Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3173
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: 28049
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Found at i:2086 original size:39 final size:40
Alignment explanation
Indices: 1840--2063 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
1830 TATTCGAATG
* *
1840 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
1881 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* *
1921 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
1961 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * *
2001 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
2040 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
2064 CTTGTGCAAG
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 35 0.22
40 93 0.59
41 29 0.18
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:10108 original size:40 final size:41
Alignment explanation
Indices: 10014--10235 Score: 219
Period size: 40 Copynumber: 5.6 Consensus size: 41
10004 TATTCGAATG
* *
10014 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTTGACT
* * * * *
10055 ATAACCGGACTAAGATCCAAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTTGACT
* *
10095 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA---G-CG
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTTGACT
* * *
10132 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAG-CGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTTGACT
* *
10172 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAG-TGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTTGACT
* *
10212 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
10236 CTTGTGCAAG
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
37 35 0.23
39 1 0.01
40 86 0.57
41 29 0.19
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTTGACT
Found at i:10191 original size:77 final size:78
Alignment explanation
Indices: 10014--10271 Score: 272
Period size: 77 Copynumber: 3.3 Consensus size: 78
10004 TATTCGAATG
* * * * *
10014 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCAAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGGCGA-TAT--CCGGGCTAAGACCCGAAGGC
*
10079 ATTCGTGCGAGTTGCT
63 ATTCGTGCGAGTCGCT
* *
10095 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGATATCCGGGCTAAAACCCGAAGGCATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGGCGATATCCGGGCTAAGACCCGAAGGCATT
* *
10159 TGTGCTAG-CGACT
66 CGTGCGAGTCG-CT
* * * *
10172 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-G-CGATATCCGGGCTAAGACCCGAAGGCA
* * *
10237 TT-GTGCAAGTAGTT
64 TTCGTGCGAGTCGCT
*
10251 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
10272 ATTTCTTGAG
Statistics
Matches: 152, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
76 1 0.01
77 59 0.39
78 14 0.09
79 17 0.11
80 29 0.19
81 32 0.21
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (78 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGGCGATATCCGGGCTAAGACCCGAAGGCATT
CGTGCGAGTCGCT
Found at i:10226 original size:117 final size:118
Alignment explanation
Indices: 10013--10235 Score: 299
Period size: 117 Copynumber: 1.9 Consensus size: 118
10003 TTATTCGAAT
** * *
10013 GATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCAAAGG
1 GATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCAAAGG
* * *
10078 CATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGC
66 CATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGC
* * *
10131 GATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCCCGAAG
1 GATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCAAAG
* *
10194 GCATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 GCATTCATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
10236 CTTGTGCAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
116 3 0.03
117 56 0.62
118 32 0.35
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (118 bp):
GATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCAAAGG
CATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGC
Found at i:17076 original size:6 final size:6
Alignment explanation
Indices: 17065--17095 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
17055 ACTCAGTGTA
17065 ATTCTG ATTCTG ATTCTG ATTCTG AATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG -ATTCTG
17096 GATAGATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:21861 original size:30 final size:29
Alignment explanation
Indices: 21804--21863 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
21794 TTCCCGATCC
* *
21804 TAGGGGCAAAGTGTAATTATGTAAAAGTT
1 TAGGGGCAAAATGTAATTATGCAAAAGTT
* *
21833 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAT-GTAATTATGCAAAAGTT
21863 T
1 T
21864 GTATTAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.32
Consensus pattern (29 bp):
TAGGGGCAAAATGTAATTATGCAAAAGTT
Found at i:22575 original size:49 final size:49
Alignment explanation
Indices: 22516--22703 Score: 259
Period size: 49 Copynumber: 3.8 Consensus size: 49
22506 TGAGGTCACG
**
22516 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * *
22565 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
* *
22616 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
*
22665 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
22704 GCTTCGGCTA
Statistics
Matches: 119, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 75 0.63
50 4 0.03
51 40 0.34
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:22684 original size:100 final size:100
Alignment explanation
Indices: 22511--22709 Score: 335
Period size: 100 Copynumber: 2.0 Consensus size: 100
22501 TATTGTGAGG
**
22511 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
*
22576 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCAGATAACTTCGA
* *
22611 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGGATAATTGGTCGCATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
* *
22676 AAGTGCAGGCTACTATGTGTACCAGATAGCTTCG
66 AAGTGCAGGCTACTATGCGTACCAGATAACTTCG
22710 GCTATAAGTG
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCAGATAACTTCGA
Done.