Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1623
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: 60066
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:6129 original size:79 final size:82
Alignment explanation
Indices: 6018--6202 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
6008 GCTACTCGTT
* *
6018 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
6081 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
6098 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
6161 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
6178 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6203 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:6202 original size:40 final size:40
Alignment explanation
Indices: 5999--6202 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
5989 CGGAATTTAA
** *
5999 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6039 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
6079 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
6118 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
6158 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
6198 CCGGA
1 CCGGA
6203 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:17067 original size:47 final size:46
Alignment explanation
Indices: 16999--17310 Score: 231
Period size: 47 Copynumber: 6.7 Consensus size: 46
16989 TTTGTGCGCT
* *
16999 AGTGTAAGGCATGTCTGGGACATGCTTCGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
* * * * * *
17045 AGTGTAAGACCATGTCTGGGACATGGCATCGG-TATCTAGACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATAT-TATGAGAGCC
* * * * *
17093 AGTGTAAGACATGTCTAGGACATGCTTCAGCTATATTATGAGTGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
* * ** * *
17139 AGAGTAAGACATGTTTGGGACATGCATCGGCC-TCGACAAAGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAT--ATTATGAGAGCC
** * * * * *
17186 AGTGTAAGATGTGTCTGGGACACGCATCGGCCA-A-GA-GTTGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATG-AGAGCC
*
17230 AGTGTAAGACATGTCTGGGACATGCATCAGCACGCATA-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-G-GC-CATATTATGAGAGCC
*
17278 AGTATAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
17311 ATTTTATTCC
Statistics
Matches: 204, Mismatches: 47, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
43 1 0.00
44 28 0.14
45 3 0.01
46 46 0.23
47 70 0.34
48 35 0.17
49 16 0.08
50 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGAGAGCC
Found at i:17160 original size:46 final size:45
Alignment explanation
Indices: 16999--17163 Score: 168
Period size: 46 Copynumber: 3.6 Consensus size: 45
16989 TTTGTGCGCT
* *
16999 AGTGTAAGGCATGTCTGGGACATGCTTCGGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCTTC-GCTATATTATGAGAGCC
* * * * * * *
17045 AGTGTAAGACCATGTCTGGGACATGGCATCGGTATCTAGACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCTTCGCTATAT-TATGAGAGCC
* *
17093 AGTGTAAGACATGTCTAGGACATGCTTCAGCTATATTATGAGTGCC
1 AGTGTAAGACATGTCTGGGACATGCTTC-GCTATATTATGAGAGCC
* *
17139 AGAGTAAGACATGTTTGGGACATGC
1 AGTGTAAGACATGTCTGGGACATGC
17164 ATCGGCCTCG
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
46 40 0.42
47 36 0.38
48 19 0.20
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCTTCGCTATATTATGAGAGCC
Found at i:17207 original size:93 final size:94
Alignment explanation
Indices: 16999--17302 Score: 246
Period size: 93 Copynumber: 3.3 Consensus size: 94
16989 TTTGTGCGCT
* * *
16999 AGTGTAAGGCATGTCTGGGACATGCTTCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGAGTAAGACCATGTCTGG
* * * * * *
17064 GACATGGCATCGGTATCTAGACGAGGGCT
66 GACATGGCATCGGCATCGAAAAGAGAGCC
* * * *
17093 AGTGTAAGACATGTCTAGGACATGCTTCAGCTATATTATGAGTGCCAGAGTAAGA-CATGTTTGG
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGAGTAAGACCATGTCTGG
* *
17157 GACAT-GCATCGGCCTCGACAAAGATAGCC
66 GACATGGCATCGGCATCGA-AAAGAGAGCC
** * * * * * * * *
17186 AGTGTAAGATGTGTCTGGGACACGCATCGGCCA-A-GA-GTTGTGCTAGTGTAAGA-CATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATG-AGAGCCAGAGTAAGACCATGTCTG
* *
17247 GGACAT-GCATCAGCA-CGCATATATGAGAGCC
65 GGACATGGCATCGGCATCG-A-A-AAGAGAGCC
*
17278 AGTATAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
17303 GCATCGGCAT
Statistics
