Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold272
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: 52784
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:7081 original size:40 final size:40
Alignment explanation
Indices: 7007--7227 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
6997 AACCCAAGTA
* * *
7007 CCTTCGTGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
7046 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
7086 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
7126 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
7166 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
7205 CCTTCAGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
7228 CATCCGAATA
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 123 0.77
41 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:10720 original size:25 final size:25
Alignment explanation
Indices: 10681--10754 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
10671 GTAAGGAGGG
10681 GATAA-GGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
10705 GATAAGGGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
10730 GATAAGGGGAGAAGATTTAGGAGCT
1 GATAAGGGGAGAAGATTTAGGAGCT
10755 TATCAAGGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 5 0.10
25 44 0.90
ACGTcount: A:0.36, C:0.04, G:0.39, T:0.20
Consensus pattern (25 bp):
GATAAGGGGAGAAGATTTAGGAGCT
Found at i:12204 original size:27 final size:26
Alignment explanation
Indices: 12164--12274 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
12154 AGGAAGCGTC
* *
12164 CTGGTGGCTATGCCACATTTATCTGAT
1 CTGGTGGCTCTGCCACA-TTATCTGTT
* *
12191 CTGGTGGCTCTGCCACACATATTTGTT
1 CTGGTGGCTCTGCCACA-TTATCTGTT
12218 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* * *
12245 CTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
12271 CTGG
1 CTGG
12275 CAGTCATGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
26 13 0.18
27 59 0.81
28 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:24933 original size:69 final size:68
Alignment explanation
Indices: 24838--25285 Score: 527
Period size: 69 Copynumber: 6.5 Consensus size: 68
24828 GGGAAAGGTC
* * * * *
24838 CATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAGAGC
1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
24903 TCAT
65 TCAT
** * * * * *
24907 CAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGGGAAGGGC
1 CA-TTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
24972 TCAT
65 TCAT
* * * * *
24976 CTGTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTAAGGGGAAGAGT
1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
*
25041 TCGT
65 TCAT
* * * ** * *
25045 CCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGGGT
1 CATT-TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
25110 TCAT
65 TCAT
* * * * *
25114 CCATATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGGGAAGGGT
1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
*
25179 TCGT
65 TCAT
* *
25183 CCATATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
1 -CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGC
25248 TCAT
65 TCAT
*
25252 CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
1 C-ATTTTTGCAGATTCTGTTCCAAGCACTCCTGC
25286 TTATCATTAT
Statistics
Matches: 329, Mismatches: 45, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
68 3 0.01
69 322 0.98
70 4 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (68 bp):
CATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCT
CAT
Found at i:25195 original size:207 final size:207
Alignment explanation
Indices: 24835--25285 Score: 591
Period size: 207 Copynumber: 2.2 Consensus size: 207
24825 CCAGGGAAAG
* * *
24835 GTCCATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAGGGGAAG
1 GTCC-TTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAG
* * * *
24900 AGCTCATCAGTTTTTGGGGAATCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGTTCCAGGG
65 AGCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
** * * * *
24965 GAAGGGCTCATCTGTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTA
130 GAAGGGCTCATCCATATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA
*
25030 AGGGGAAGAGTTC
195 AGGGGAAGAGCTC
* * * * ** *
25043 GTCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGG
1 GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA
* * * *
25108 GTTCATCCA-TATTTGGAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTCAAGGG
66 GCTCAT-CAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGG
