Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3015
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: 26248
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:1735 original size:39 final size:39
Alignment explanation
Indices: 1631--1847 Score: 275
Period size: 39 Copynumber: 5.6 Consensus size: 39
1621 CGGATGATAA
* * **
1631 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAAT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTAAT
* * *
1670 TCGGGCTAAGT--CGAAGGCATTAGTGCGAGCTACTAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
1707 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
1745 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-TTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
1782 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AT
1823 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1848 AGCTAGTGGC
Statistics
Matches: 157, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
36 1 0.01
37 51 0.32
38 26 0.17
39 52 0.33
40 26 0.17
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:1761 original size:76 final size:76
Alignment explanation
Indices: 1630--1845 Score: 276
Period size: 76 Copynumber: 2.8 Consensus size: 76
1620 TCGGATGATA
* * ** *
1630 ACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTAATTCGGGCTAAGT-CGAAGGCATTAG
1 ACCGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTTACT-ATCCGGGCTAAGTCCGAAGGCATTAG
1693 TGCGAGCTACTAAT
64 TGCGAGCTA-TAAT
* *
1707 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCCGGGCTAAGTCCGAAGGCATTTGTG
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATCCGGGCTAAGTCCGAAGGCATTAGTG
* *
1771 CGAGTTATTAT
66 CGAGCTATAAT
1782 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT--CCGGGCTAAGT-CCGAAGGCATT
1846 TGAGCTAGTG
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
75 15 0.12
76 85 0.69
77 2 0.02
78 11 0.09
79 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (76 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATCCGGGCTAAGTCCGAAGGCATTAGTG
CGAGCTATAAT
Found at i:1880 original size:39 final size:40
Alignment explanation
Indices: 1627--1880 Score: 163
Period size: 39 Copynumber: 6.6 Consensus size: 40
1617 TGTTCGGATG
* * *
1627 ATAACCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAACTCCCGAAG-GCATTTGAGCAAGTGACT
** * * * *
1667 A-ATTCGGGCTAAGT--CGAAGGCATTAGTGCGAGCT-ACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAG-TGACT
* * * * *
1704 A-ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAGTGACT
* * * * *
1743 AT--CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAGTGACT
* * *
1780 AT-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAGTGACT
* * *
1819 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCT
1 ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAGTGACT
*
1859 ATATCC-GGCTAAACT-CCGAAGG
1 ATAACCGGGCT-AACTCCCGAAGG
1881 TACTTGGTTT
Statistics
Matches: 187, Mismatches: 17, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
37 52 0.28
38 26 0.14
39 67 0.36
40 42 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAACTCCCGAAGGCATTTGAGCAAGTGACT
Found at i:9828 original size:39 final size:39
Alignment explanation
Indices: 9693--9916 Score: 306
Period size: 40 Copynumber: 5.7 Consensus size: 39
9683 TCGGATGATA
** * **
9693 ACCGGGCTAAGTCCCG-AGAGCATTTGAACTAGTGGCTAAT
1 ACCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACT-AT
* * *
9733 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
9772 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
1 A-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
9812 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
*
9851 ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT
1 ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
9890 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -ACCGGGCTAAGTCCCGAAGGCATTTG
9917 AGCTAGTGGC
Statistics
Matches: 167, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
39 77 0.46
40 88 0.53
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT
Found at i:9915 original size:79 final size:79
Alignment explanation
Indices: 9694--9916 Score: 306
Period size: 79 Copynumber: 2.8 Consensus size: 79
9684 CGGATGATAA
** * ** * *
9694 CCGGGCTAAGTCCCG-AGAGCATTTGAACTAGTGGCTAATTCCGGGCTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCAAGTTACT-ATACCGGGCTAAGTCCCGAAGGCATTT
9758 GTGCGAGCTACTATAT
64 GTGCGAGCTACTATAT
* *
9774 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
* *
9839 GCGAGTTATTATA-
66 GCGAGCTACTATAT
9852 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTAT-ACCGGGCTAAGTCCCGAAGGCATTTG
9917 AGCTAGTGGC
Statistics
Matches: 129, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
78 36 0.28
79 64 0.50
80 27 0.21
81 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATACCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGCTACTATAT
Found at i:9947 original size:118 final size:118
Alignment explanation
Indices: 9734--9949 Score: 308
Period size: 118 Copynumber: 1.8 Consensus size: 118
9724 GTGGCTAATT
* *
9734 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
* * * *
9799 TGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA
66 AGCGAGTGACTATACCGGGCTAACTCCCGAAGGCATTTGTGCGAGTTATTATA
* *
9852 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
* * * *
9917 AGCTAGTGGCTATATCTGGCTAAACT-CCGAAGG
66 AGCGAGTGACTATACCGGGCT-AACTCCCGAAGG
9950 TACTTGGTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 82 0.96
119 3 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (118 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCAAGCTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
AGCGAGTGACTATACCGGGCTAACTCCCGAAGGCATTTGTGCGAGTTATTATA
Found at i:9949 original size:79 final size:77
Alignment explanation
Indices: 9734--9939 Score: 286
Period size: 79 Copynumber: 2.6 Consensus size: 77
9724 GTGGCTAATT
*
9734 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT-CGGGCTAAGTCCCGAAGGCATTTG
* *
9799 TGCGAGTTATTATA
64 TGCAAGTTACTATA
* *
9813 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCGGGCTAAGTCCCGAAGGCATTTGT
9878 GCAAGTTACTATAA
65 GCAAGTTACTAT-A
* * * *
9892 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATATCTGGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATATCGGGCTAA
9940 ACTCCGAAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
78 36 0.32
79 77 0.68
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (77 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCGGGCTAAGTCCCGAAGGCATTTGTG
CAAGTTACTATA
Found at i:21114 original size:18 final size:18
Alignment explanation
Indices: 21093--21131 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21083 TCTCATCAAG
21093 TTTTTAAGATTCATTTAT
1 TTTTTAAGATTCATTTAT
*
21111 TTTTTAAGATTCATTTGT
1 TTTTTAAGATTCATTTAT
21129 TTT
1 TTT
21132 CCTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (18 bp):
TTTTTAAGATTCATTTAT
Done.