Matches: 169, Mismatches: 36, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
90 3 0.02
91 35 0.21
92 26 0.15
93 56 0.33
94 49 0.29
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCCAGAGTAAGACCATGTCTGG
GACATGGCATCGGCATCGAAAAGAGAGCC
Found at i:23176 original size:3 final size:3
Alignment explanation
Indices: 23163--23195 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
23153 ATACTAATTA
23163 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
23196 GAGACTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:25860 original size:26 final size:27
Alignment explanation
Indices: 25818--25996 Score: 124
Period size: 26 Copynumber: 6.9 Consensus size: 27
25808 AATGGCTAAT
* *
25818 GTGATTAATTAACAGGCCT-TGAGTCG
1 GTGATTACTTAGCAGGCCTATGAGTCG
*
25844 GTGATTACTTAGTAGG-CTATGAGTCG
1 GTGATTACTTAGCAGGCCTATGAGTCG
* *
25870 GTGATTACTTAGCAGG-CTATAAG-CTA
1 GTGATTACTTAGCAGGCCTATGAGTC-G
* * *
25896 GTGACTACTTAGCAGG-TTATGAGTTG
1 GTGATTACTTAGCAGGCCTATGAGTCG
* * *
25922 GTGATCATTTAGCAGG--TATTGAGACG
1 GTGATTACTTAGCAGGCCTA-TGAGTCG
* * * *
25948 ATGATTATTTAACAGGCCT-TGAGCCG
1 GTGATTACTTAGCAGGCCTATGAGTCG
* *
25974 GTGATTACTAAGCA-GACTATGAG
1 GTGATTACTTAGCAGGCCTATGAG
25997 CCGATAATTA
Statistics
Matches: 121, Mismatches: 25, Indels: 14
0.76 0.16 0.09
Matches are distributed among these distances:
25 8 0.07
26 112 0.93
28 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (27 bp):
GTGATTACTTAGCAGGCCTATGAGTCG
Found at i:37309 original size:35 final size:35
Alignment explanation
Indices: 37261--37333 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
37251 CTTCTGAGTG
* **
37261 CAAATCTATATCTGTCTCTG-AGATGGGCTAAGGCC
1 CAAATCTACATCTGAATCTGTA-ATGGGCTAAGGCC
*
37296 CAAATCTACATCTGAATCTGTAATGGGCTTAGGCC
1 CAAATCTACATCTGAATCTGTAATGGGCTAAGGCC
37331 CAA
1 CAA
37334 GTCTGTATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (35 bp):
CAAATCTACATCTGAATCTGTAATGGGCTAAGGCC
Found at i:37757 original size:18 final size:18
Alignment explanation
Indices: 37734--37769 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
37724 TACATTTTAT
37734 CGTTAGATAATTAAATGA
1 CGTTAGATAATTAAATGA
37752 CGTTAGATAATTAAATGA
1 CGTTAGATAATTAAATGA
37770 AAGAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
CGTTAGATAATTAAATGA
Found at i:38007 original size:21 final size:21
Alignment explanation
Indices: 37968--38007 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
37958 GTTATTTTTG
* **
37968 AATTTGTTTAATTTTGTATTT
1 AATTTGTTAAATTAGGTATTT
37989 AATTTGTTAAATTAGGTAT
1 AATTTGTTAAATTAGGTAT
38008 GATGGTTGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
AATTTGTTAAATTAGGTATTT
Found at i:44282 original size:12 final size:12
Alignment explanation
Indices: 44262--44302 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
44252 TTGTGACTGC
44262 ATCTGTATCTGA
1 ATCTGTATCTGA
* *
44274 ATCTATATCTGC
1 ATCTGTATCTGA
*
44286 ATTTGTATCTGA
1 ATCTGTATCTGA
44298 ATCTG
1 ATCTG
44303 AATATGCATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (12 bp):
ATCTGTATCTGA
Found at i:44310 original size:24 final size:24
Alignment explanation
Indices: 44259--44312 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
44249 GATTTGTGAC
*
44259 TGCATCTGTATCTGAATCTATATC
1 TGCATCTGTATCTGAATCTATATA
*
44283 TGCATTTGTATCTGAATCTGA-ATA
1 TGCATCTGTATCTGAATCT-ATATA
44307 TGCATC
1 TGCATC
44313 CATACCTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (24 bp):
TGCATCTGTATCTGAATCTATATA
Found at i:46272 original size:18 final size:18
Alignment explanation
Indices: 46258--46300 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 18
46248 ATATATTATG
*
46258 ATTGTATTGATTATTTGA
1 ATTGAATTGATTATTTGA
46276 ATTGAATTGA--A-TTGA
1 ATTGAATTGATTATTTGA
46291 ATTGAATTGA
1 ATTGAATTGA
46301 ATTCACGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 14 0.58
16 1 0.04
18 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (18 bp):
ATTGAATTGATTATTTGA
Found at i:46280 original size:5 final size:5
Alignment explanation
Indices: 46272--46303 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
46262 TATTGATTAT
46272 TTGAA TTGAA TTGAA TTGAA TTGAA TTGAA TT
1 TTGAA TTGAA TTGAA TTGAA TTGAA TTGAA TT
46304 CACGTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (5 bp):
TTGAA
Done.