Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3377
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: 23701
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Found at i:2750 original size:40 final size:40
Alignment explanation
Indices: 2672--2874 Score: 268
Period size: 40 Copynumber: 5.1 Consensus size: 40
2662 GGGATTTAAT
* *
2672 CGGATATAGCT-ACTCGCTC-AATGCCTTCGGGACATAGCC
1 CGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
2711 CGGATATAGTAACTCGCACCATTGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
*
2751 CGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
2791 CGGATGTAATAACTCGCACAAATACCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
2831 CGGA-ACTAGTCACTAGCACAAAATGCCTTCGGGACTTAGCC
1 CGGATA-TAGTAACTCGCAC-AAATGCCTTCGGGACTTAGCC
2872 CGG
1 CGG
2875 TTATCATCCA
Statistics
Matches: 145, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 16 0.11
40 105 0.72
41 23 0.16
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
Found at i:14255 original size:27 final size:27
Alignment explanation
Indices: 14225--14402 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
14215 ATATTGAGCC
* * *
14225 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
14252 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
14279 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
14307 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
14334 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
14361 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
14388 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
14403 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:14318 original size:55 final size:55
Alignment explanation
Indices: 14225--14402 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
14215 ATATTGAGCC
* * *
14225 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
14279 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
14334 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
14388 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
14403 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:14364 original size:82 final size:81
Alignment explanation
Indices: 14246--14401 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
14236 TGCTATACAA
* * *
14246 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
14311 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
14328 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
14392 CACTTAGTGC
65 CACTTAGTGC
14402 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:22391 original size:27 final size:27
Alignment explanation
Indices: 22355--22510 Score: 161
Period size: 27 Copynumber: 5.7 Consensus size: 27
22345 CTATATACAA
* * *
22355 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAAATCGCACACTTAGTGCCACATAG
*
22382 TCAAATCGCACACTTAGTGCTACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
* * * *
22409 TTAGACTCGCACACTTAGTGCCGCATGG
1 TCA-AATCGCACACTTAGTGCCACATAG
* *
22437 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAAATCGCACACTTAGTGCCA-CATAG
** *
22464 TCATTTCGCACACTTAGTGCAACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
*
22491 TCGAATCGCACACTTAGTGC
1 TCAAATCGCACACTTAGTGC
22511 TGTACAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.01
27 82 0.77
28 23 0.22
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (27 bp):
TCAAATCGCACACTTAGTGCCACATAG
Found at i:22427 original size:55 final size:55
Alignment explanation
Indices: 22332--22511 Score: 197
Period size: 55 Copynumber: 3.3 Consensus size: 55
22322 ATATTGAGCC
* * * *
22332 CGCACACTCAGTGCTAT-ATACAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTATCAT--ATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
22388 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
22443 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
22497 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22512 GTACAATTTA
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
54 42 0.40
55 45 0.43
56 17 0.16
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:22454 original size:82 final size:81
Alignment explanation
Indices: 22355--22510 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
22345 CTATATACAA
* * *
22355 TCAACTCGCACACTTAGTGCCA-CGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGC
1 TCAACTCGCACACTTAGTG-CATCATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGC
22419 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * ** *
22437 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
22502 ACTTAGTGC
66 ACTTAGTGC
22511 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Done.