Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2313
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: 40040
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3853 original size:26 final size:26
Alignment explanation
Indices: 3817--3868 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3807 GAAATGTGAA
*
3817 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
3843 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
3869 GTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:3917 original size:102 final size:104
Alignment explanation
Indices: 3741--3962 Score: 360
Period size: 102 Copynumber: 2.2 Consensus size: 104
3731 TGTATATAAA
** * *
3741 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
3806 TGAAATGTGAAA-GGGGTTGCTATGTGCTGATT-CCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
3843 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
3907 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
3947 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
3963 GATATCCATT
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
102 69 0.62
103 21 0.19
104 21 0.19
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:4014 original size:71 final size:72
Alignment explanation
Indices: 3881--4032 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
3871 TCATTGGTGG
* *
3881 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
3946 GAGGGGT
66 GAGGGGT
***
3953 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4017 GAGGGGT
66 GAGGGGT
4024 TGCTAAGTG
1 TGCTAAGTG
4033 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:7531 original size:6 final size:6
Alignment explanation
Indices: 7494--7523 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7484 AGTTCAGATT
7494 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
7524 AACAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:7939 original size:54 final size:54
Alignment explanation
Indices: 7857--7969 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
7847 TTTTTTATTA
7857 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
7911 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
7965 AATTT
1 AATTT
7970 CTTTGTTATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.45
Consensus pattern (54 bp):
AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
Found at i:8863 original size:14 final size:14
Alignment explanation
Indices: 8844--8878 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
8834 ATCGAGCGGA
8844 GCAAATCAAAGATG
1 GCAAATCAAAGATG
*
8858 GCAAATCGAAGATG
1 GCAAATCAAAGATG
8872 GCAAATC
1 GCAAATC
8879 TTATCTCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (14 bp):
GCAAATCAAAGATG
Found at i:9135 original size:163 final size:163
Alignment explanation
Indices: 8865--9164 Score: 494
Period size: 163 Copynumber: 1.8 Consensus size: 163
8855 ATGGCAAATC
* *
8865 GAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCGATAATCCTATCCC
1 GAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGATTAAAGCCGATAATCCTATCCC
* ** *
8930 CTTGAAGTTGCAGTGGAGCGGATCACAACCTTGGATCTTATCTCTTTGAAGTTGCAGAGAGCAGA
66 CTTGAAGTTGCAGTGGAGCGGATCAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
8995 TCCCATCCTCCTGAAGTTGCAGTGGGGCAGACT
131 TCCCATCCTCCTGAAGTTGCAGTGGGGCAGACT
* *
9028 GAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAGCCGATAATCCTATCTC
1 GAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGATTAAAGCCGATAATCCTATC-C
*
9093 CC-TGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
65 CCTTGAAGTTGCAGTGGAGCGGATCAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAG
*
9157 ATCGCATC
130 ATCCCATC
9165 TAGTCTTATC
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
163 123 0.98
164 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (163 bp):
GAAGATGGCAAATCTTATCTCCCTAAAGTTGCAGAGGAGCAGATTAAAGCCGATAATCCTATCCC
CTTGAAGTTGCAGTGGAGCGGATCAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGA
TCCCATCCTCCTGAAGTTGCAGTGGGGCAGACT
Found at i:9216 original size:84 final size:86
Alignment explanation
Indices: 9004--9230 Score: 239
Period size: 84 Copynumber: 2.6 Consensus size: 86
8994 ATCCCATCCT
* * *
9004 CCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTTGCAGAGGAGCA
1 CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTCTCTGAAGTTGCAGAGGAGCA
*
9069 GATTAAAGCCGATAATCCTATCTC
64 GATT-AAGCAGATAATCCTATCTC
* * * *
9093 CCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTTATCTCTCTGAAGTTGCAGA-GAGCA
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCTTATCTCTCTGAAGTTGCAGAGGAGCA
* ** * *
