Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2132
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: 28695
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1933 original size:21 final size:21
Alignment explanation
Indices: 1900--1949 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1890 TTGCAAGTTG
*
1900 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1922 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1943 AAATAAA
1 AAATAAA
1950 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5870 original size:13 final size:13
Alignment explanation
Indices: 5852--5889 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5842 CATTTTTCTT
5852 TGTATCGATACAA
1 TGTATCGATACAA
*
5865 TGTATCGATACAC
1 TGTATCGATACAA
5878 TGTATCGATACA
1 TGTATCGATACA
5890 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6044 original size:20 final size:20
Alignment explanation
Indices: 6001--6046 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
5991 AAATCTTTTG
6001 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
6022 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
6042 CAAAA
1 CAAAA
6047 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:9717 original size:78 final size:76
Alignment explanation
Indices: 9530--9757 Score: 305
Period size: 79 Copynumber: 2.9 Consensus size: 76
9520 TGGGGATAAC
* *
9530 AACGGGGCTGGAGTAT-CTGCGATTATGAAAAATTGGTGTTCTGGAAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCT-CGATTGTGAAAAATTGGTGTT-TGGAAATAAAAT-GGGGTTGGAG
*
9594 TATCCCTTTGAAAAT
63 TAT-CCTTTAAAAAT
*
9609 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTATGGAAATAAAACTGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTT-TGGAAATAAAA-TGGGGTTGGAGT
9674 ATCCTTTAAAAAT
64 ATCCTTTAAAAAT
* * *
9687 AACGGGGTTGGAGTATCCTTGATTGTGAAAAGATTGGTGTTTCAGAAATAAAATTGGGGTTGGAC
1 AACGGGGTTGGAGTATCCTCGATTGTGAAAA-ATTGGTGTTT-GGAAATAAAA-TGGGGTTGGAG
9752 TATCCT
63 TATCCT
9758 CGATTGTGAG
Statistics
Matches: 135, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
78 41 0.30
79 91 0.67
80 3 0.02
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (76 bp):
AACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTGGAAATAAAATGGGGTTGGAGTAT
CCTTTAAAAAT
Found at i:9772 original size:130 final size:130
Alignment explanation
Indices: 9611--9886 Score: 347
Period size: 130 Copynumber: 2.1 Consensus size: 130
9601 TTGAAAATAA
** * * *
9611 CGGGGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTATGGAAATAAAACTGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCTCGATTGTGAAAAATCAATATTATAGAAATAAAACCGGGGTTGGAGTAT
* * ** * * *
9676 -CCTTTAAAAATAACGGGGTTGGAGTATCCTTGATTGTGAAAAGATTGGTGTTTCAGAAATAAAA
66 CCCTTCAAAAATAACGGGATTGGAGTATCCCCGATTATGAAAA-ATTGATATTTCAGAAATAAAA
9740 T
130 T
* * * * *
9741 TGGGGTTGGACTATCCTCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCTCGATTGTGAAAAATCAATATTATAGAAATAAAACCGGGGTTGGAGTAT
* **
9806 CCCTTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATATTTTGGAAATAAAAT
66 CCCTTCAAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATATTTCAGAAATAAAAT
*
9871 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
9887 CTGAGATGAA
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
130 86 0.70
131 36 0.30
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCTCGATTGTGAAAAATCAATATTATAGAAATAAAACCGGGGTTGGAGTAT
CCCTTCAAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGATATTTCAGAAATAAAAT
Found at i:9807 original size:51 final size:52
Alignment explanation
Indices: 9689--9807 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 52
9679 TTAAAAATAA
* *** * *
9689 CGGGGTTGGAGTATCCTTGATTGTGAAAAGATTGGTGTTTCAGAAATAAAAT
1 CGGGGTTGGAGTATCCTCGATTGTGAAAAGATCAATATTTCAGAAATAAAAC
* * * * *
9741 TGGGGTTGGACTATCCTCGATTGTGAGAA-ATCAATATTTTAGAAATAAAGC
1 CGGGGTTGGAGTATCCTCGATTGTGAAAAGATCAATATTTCAGAAATAAAAC
