Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold987
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: 40054
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Found at i:3528 original size:38 final size:39
Alignment explanation
Indices: 3427--3601 Score: 199
Period size: 38 Copynumber: 4.6 Consensus size: 39
3417 TTGAATGCTG
* *
3427 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-ATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTA-A
**
3466 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAA
3505 TTCCGGG-TAAG-CCCGAAGGCATTTGTGCGAGATACTAA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
3543 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGA-ATA--AA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
3578 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3602 GTGAGTTACT
Statistics
Matches: 124, Mismatches: 3, Indels: 21
0.84 0.02 0.14
Matches are distributed among these distances:
35 24 0.19
36 1 0.01
37 9 0.07
38 38 0.31
39 35 0.28
40 16 0.13
41 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAA
Found at i:3547 original size:77 final size:75
Alignment explanation
Indices: 3427--3601 Score: 193
Period size: 77 Copynumber: 2.3 Consensus size: 75
3417 TTGAATGCTG
*
3427 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACATATCCGGACTAAG-TCCCGAAGGCA-T
3490 TGTGCGAGATACTAA
64 TGTGCGA-ATA--AA
**
3505 TTCCGGG-TAAG-CCCGAAGGCATTTGTGCG-AGAT-AC-TAATCCGGGTTAAGTCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TGACAT-ATCCGGACTAAGTCCCGAAGGCA
3565 TTGTGCGAATAAA
63 TTGTGCGAATAAA
*
3578 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
3602 GTGAGTTACT
Statistics
Matches: 87, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
72 6 0.07
73 6 0.07
74 12 0.14
75 3 0.03
76 10 0.11
77 32 0.37
78 12 0.14
79 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (75 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACATATCCGGACTAAGTCCCGAAGGCATTG
TGCGAATAAA
Found at i:9683 original size:41 final size:40
Alignment explanation
Indices: 9531--9700 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 40
9521 GCTAATCGGG
*
9531 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* *
9572 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* * *
9615 GACATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT
* *
9655 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
9696 G-CTAA
1 GTCTAA
9701 GAGTCGGACT
Statistics
Matches: 106, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
39 7 0.07
40 14 0.13
41 49 0.46
42 23 0.22
43 9 0.08
44 1 0.01
45 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:18091 original size:34 final size:34
Alignment explanation
Indices: 18043--18123 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
18033 GCATGACTGC
* * *
18043 TACTAATACTGTGATGGGTTAAGGCCCTAATGCA
1 TACTGATACTGTGATGGGCTAAGGCCCTAATACA
* *
18077 TACTGATACTGTGATGGGCTAAGTCCCTACTACA
1 TACTGATACTGTGATGGGCTAAGGCCCTAATACA
*
18111 TATTTGATACTGT
1 TA-CTGATACTGT
18124 ACTGAGATGG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 31 0.77
35 9 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (34 bp):
TACTGATACTGTGATGGGCTAAGGCCCTAATACA
Found at i:20880 original size:22 final size:22
Alignment explanation
Indices: 20848--20891 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20838 TACTTTAGCC
20848 ATTTTTATTTTTATTGTAATTT
1 ATTTTTATTTTTATTGTAATTT
* *
20870 ATTTTTCTTTTTATTTTAATTT
1 ATTTTTATTTTTATTGTAATTT
20892 GCTAGTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
ATTTTTATTTTTATTGTAATTT
Found at i:22694 original size:68 final size:67
Alignment explanation
Indices: 22622--22771 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
22612 CATCATGTGT
* * * *
22622 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
22684 ATGTAG
62 ATGTAG
** * *
22690 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
22755 AG
66 AG
22757 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
22772 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:22727 original size:64 final size:64
Alignment explanation
Indices: 22646--22829 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
22636 AGACATTATG
* *
22646 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
22710 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
22775 AA
63 AA
* * * *
22777 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
22830 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:30210 original size:13 final size:13
Alignment explanation
Indices: 30192--30220 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
30182 TTTAGTTTAA
30192 TTAGTTAATTAGT
1 TTAGTTAATTAGT
30205 TTAGTTAATTAGT
1 TTAGTTAATTAGT
30218 TTA
1 TTA
30221 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:35047 original size:29 final size:29
Alignment explanation
Indices: 34984--35051 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
34974 TAATCAACCA
34984 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
35013 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
35042 CGCACACTTA
1 CGCACACTTA
35052 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:35192 original size:29 final size:30
Alignment explanation
Indices: 35153--35231 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
35143 CTTAATAATC
35153 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
35183 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
35212 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35232 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Done.