Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1144
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: 6264
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Found at i:1294 original size:78 final size:78
Alignment explanation
Indices: 1162--1720 Score: 483
Period size: 78 Copynumber: 7.1 Consensus size: 78
1152 TCCAGAACAT
* * * * *
1162 CGTTATTTTCGAG-GGAATACTCTAACCCCGATTTTATTTTTAGAACACC-AATTTTCTACAATC
1 CGTTATTTT-GAGAGG-ATACTCCAACCCCGGTTTTATTTCTAAAACACCGATTTTTC-ACAATC
*
1225 GGGGATACTCTAACCC
63 GGGGATACTCCAACCC
* * * * *
1241 CGTTATTTTGAGAGGATACTCCAACCTCGGTTTTATTTCTAAAATACTGATTTTCCACCATCGGG
1 CGTTATTTTGAGAGGATACTCCAACCCCGGTTTTATTTCTAAAACACCGATTTTTCACAATCGGG
** *
1306 GATACTTTAACCA
66 GATACTCCAACCC
* * * * *
1319 CGTTGGTTTCGAGAGGATACTTCAACCCCGGTTTTATTT-TCAAAACACTGATTTTTCACAATCA
1 CGTT-ATTTTGAGAGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCGATTTTTCACAATCG
*
1383 GGAATACTCCAA-CC
64 GGGATACTCCAACCC
* *
1397 CGTTATTTTTGAGAGGATACTCCAACCCTGGTTTTATTTCTAAAACACCGATATTTTCACAATCA
1 CGTTA-TTTTGAGAGGATACTCCAACCCCGGTTTTATTTCTAAAACACCGAT-TTTTCACAATCG
* *
1462 TGGATATTCCAACCC
64 GGGATACTCCAACCC
* * * *
1477 CGTTATTTCTGAAGAGGATACTCAAACCCCAGCTTTATTTCTAAAACATCGATTTTTCACAATCG
1 CGTTATTT-TG-AGAGGATACTCCAACCCCGGTTTTATTTCTAAAACACCGATTTTTCACAATCG
* *
1542 AGGATACTCCAATCC
64 GGGATACTCCAACCC
* * *
1557 CATTATTTTCA-AGGGATACTCCAA-CCCGGATTTTATTTTTAAAACACCGA-TTTTCACCAA-C
1 CGTTATTTTGAGA-GGATACTCCAACCCCGG-TTTTATTTCTAAAACACCGATTTTTCA-CAATC
*
1618 -AGGATACTCCAACCCC
63 GGGGATACTCCAA-CCC
* * * * * * * * * *
1634 CGTTATTTTTGA-AGGGATACACTAACCTCGATTTTGTTTCCAAAATATCAATTTTTCACCATCG
1 CGTTA-TTTTGAGA-GGATACTCCAACCCCGGTTTTATTTCTAAAACACCGATTTTTCACAATCG
** *
1698 AAGATTCTCCAACCC
64 GGGATACTCCAACCC
1713 CGTT-TTTT
1 CGTTATTTT
1721 CTCCAACATA
Statistics
Matches: 397, Mismatches: 64, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
76 12 0.03
77 22 0.06
78 161 0.41
79 117 0.29
80 49 0.12
81 36 0.09
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (78 bp):
CGTTATTTTGAGAGGATACTCCAACCCCGGTTTTATTTCTAAAACACCGATTTTTCACAATCGGG
GATACTCCAACCC
Found at i:1539 original size:159 final size:158
Alignment explanation
Indices: 1213--1653 Score: 464
Period size: 157 Copynumber: 2.8 Consensus size: 158
1203 AGAACACCAA
* *
1213 TTTTCTACAATCGGGGATACTCTAACCCCGTTA-TTTTGAGAGGATACTCCAA-CCTCGGTTTTA
1 TTTTC-ACAATC-AGGATACTCCAACCCCGTTATTTTTGAGAGGATACTCCAACCCT-GGTTTTA
* * * * * * * *
1276 TTTCTAAAATACTGAT-TTTCCACCATCGGGGATACTT-TAACCACGTTGGTTTC-G-AGAGGAT
63 TTTCTAAAACACCGATATTTTCACAATC-AGGATA-TTCCAACCCCGTT-ATTTCTGAAGAGGAT
* *
1337 ACTTCAACCCCGGTTTTATTTTCAAAACACTGAT
125 ACTTCAACCCCAGCTTTATTTTCAAAACACTGAT
1371 TTTTCACAATCAGGAATACTCCAA-CCCGTTATTTTTGAGAGGATACTCCAACCCTGGTTTTATT
1 TTTTCACAATCAGG-ATACTCCAACCCCGTTATTTTTGAGAGGATACTCCAACCCTGGTTTTATT
1435 TCTAAAACACCGATATTTTCACAATCATGGATATTCCAACCCCGTTATTTCTGAAGAGGATAC-T
65 TCTAAAACACCGATATTTTCACAATCA-GGATATTCCAACCCCGTTATTTCTGAAGAGGATACTT
1499 CAAACCCCAGCTTTA-TTTCTAAAACA-TCGAT
129 C-AACCCCAGCTTTATTTTC-AAAACACT-GAT
* * **
1530 TTTTCACAATCGAGGATACTCCAATCCCATTATTTTCAAG-GGATACTCCAACCC-GGATTTTAT
1 TTTTCACAATC-AGGATACTCCAACCCCGTTATTTTTGAGAGGATACTCCAACCCTGG-TTTTAT
* * *
1593 TTTTAAAACACCG--ATTTTCACCAA-CAGGATACTCCAACCCCCGTTATTTTTGAAG-GGATAC
64 TTCTAAAACACCGATATTTTCA-CAATCAGGATATTCCAA-CCCCGTTATTTCTGAAGAGGATAC
1654 ACTAACCTCG
Statistics
Matches: 249, Mismatches: 18, Indels: 34
0.83 0.06 0.11
Matches are distributed among these distances:
156 25 0.10
157 85 0.34
158 43 0.17
159 81 0.33
160 15 0.06
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (158 bp):
TTTTCACAATCAGGATACTCCAACCCCGTTATTTTTGAGAGGATACTCCAACCCTGGTTTTATTT
CTAAAACACCGATATTTTCACAATCAGGATATTCCAACCCCGTTATTTCTGAAGAGGATACTTCA
ACCCCAGCTTTATTTTCAAAACACTGAT
Found at i:3722 original size:4 final size:4
Alignment explanation
Indices: 3713--3780 Score: 113
Period size: 4 Copynumber: 17.2 Consensus size: 4
3703 TTGAGGTGTG
3713 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT CT-TT TA-T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT -TATT TATT
3760 TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT T
3781 TGTTTGTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
3 4 0.07
4 56 0.92
5 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Done.