9792 CGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
9808 CTTCGAAAAT
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
51 29 0.54
52 25 0.46
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (52 bp):
CGGGGTTGGAGTATCCTCGATTGTGAAAAGATCAATATTTCAGAAATAAAAC
Found at i:13643 original size:18 final size:18
Alignment explanation
Indices: 13622--13664 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
13612 CAAAAACAAA
* *
13622 AAAAATATGAAAAAATAG
1 AAAAATATAAAAAAAGAG
* *
13640 AAAAATTTAAAAAAAGAT
1 AAAAATATAAAAAAAGAG
13658 AAAAATA
1 AAAAATA
13665 AGACAACTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (18 bp):
AAAAATATAAAAAAAGAG
Found at i:17051 original size:18 final size:18
Alignment explanation
Indices: 17030--17065 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
17020 TGGTCACCAT
17030 CCTATGCTTTTGTGATTA
1 CCTATGCTTTTGTGATTA
17048 CCTATGCTTTTGTGATTA
1 CCTATGCTTTTGTGATTA
17066 ATAGTCCACA
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:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (18 bp):
CCTATGCTTTTGTGATTA
Found at i:20056 original size:16 final size:16
Alignment explanation
Indices: 20035--20065 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20025 ATTTTTGTTC
*
20035 AAATGTATTGATACAG
1 AAATGTATCGATACAG
20051 AAATGTATCGATACA
1 AAATGTATCGATACA
20066 AGGTCTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (16 bp):
AAATGTATCGATACAG
Found at i:20232 original size:50 final size:51
Alignment explanation
Indices: 20105--20233 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
20095 TTACTGATTA
* *
20105 TATCAATACATTATTCATTGTATCGATACATTATAGGTTTTTACCCAAATG
1 TATCGATACATTATTCATTGTATAGATACATTATAGGTTTTTACCCAAATG
* * * *
20156 TATCGATTCATTCTTCATTGTATAGATACATTATGGGTTTTTA-CCAGATG
1 TATCGATACATTATTCATTGTATAGATACATTATAGGTTTTTACCCAAATG
* * *
20206 TATTGATACATTATTTAATGTATAGATA
1 TATCGATACATTATTCATTGTATAGATA
20234 TATGCAAGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 29 0.43
51 38 0.57
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (51 bp):
TATCGATACATTATTCATTGTATAGATACATTATAGGTTTTTACCCAAATG
Found at i:21184 original size:20 final size:21
Alignment explanation
Indices: 21147--21185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21137 AGCCCATGTC
*
21147 CATGTATTTTGAGCTATGTTT
1 CATGCATTTTGAGCTATGTTT
*
21168 CATGCATTTTTAG-TATGT
1 CATGCATTTTGAGCTATGT
21186 CCAGCACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (21 bp):
CATGCATTTTGAGCTATGTTT
Found at i:24020 original size:21 final size:20
Alignment explanation
Indices: 23988--24039 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
23978 CAATCTCAAT
*
23988 CATTTGTTTATATTTTATAA
1 CATTTCTTTATATTTTATAA
24008 CAGTTTCTTTATATTTTATAA
1 CA-TTTCTTTATATTTTATAA
*
24029 CATTTGTTTAT
1 CATTTCTTTAT
24040 GATCATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.60
Consensus pattern (20 bp):
CATTTCTTTATATTTTATAA
Found at i:26040 original size:29 final size:29
Alignment explanation
Indices: 25997--26064 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
25987 TCTCACGTGA
*
25997 TAAAATAAAAATATTTTAGTAAAATGTTT
1 TAAAATAAAAATATTTTAATAAAATGTTT
* * **
26026 TAAAATAATATTATTTTAATAATTTGTTT
1 TAAAATAAAAATATTTTAATAAAATGTTT
*
26055 AAAAATAAAA
1 TAAAATAAAA
26065 GATAGTTTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
TAAAATAAAAATATTTTAATAAAATGTTT
Found at i:27121 original size:32 final size:33
Alignment explanation
Indices: 27080--27142 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
27070 TAGCCAAACT
27080 TGTATCGATACAC-AAAATATGTATCGATATAA
1 TGTATCGATACACAAAAATATGTATCGATATAA
27112 TGTATCGATACACAAAAAATATGTATCGATA
1 TGTATCGATACAC-AAAAATATGTATCGATA
27143 CATTGGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.45
34 16 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATATAA
Done.