Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2077
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: 22258
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Found at i:1192 original size:68 final size:67
Alignment explanation
Indices: 1146--1303 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 67
1136 ATACTATATA
1146 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
1211 AAT
65 AAT
1214 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
1279 AAT
65 AAT
* *
1282 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
1304 TCCAAGTGAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:1377 original size:66 final size:67
Alignment explanation
Indices: 1180--1377 Score: 192
Period size: 68 Copynumber: 2.9 Consensus size: 67
1170 GGGATGTATC
* * *
1180 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATA-C--GGGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
* *
1242 TGTATC-
62 AGGA-CA
*
1248 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
1313 AGGACA
62 AGGACA
* *
1319 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
1378 TTCACCATGT
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
66 24 0.21
67 9 0.08
68 55 0.47
69 1 0.01
70 1 0.01
71 26 0.22
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:8682 original size:68 final size:64
Alignment explanation
Indices: 8610--8789 Score: 222
Period size: 66 Copynumber: 2.7 Consensus size: 64
8600 CATCATGTGT
* *
8610 ACAAGA-AGGCTACGAGATACTATATAGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
1 ACAAGAGA-GCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGAT--GGGATGTATCCCAT
8674 GTAG
61 GTAG
8678 ACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATGGGATGTATCCCATGTA
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATGGGATGTATCCCATGTA
8743 G
64 G
* *
8744 ACAAGAGAGCTACGTGAGAGATAAA--TAGCTAGGTCGCATGAGTGAT
1 ACAAGAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGAT
8790 TCCAAGTGAA
Statistics
Matches: 105, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
64 19 0.18
66 43 0.41
68 33 0.31
69 5 0.05
70 5 0.05
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGAGATAAATGTAGCTAGGTCACATGTGTGATGGGATGTATCCCATGTAG
Found at i:8753 original size:66 final size:66
Alignment explanation
Indices: 8635--8789 Score: 260
Period size: 66 Copynumber: 2.3 Consensus size: 66
8625 GATACTATAT
8635 AGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGAT
1 AGTAGCTAGGTCACATGTGTGATA-GGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGAT
8700 AA
65 AA
8702 ATGTAGCTAGGTCACATGTGTGAT-GGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGAT
1 A-GTAGCTAGGTCACATGTGTGATAGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGAT
8766 AA
65 AA
* *
8768 A-TAGCTAGGTCGCATGAGTGAT
1 AGTAGCTAGGTCACATGTGTGAT
8790 TCCAAGTGAA
Statistics
Matches: 85, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
64 19 0.22
66 43 0.51
67 1 0.01
68 22 0.26
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (66 bp):
AGTAGCTAGGTCACATGTGTGATAGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
A
Found at i:8863 original size:66 final size:66
Alignment explanation
Indices: 8736--8863 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
8726 GGGATGTATC
*
8736 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATAGCTAGGTCGCATGAGTGATTCCAAGTGAAG
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATAGCTAGGTCGCATGAGTGATACCAAGTGAAG
8801 GACA
63 GACA
* * *
8805 CCATGTAGACAAGAGAGCTAC-GAGATAAATCGGCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-AGCTAGGTCGCATGAGTGATACCAAGTG
8864 TTCACCATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
65 9 0.17
66 24 0.44
69 21 0.39
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (66 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATAGCTAGGTCGCATGAGTGATACCAAGTGAAGGAC
A
Found at i:10762 original size:10 final size:10
Alignment explanation
Indices: 10747--10773 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10737 TAAGTTGAAG
10747 TTGAGCTGAT
1 TTGAGCTGAT
10757 TTGAGCTGAT
1 TTGAGCTGAT
10767 TTGAGCT
1 TTGAGCT
10774 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:11128 original size:20 final size:20
Alignment explanation
Indices: 11105--11158 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
11095 AGTTTTACCC
*
11105 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
11125 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
11145 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
11159 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:11140 original size:30 final size:30
Alignment explanation
Indices: 11105--11178 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
11095 AGTTTTACCC
11105 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
11135 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
11165 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
11179 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:11168 original size:20 final size:20
Alignment explanation
Indices: 11105--11169 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
11095 AGTTTTACCC
* * * *
11105 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
11125 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
11144 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
11165 AGCTC
1 AGCTC
11170 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:12821 original size:10 final size:10
Alignment explanation
Indices: 12808--12846 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
12798 AAAAAGGAGC
12808 AAAAAAGAAA
1 AAAAAAGAAA
12818 AAAAAAGTAAA
1 AAAAAAG-AAA
12829 AAAAGAAGAAA
1 AAAA-AAGAAA
12840 AAAAAAG
1 AAAAAAG
12847 TGAAAAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:12845 original size:22 final size:21
Alignment explanation
Indices: 12808--12852 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
12798 AAAAAGGAGC
12808 AAAAAAGAAAAAAAAAGTAAA
1 AAAAAAGAAAAAAAAAGTAAA
*
12829 AAAAGAAGAAAAAAAAAGTGAA
1 AAAA-AAGAAAAAAAAAGTAAA
12851 AA
1 AA
12853 GTCTTGCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAGTAAA
Found at i:13878 original size:6 final size:6
Alignment explanation
Indices: 13858--13953 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
13848 AAAGAAATTG
* ** * **
13858 AAAG-A AAACAA AAAGAA AAAGAA ATTGCA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** * * *
13905 AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAG
13954 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 22, Indels: 7
0.69 0.23 0.07
Matches are distributed among these distances:
5 3 0.05
6 51 0.78
7 7 0.11
8 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:13907 original size:18 final size:18
Alignment explanation
Indices: 13858--13908 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
13848 AAAGAAATTG
*
13858 AAAGAAAAC-AAAAAGAA
1 AAAGAAATCGAAAAAGAA
* *
13875 AAAGAAATTGCAAAAGAA
1 AAAGAAATCGAAAAAGAA
13893 AAAGAAATCGAAAAAG
1 AAAGAAATCGAAAAAG
13909 TGAGAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.73, C:0.06, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAGAAATCGAAAAAGAA
Found at i:13935 original size:14 final size:13
Alignment explanation
Indices: 13914--13951 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
13904 AAAAGTGAGA
13914 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
13926 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
13941 GAAAAAGAAAA
1 GAAAAAGAAAA
13952 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:13965 original size:21 final size:21
Alignment explanation
Indices: 13915--13965 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
13905 AAAGTGAGAG
*
13915 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
13936 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
13957 AAAAAGAAA
1 AAAAAGAAA
13966 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:14005 original size:33 final size:33
Alignment explanation
Indices: 13968--14030 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
13958 AAAAGAAATT
13968 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
14001 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
14031 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:15829 original size:20 final size:20
Alignment explanation
Indices: 15806--15859 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
15796 AGTTTTTCCC
*
15806 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
15826 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
15846 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15860 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:15841 original size:30 final size:30
Alignment explanation
Indices: 15806--15879 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
15796 AGTTTTTCCC
15806 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
15836 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
15866 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
15880 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:15869 original size:20 final size:20
Alignment explanation
Indices: 15806--15870 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
15796 AGTTTTTCCC
* * * *
15806 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
15826 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
15845 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
15866 AGCTC
1 AGCTC
15871 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.