Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2549
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: 19141
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Found at i:3311 original size:28 final size:27
Alignment explanation
Indices: 3248--3399 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
3238 ATATTAAGTC
* * *
3248 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
3275 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
3303 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
3330 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
3358 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
3385 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3400 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:3332 original size:55 final size:55
Alignment explanation
Indices: 3248--3399 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
3238 ATATTAAGTC
* * *
3248 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
3303 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
3358 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
3400 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:11314 original size:28 final size:27
Alignment explanation
Indices: 11251--11402 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
11241 ATATTAAGTC
* * *
11251 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
11278 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
11306 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
11333 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
11361 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
11388 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
11403 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:11335 original size:55 final size:55
Alignment explanation
Indices: 11251--11402 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
11241 ATATTAAGTC
* * *
11251 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
11306 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
11361 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
11403 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:14116 original size:39 final size:39
Alignment explanation
Indices: 14071--14293 Score: 211
Period size: 39 Copynumber: 5.7 Consensus size: 39
14061 GCTCCTCGTT
* * * *
14071 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCA
14111 C-AATGCCTTCGGGACTTAACCCGGATTTA-ATACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTATA-ACTCGCA
* *
14149 CGAATGCCTTCGGGACTTAACCCGGATTTATATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCA
* * * * *
14188 CAAAGGCCTTCGGGGCTTAACCCGGAACTTGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTATAACTCGCA
** * * *
14228 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-TAAC-TCGCA
*
14269 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
14294 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.01
38 7 0.05
39 85 0.55
40 50 0.32
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCA
Found at i:14173 original size:78 final size:77
Alignment explanation
Indices: 14071--14294 Score: 238
Period size: 78 Copynumber: 2.8 Consensus size: 77
14061 GCTCCTCGTT
* * *
14071 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTA-TAACTCACACAAAGCCTTCGGGACTTAACCCGGA
14136 -TT-TAATACTCGCA
65 CTTGT-AT-CTCGCA
* * * * *
14149 CGAATGCCTTCGGGACTTAACCCGGATTTATATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTATAACTCACACAAA-GCCTTCGGGACTTAACCCGG-
14214 ACTTGTATCTCGCA
64 ACTTGTATCTCGCA
* * * * *
14228 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTA-TAACTCA-CACAAAGCCTTCGGGACTTAACCCG
14292 GAC
63 GAC
14295 AGCATTCAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
77 10 0.08
78 48 0.40
79 31 0.26
80 25 0.21
81 7 0.06
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTATAACTCACACAAAGCCTTCGGGACTTAACCCGGAC
TTGTATCTCGCA
Found at i:14302 original size:41 final size:41
Alignment explanation
Indices: 14225--14302 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
14215 CTTGTATCTC
* * *
14225 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
14266 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
14303 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.