Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3454
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: 40617
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:6890 original size:79 final size:81
Alignment explanation
Indices: 6754--6938 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
6744 TTGAATGATG
* *
6754 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
6818 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
6833 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
6895 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
6913 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6939 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:6952 original size:40 final size:40
Alignment explanation
Indices: 6755--6938 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
6745 TGAATGATGT
* * * *
6755 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
6795 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
6835 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
6873 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
6914 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
6939 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:6960 original size:79 final size:79
Alignment explanation
Indices: 6807--6971 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
6797 GGACTAAGAT
* * **
6807 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
6872 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
6886 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
6949 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
6965 CCGAAGG
1 CCGAAGG
6972 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:8804 original size:14 final size:15
Alignment explanation
Indices: 8769--8814 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
8759 ACAAAAAAGT
*
8769 AAAACATTTT-CTAG
1 AAAACATTTTACTGG
* *
8783 AGATCATTTTAC-GG
1 AAAACATTTTACTGG
8797 AAAACATTTTACTGG
1 AAAACATTTTACTGG
8812 AAA
1 AAA
8815 TCAAACAGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
AAAACATTTTACTGG
Found at i:15083 original size:13 final size:13
Alignment explanation
Indices: 15065--15098 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
15055 GTTGCCGAAT
15065 TCTCTCTTCTCTC
1 TCTCTCTTCTCTC
15078 TCTCTCTT-TCTC
1 TCTCTCTTCTCTC
15090 T-TCTCTTCT
1 TCTCTCTTCT
15099 TCTTTTCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 6 0.30
13 8 0.40
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
TCTCTCTTCTCTC
Found at i:15091 original size:19 final size:17
Alignment explanation
Indices: 15067--15103 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
15057 TGCCGAATTC
15067 TCTCTTCTCTCTCTCTCTT
1 TCTCTTCTCT-TCT-TCTT
15086 TCTCTTCTCTTCTTCTT
1 TCTCTTCTCTTCTTCTT
15103 T
1 T
15104 TCTAGCCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTCTTCTCTTCTTCTT
Found at i:15791 original size:27 final size:27
Alignment explanation
Indices: 15752--16038 Score: 258
Period size: 27 Copynumber: 10.7 Consensus size: 27
15742 GATTCATTGG
* *
15752 AAAATGACTGAAATACCCTTGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * *
15779 AAAAAGACCGAAATATCC-AGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
15805 AAAATGATCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * *
15832 AAATTAACCAAAATACCCTCGAAGGAT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
15859 AAAATGACCGAAATACCCTCAAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * * *
15886 ATAATTACTGAAATGCCCTCGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * *
15913 AAAATGATCGAAATACCCTCAAAGTGT
1 AAAATGACCGAAATACCCTCGAAGGGT
** *
15940 AAAATGATTGAAATACCC-CTGAACGGT
1 AAAATGACCGAAATACCCTC-GAAGGGT
* * *
15967 AAAATGACTGAAATACCC-CCATAAGGT
1 AAAATGACCGAAATACCCTCGA-AGGGT
* *
15994 AAAATGACTGAAATACCC-CCATAGGGT
1 AAAATGACCGAAATACCCTCGA-AGGGT
* *
16021 AAAATGACTGTAATACCC
1 AAAATGACCGAAATACCC
16039 CTAAGAGATT
Statistics
Matches: 216, Mismatches: 41, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 24 0.11
27 192 0.89
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCGAAGGGT
Found at i:16417 original size:28 final size:28
Alignment explanation
Indices: 16379--16505 Score: 110
Period size: 28 Copynumber: 4.4 Consensus size: 28
16369 CACTGTACTG
16379 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *** * **
16407 GTTACTATATTTAACAAAGGCCTGCACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
16435 GTTACTGTATTGGGCTAAGGCCCACACTATATT
1 GTTACTGTATTGGGCTAAGGCCCACAC-----T
* * *
16468 GTTACTGTATAGGGCTCAGGCCCAGACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
16496 GATACTGTAT
1 GTTACTGTAT
16506 GATTACTGAT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
28 51 0.67
33 25 0.33
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:18269 original size:25 final size:25
Alignment explanation
Indices: 18238--18288 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
18228 AGGAGATAGG
18238 AGCCAAAGGTATAAGGGTGAACGCC
1 AGCCAAAGGTATAAGGGTGAACGCC
18263 AGCCAAAGGTATAAGGGTGAACGCC
1 AGCCAAAGGTATAAGGGTGAACGCC
18288 A
1 A
18289 CACTCGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (25 bp):
AGCCAAAGGTATAAGGGTGAACGCC
Found at i:18610 original size:11 final size:11
Alignment explanation
Indices: 18594--18627 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18584 AGAACATCTT
18594 TTGAAGCTTCC
1 TTGAAGCTTCC
*
18605 TTGAAGGTTCC
1 TTGAAGCTTCC
*
18616 TTGAAGTTTCC
1 TTGAAGCTTCC
18627 T
1 T
18628 AGCATGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (11 bp):
TTGAAGCTTCC
Found at i:24846 original size:79 final size:81
Alignment explanation
Indices: 24710--24894 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
24700 TTGAATGATG
*
24710 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
24774 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
24789 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
24851 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
24869 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24895 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:24908 original size:40 final size:40
Alignment explanation
Indices: 24711--24894 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
24701 TGAATGATGT
* * * *
24711 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
24751 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
24791 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
24829 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
24870 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
24895 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:24916 original size:79 final size:79
Alignment explanation
Indices: 24763--24927 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
24753 GGACTAAGAT
* **
24763 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
24828 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
24842 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
24905 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
24921 CCGAAGG
1 CCGAAGG
24928 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:32790 original size:79 final size:81
Alignment explanation
Indices: 32654--32838 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
32644 TTGAATGATG
*
32654 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
32718 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
32733 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
32795 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
32813 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
32839 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:32852 original size:40 final size:40
Alignment explanation
Indices: 32655--32838 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
32645 TGAATGATGT
* * * *
32655 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
32695 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
32735 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
32773 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
32814 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
32839 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:32860 original size:79 final size:79
Alignment explanation
Indices: 32707--32871 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
32697 GGACTAAGAT
* **
32707 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
32772 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
32786 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
32849 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
32865 CCGAAGG
1 CCGAAGG
32872 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.