Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5387.1
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: 25071
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:7138 original size:37 final size:37
Alignment explanation
Indices: 7088--7166 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
7078 TTATTACGAA
* * *
7088 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
7125 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
7162 GTCTT
1 GTCTT
7167 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:7372 original size:47 final size:47
Alignment explanation
Indices: 7285--7758 Score: 849
Period size: 47 Copynumber: 10.1 Consensus size: 47
7275 CCCTTCGGGA
* * * * * * *
7285 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
7332 CCTGTCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7379 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7426 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7473 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7520 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7567 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7614 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7661 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
7708 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
7755 CTTA
1 CTTA
7759 CTATCATTTC
Statistics
Matches: 415, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 415 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:18274 original size:100 final size:100
Alignment explanation
Indices: 18101--18300 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
18091 TCGGCTTTGC
18101 ACATAAATATTAAGAGTTTGATATTTTTATGATTTTTGGAAGGTAAATAAGGTTATGCTCAAGTT
1 ACATAAATATTAAGAGTTTGATATTTTTATGATTTTTGGAAGGTAAATAAGGTTATGCTCAAGTT
18166 AAATACAAGATTATGGCTGATTTGTGTTTAGTGAG
66 AAATACAAGATTATGGCTGATTTGTGTTTAGTGAG
18201 ACATAAATATTAAGAGTTTGATATTTTTATGATTTTTGGAAGGTAAATAAGGTTATGCTCAAGTT
1 ACATAAATATTAAGAGTTTGATATTTTTATGATTTTTGGAAGGTAAATAAGGTTATGCTCAAGTT
18266 AAATACAAGATTATGGCTGATTTGTGTTTAGTGAG
66 AAATACAAGATTATGGCTGATTTGTGTTTAGTGAG
18301 TTTCGGCCAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (100 bp):
ACATAAATATTAAGAGTTTGATATTTTTATGATTTTTGGAAGGTAAATAAGGTTATGCTCAAGTT
AAATACAAGATTATGGCTGATTTGTGTTTAGTGAG
Found at i:19268 original size:43 final size:40
Alignment explanation
Indices: 19169--19352 Score: 223
Period size: 40 Copynumber: 4.6 Consensus size: 40
19159 TATTCGGATG
*
19169 ATATCCGGGCTAAGTCCCGAAGCCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
19209 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC---TAG-TGACT
*
19252 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * *
19292 ACATCCGGGCTAAGACCCAAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
19332 AT-TCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
19353 TACTTGGGTT
Statistics
Matches: 125, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
38 13 0.10
39 5 0.04
40 68 0.54
41 2 0.02
43 35 0.28
44 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:19315 original size:83 final size:79
Alignment explanation
Indices: 19173--19352 Score: 254
Period size: 83 Copynumber: 2.2 Consensus size: 79
19163 CGGATGATAT
* * * *
19173 CCGGGCTAAGTCCCGAAGCCATTTGTGCTAGTGACTATATCCGGGCGAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCCGGGCGAAGACCCAAAGGCATTTG
19238 TGCGAGTAGTTGCTATAC
66 TGC-A--AGTTGCTAT-C
*
19256 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCCGGGCTAAGACCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCCGGGCGAAGACCCAAAGGCATTTG
*
19321 TGCAAGTTGCTATT
66 TGCAAGTTGCTATC
*
19335 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
19353 TACTTGGGTT
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
78 15 0.17
79 2 0.02
80 9 0.10
82 1 0.01
83 63 0.70
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTACATCCGGGCGAAGACCCAAAGGCATTTG
TGCAAGTTGCTATC
Done.