Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold993
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: 29205
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Found at i:3098 original size:40 final size:40
Alignment explanation
Indices: 3004--3148 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
2994 TACTCGAATG
*
3004 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
3045 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
3085 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
3125 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
3149 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:9839 original size:38 final size:38
Alignment explanation
Indices: 9796--9871 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
9786 TTCATCCTTT
9796 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
9834 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
9872 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:11151 original size:40 final size:40
Alignment explanation
Indices: 11057--11201 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
11047 TACTCGAATG
*
11057 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
11098 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
11138 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
11178 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
11202 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:18433 original size:46 final size:46
Alignment explanation
Indices: 18378--18594 Score: 233
Period size: 46 Copynumber: 4.7 Consensus size: 46
18368 GATATTTGGG
* * * * *
18378 CATCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAG
1 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
** * * * *
18424 TGTCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGG
1 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTGATGGATG---CGA-A
*
18471 CATCCGAGCTCCTTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
1 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
* *
18517 CACCCGAGCTCATTGAGTTGAGTCTGAGTTCACTGATGGATGCGAA
1 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
* *
18563 CACCCGAGCTCATTCAGTTGAGTCCGAGTTCA
1 CATCCGAGCTCATTGAGTTGAGTCCGAGTTCA
18595 TTTATGGACG
Statistics
Matches: 148, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
43 4 0.03
45 2 0.01
46 104 0.70
47 31 0.21
48 3 0.02
50 4 0.03
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (46 bp):
CATCCGAGCTCATTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
Found at i:18535 original size:93 final size:93
Alignment explanation
Indices: 18376--18548 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
18366 AGGATATTTG
* * **** *
18376 GGCATCCGAACTCGTTGAGTTGAGTCCCAGTTCACTTATGGATGCGAGTGTCCGAACTCGTTGAG
1 GGCATCCGAACTCCTTGAGTTGAGTCCCAGTTCACTGATGGATGCGAACACCCGAACTCATTGAG
18441 TTGAGTCCGAGTTCATGAGATGTAACTA
66 TTGAGTCCGAGTTCATGAGATGTAACTA
* * *
18469 GGCATCCGAGCTCCTTGAGTTGAGTCCGAGTTCACTGATGGATGCGAACACCCGAGCTCATTGAG
1 GGCATCCGAACTCCTTGAGTTGAGTCCCAGTTCACTGATGGATGCGAACACCCGAACTCATTGAG
*
18534 TTGAGTCTGAGTTCA
66 TTGAGTCCGAGTTCA
18549 CTGATGGATG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCCTTGAGTTGAGTCCCAGTTCACTGATGGATGCGAACACCCGAACTCATTGAG
TTGAGTCCGAGTTCATGAGATGTAACTA
Found at i:27995 original size:27 final size:27
Alignment explanation
Indices: 27965--28169 Score: 243
Period size: 27 Copynumber: 7.6 Consensus size: 27
27955 ATATTTAGTC
* * * *
27965 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27992 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28019 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28047 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28074 CGCACACTTAGTGC-ATCAATATTCATTT
1 CGCACACTTAGTGCTA-C-ATAGTCAAAT
*
28102 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28129 CGCACACTTAGTGCTACAT-GTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28155 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28170 GTACAATTTA
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
26 22 0.14
27 88 0.56
28 45 0.29
29 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28057 original size:55 final size:54
Alignment explanation
Indices: 27965--28169 Score: 243
Period size: 55 Copynumber: 3.8 Consensus size: 54
27955 ATATTTAGTC
* * * * *
27965 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
** * *
28019 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTCAAAT
* ** *
28074 CGCACACTTAGTGC-ATCAATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-C-ATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
*
28129 CGCACACTTAGTGCTACAT-GTCAAATCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
28170 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
53 18 0.14
54 23 0.18
55 80 0.63
56 6 0.05
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAAT
Done.