* * *
25172 GAAGGGTTCGTCCATATTTGCAGATTCTATTCCAAGCACTCCTGCCTATGCAGATAACATGTTCA
130 GAAGGGCTCATCCATATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCA
25237 AGGGGAAGAGCTC
195 AGGGGAAGAGCTC
* *
25250 AT-CTATTTTTGCAGATTCTGTTCCAAGCACCCCTGC
1 GTCCT-TGTTTGCAGATTCTGTTCCAAGCACCCCTGC
25286 TTATCATTAT
Statistics
Matches: 210, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
206 2 0.01
207 202 0.96
208 6 0.03
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (207 bp):
GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCAAGGGGAAGA
GCTCATCAGTATTTGGAGAATCTGTTCCAAGCACCCCTGCCTATGCAGATAACATGTTCAAGGGG
AAGGGCTCATCCATATTTGCAGATTCTATTCCAAGCACTCCGGCCTATGCAGATAACATGTTCAA
GGGGAAGAGCTC
Found at i:31375 original size:26 final size:22
Alignment explanation
Indices: 31329--31373 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31319 ACTAAATAAG
31329 TATGATTGTAACTTGTTTTCTT
1 TATGATTGTAACTTGTTTTCTT
31351 TATGATTGTAACTTGTTTTCTT
1 TATGATTGTAACTTGTTTTCTT
31373 T
1 T
31374 CTCCTAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (22 bp):
TATGATTGTAACTTGTTTTCTT
Found at i:42776 original size:21 final size:22
Alignment explanation
Indices: 42741--42788 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
42731 TTTTTAAAAA
* * *
42741 TAAAAAATATTATATATTTTTT
1 TAAATAATATTATATATATATT
42763 TAAATAAT-TTATATATATATT
1 TAAATAATATTATATATATATT
42784 TAAAT
1 TAAAT
42789 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATAATATTATATATATATT
Found at i:42922 original size:15 final size:15
Alignment explanation
Indices: 42885--42922 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
42875 GTGATTTGAC
*
42885 AAATAATATAAATTTA
1 AAATAAT-TAAAATTA
42901 AAA-AATTAAAATTA
1 AAATAATTAAAATTA
42915 AAATAATT
1 AAATAATT
42923 CTTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 7 0.35
16 3 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAATTAAAATTA
Found at i:46269 original size:31 final size:31
Alignment explanation
Indices: 46234--46297 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
46224 CCTTTTCATA
*
46234 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
46265 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
46296 TT
1 TT
46298 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:46537 original size:24 final size:23
Alignment explanation
Indices: 46505--46635 Score: 163
Period size: 25 Copynumber: 5.4 Consensus size: 23
46495 CTGGAGGTCT
* * *
46505 AGCCTCTTTTAGTAACTGAGGAAAA
1 AGCC-CTTTTA-TAACTGGGGCATA
46530 AGCCCTTTTTATAACTGGGGCATA
1 AGCCC-TTTTATAACTGGGGCATA
46554 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-T-ATAACTGGGGCATA
46579 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-T-ATAACTGGGGCATA
*
46604 AGCCCTTTAATAACTGGGGCATA
1 AGCCCTTTTATAACTGGGGCATA
46627 AGCCCTTTT
1 AGCCCTTTT
46636 GCACTTTCTC
Statistics
Matches: 98, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
23 25 0.26
24 17 0.17
25 56 0.57
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (23 bp):
AGCCCTTTTATAACTGGGGCATA
Found at i:46573 original size:25 final size:25
Alignment explanation
Indices: 46529--46634 Score: 182
Period size: 25 Copynumber: 4.4 Consensus size: 25
46519 ACTGAGGAAA
*
46529 AAGCCCTTT-TTATAACTGGGGCAT
1 AAGCCCTTTATCATAACTGGGGCAT
46553 AAGCCCTTTATCATAACTGGGGCAT
1 AAGCCCTTTATCATAACTGGGGCAT
46578 AAGCCCTTTATCATAACTGGGGCAT
1 AAGCCCTTTATCATAACTGGGGCAT
46603 AAGCCCTTTA--ATAACTGGGGCAT
1 AAGCCCTTTATCATAACTGGGGCAT
46626 AAGCCCTTT
1 AAGCCCTTT
46635 TGCACTTTCT
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
23 22 0.28
24 9 0.11
25 49 0.61
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (25 bp):
AAGCCCTTTATCATAACTGGGGCAT
Found at i:46709 original size:20 final size:20
Alignment explanation
Indices: 46681--46731 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
46671 GCATTTATGA
*
46681 ACATCTCATGTGAATATCAT
1 ACATATCATGTGAATATCAT
* *
46701 ACATGTCATGTGCATATCAT
1 ACATATCATGTGAATATCAT
46721 ACATATCATGT
1 ACATATCATGT
46732 TTATCAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGAATATCAT
Found at i:46796 original size:25 final size:25
Alignment explanation
Indices: 46768--46815 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
46758 ATATATAAAC
*
46768 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGTAAAATGGTCATTTTTA
46793 CCTAGGGGTAAAATGGTCATTTT
1 CCTAGGGGTAAAATGGTCATTTT
46816 CATGTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (25 bp):
CCTAGGGGTAAAATGGTCATTTTTA
Done.