TTGTGGTTAT
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 134 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:18531 original size:16 final size:17
Alignment explanation
Indices: 18502--18538 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
18492 ACTAAAATTT
18502 GTAG-GAATAGAATTAA
1 GTAGTGAATAGAATTAA
*
18518 GTAGTGAATA-AATTAT
1 GTAGTGAATAGAATTAA
18534 GTAGT
1 GTAGT
18539 CGAACCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.32
Consensus pattern (17 bp):
GTAGTGAATAGAATTAA
Found at i:25757 original size:79 final size:79
Alignment explanation
Indices: 25619--25829 Score: 230
Period size: 79 Copynumber: 2.7 Consensus size: 79
25609 CATTTGAATG
* * * * *
25619 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAG-ACCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
* *
25684 TTTATGCTAG-TGATT
65 TTTATGCGAGTTG-CT
*
25699 TTATCCGGGCTAAGACCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCGAAGGCATTTGTGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGCA
*
25763 TTTGTGCGAGTTGCT
65 TTTATGCGAGTTGCT
* * * ** *
25778 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAA
25830 ATTCGAAGAA
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
79 70 0.63
80 41 0.37
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCGAAGGCATTTGTGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCAT
TTATGCGAGTTGCT
Found at i:25769 original size:40 final size:40
Alignment explanation
Indices: 25619--25829 Score: 241
Period size: 40 Copynumber: 5.3 Consensus size: 40
25609 CATTTGAATG
* * *
25619 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
* * * *
25659 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
*
25699 TTATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
*
25738 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT
* * * ** *
25778 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
25818 ATATCC-GGCTAA
1 ATATCCGGGCTAA
25830 ATTCGAAGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
39 39 0.25
40 115 0.75
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT
Found at i:30172 original size:40 final size:40
Alignment explanation
Indices: 30094--30315 Score: 292
Period size: 40 Copynumber: 5.5 Consensus size: 40
30084 ACCCAAGTAT
* *
30094 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
30133 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
30173 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
30213 CTTC-GGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
30255 CTTC-GGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
30294 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
30316 CATCCGAATA
Statistics
Matches: 163, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.01
39 47 0.29
40 79 0.48
41 1 0.01
42 35 0.21
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Done.