Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1692
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: 38478
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Found at i:332 original size:43 final size:37
Alignment explanation
Indices: 240--310 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
230 TTCATGCTTT
240 TTCATTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
277 TTCATTCTTTTGGCCGAAAATTCTAAGGAAGGAG
1 TTCATTCTTTTGGCCGAAAATTCTAAGGAAGGAG
311 AAGGAGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (37 bp):
TTCATTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:7470 original size:38 final size:38
Alignment explanation
Indices: 7427--7502 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
7417 TTCATCCTTT
7427 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
7465 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
7503 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:7949 original size:40 final size:40
Alignment explanation
Indices: 7855--7999 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
7845 TACTCGAATG
*
7855 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
7896 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
7936 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
7976 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
8000 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:10114 original size:20 final size:19
Alignment explanation
Indices: 10061--10114 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
10051 ATCATATGAG
* *
10061 ACTGTTTTATTATGGGCCA
1 ACTGTATTAATATGGGCCA
*
10080 ACTGTATTAAAATGGGCCCA
1 ACTGTATTAATATGGG-CCA
* *
10100 ACTTTGTTAATATGG
1 ACTGTATTAATATGG
10115 ACAAGGCCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (19 bp):
ACTGTATTAATATGGGCCA
Found at i:15555 original size:40 final size:40
Alignment explanation
Indices: 15496--15643 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
15486 GAACATTGGA
*
15496 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
15536 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
15576 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
15616 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
15644 ATGTGTTTGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:22402 original size:40 final size:40
Alignment explanation
Indices: 22343--22490 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
22333 GAGCATTGGA
*
22343 ATATATCCGGGCTAAGACCCGAAGGCAATTACGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
22383 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
22423 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
22463 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
22491 ATGTGTTTGC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:31226 original size:43 final size:42
Alignment explanation
Indices: 31178--31303 Score: 180
Period size: 43 Copynumber: 2.9 Consensus size: 42
31168 GTTATCGAGA
31178 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTAT
*
31221 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCT-GGACATTGGCATTGTAT
* * * *
31264 TATGATTTCATGTAAGACCCTGTCTGGAACAGTGGCATTG
1 TGTGATTACATGTAAGACCATGTCTGG-ACATTGGCATTG
31304 GTAACATGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
42 2 0.03
43 73 0.97
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTGATTACATGTAAGACCATGTCTGGACATTGGCATTGTAT
Found at i:34848 original size:50 final size:50
Alignment explanation
Indices: 34785--34914 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
34775 TTATGTGAGC
* * *
34785 CAGTGTAATACCATGTCTGGGACATGGCATCAGCAC-CGATAAATGAGAGT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCAGC-CTCGATAAACGAGAGT
* * *
34835 TAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATATACGAGAGT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATAAACGAGAGT
*
34885 CAGTGTAAGACCATGTTTGGGACATTGCAT
1 CAGTGTAAGACCATGTTTGGGACATGGCAT
34915 TTACTTTGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.01
50 70 0.99
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (50 bp):
CAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATAAACGAGAGT
Found at i:36636 original size:39 final size:40
Alignment explanation
Indices: 36541--36682 Score: 165
Period size: 39 Copynumber: 3.7 Consensus size: 40
36531 TTGAATGATG
* *
36541 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
36579 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAT
36620 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAT
36659 TCCGGGCTAAG--CC-AAGGCATTTGT
1 TCCGGGCTAAGACCCGAAGGCATTTGT
36683 CGATCTACGT
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
37 11 0.12
38 2 0.02
39 56 0.60
40 12 0.13
41 11 0.12
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:36751 original size:40 final size:40
Alignment explanation
Indices: 36696--36787 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
36686 TCTACGTAAG
* *
36696 CGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTAAGTCC
*
36736 CGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCC
1 CGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCC
36776 CGAAGGCATTTG
1 CGAAGGCATTTG
36788 AACGAGGAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 46 0.96
41 2 0.04
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCC
Done.