9156 GA-T-CGCATCTAGTCTTATCTC
64 GATTAAGCAGATAATCCTATCTC
9177 CCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTG
1 CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTCT-CTGAAGTTG
9231 TAGTGAGGCA
Statistics
Matches: 116, Mismatches: 17, Indels: 15
0.78 0.11 0.10
Matches are distributed among these distances:
83 2 0.02
84 52 0.45
85 2 0.02
86 5 0.04
87 10 0.09
88 24 0.21
89 21 0.18
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (86 bp):
CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCTCTGAAGTTGCAGAGGAGCAGA
TTAAGCAGATAATCCTATCTC
Found at i:9225 original size:44 final size:43
Alignment explanation
Indices: 9004--9249 Score: 184
Period size: 44 Copynumber: 5.7 Consensus size: 43
8994 ATCCCATCCT
* *
9004 CCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTC
* * * *
9049 CCTGAAGTTGCAGAGGAGCAGA-TTA-AAGCCGATAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCTTATCTC
* * * *
9093 CCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCTTATCTC
* * * * * *
9137 TCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCTTATCTC
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTC
9177 CCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-C
1 CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTC
*
9220 TCCTGAAGTTGTAGT-GAGGCAGACTGAAGA
1 -CCTGAAGTTGCAGTGGA-GCAGACT-AAGA
9250 TTTCAGATCT
Statistics
Matches: 160, Mismatches: 28, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
40 21 0.13
41 10 0.06
42 6 0.04
43 13 0.08
44 83 0.52
45 27 0.17
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTC
Found at i:10976 original size:28 final size:27
Alignment explanation
Indices: 10922--10982 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
10912 TATATATTTT
* *
10922 TATATTTTTCTTATGTTCATAAGTGTA
1 TATATTTTTCTTATATTCATAAATGTA
*
10949 T-TATTTTTTTTATATTCATATTAATGTA
1 TATATTTTTCTTATATTCATA--AATGTA
10977 TATATT
1 TATATT
10983 ATGTGCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 17 0.61
27 1 0.04
28 6 0.21
29 4 0.14
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.61
Consensus pattern (27 bp):
TATATTTTTCTTATATTCATAAATGTA
Found at i:11178 original size:15 final size:15
Alignment explanation
Indices: 11155--11187 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11145 GTGATATGTC
11155 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
11170 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
11185 ATT
1 ATT
11188 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:11633 original size:98 final size:99
Alignment explanation
Indices: 11462--11659 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 99
11452 TTAAAAATAA
* * * *
11462 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATTGTGCCCCTAACATATTGGGTGTGATTT
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCCTAACATATTGGGTGTGATTT
11527 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
11561 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTG-GCCTAACGTATTGGGTGTGATTT
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCCTAACATATTGGGTGTGATTT
11625 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
11659 T
1 T
11660 TTTACTGTAC
Statistics
Matches: 93, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 56 0.60
99 37 0.40
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (99 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCCTAACATATTGGGTGTGATTT
CTTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:15628 original size:11 final size:11
Alignment explanation
Indices: 15612--15639 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
15602 TGTGTGTTCA
15612 TCTTCTCAATT
1 TCTTCTCAATT
15623 TCTTCTCAATT
1 TCTTCTCAATT
15634 TCTTCT
1 TCTTCT
15640 GCTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (11 bp):
TCTTCTCAATT
Found at i:18352 original size:20 final size:21
Alignment explanation
Indices: 18320--18358 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
18310 TGGTTTTGGA
18320 AAATAAATAATTA-GTTTTAT
1 AAATAAATAATTATGTTTTAT
18340 AAATAGAAT-ATTATGTTTT
1 AAATA-AATAATTATGTTTT
18359 TAATTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
AAATAAATAATTATGTTTTAT
Found at i:22287 original size:40 final size:40
Alignment explanation
Indices: 22232--22312 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22222 AAGATTGGAA
22232 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
22272 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
22312 T
1 T
22313 CTGAGTGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (40 bp):
TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
Done.