Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_333 ID=scaffold_333-JGI_221_v2.0
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: 8350
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.30
Warning! 254 characters in sequence are not A, C, G, or T
Found at i:874 original size:44 final size:44
Alignment explanation
Indices: 824--1077 Score: 222
Period size: 44 Copynumber: 5.7 Consensus size: 44
814 TACTGGTGGC
* * *
824 GAAGTAGATCCAAGAAAGCAGATCTTTTCTTTATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * *** * *
868 GAAGTAGATCGAAGATACCAGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
*** * * *
913 GGAA-TAGATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGC
1 -GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
* * * * *
958 GAAGTAGATCGAAGAGAGCAAATATTATCTTTATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * * *
1002 AAAGCAGATTGAATAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
*
1046 GAAGTAGATTGAAGAAAGCAGATCTTGTCTTC
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
1078 CCATACTGGT
Statistics
Matches: 167, Mismatches: 40, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
44 97 0.58
45 67 0.40
46 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (44 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
Found at i:1024 original size:134 final size:133
Alignment explanation
Indices: 798--1105 Score: 420
Period size: 134 Copynumber: 2.3 Consensus size: 133
788 TGAATACAAA
* * * *
798 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTTTCTTTATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATATTATCTTTATGTATT
* * * * * *
863 GGCGTGAAGTAGATCGAAGATACCAGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCGAAG
66 GGCGTAAAGCAGATCGAAGAAAACAGATCTTGTCTCCACATACTGG-CGT-GAAGTAGATCGAAG
927 AAAGC
129 AAAGC
* *
932 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGCAAATATTATCTTTATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATATTATCTTTATGTATT
* * * ** * *
997 GGCGTAAAGCAGATTGAATAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGAA
66 GGCGTAAAGCAGATCGAAGAAAACAGATCTTGTCTCCACATACTGGCGTGAAGTAGATCGAAGAA
1062 AGC
131 AGC
1065 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGA
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGA
1106 TAACAGGTCC
Statistics
Matches: 154, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
132 3 0.02
133 56 0.36
134 95 0.62
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (133 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGAAAGCAAATATTATCTTTATGTATT
GGCGTAAAGCAGATCGAAGAAAACAGATCTTGTCTCCACATACTGGCGTGAAGTAGATCGAAGAA
AGC
Found at i:1111 original size:89 final size:90
Alignment explanation
Indices: 798--1194 Score: 335
Period size: 89 Copynumber: 4.5 Consensus size: 90
788 TGAATACAAA
* * * *
798 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTTTCTTTATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATT
* *
863 GG-CGTGAAGTAGATCGAAGATACC
66 GGTCGCGAAGTAGATCGAAGATAGC
* * ** *
887 AGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCGAAGAAAGCAGATCTTGTCTTCCCATAC
1 AGATCTTGTCTTCCCATACTGGTGG-CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATAT
* *
951 TGGTGGCGAAGTAGATCGAAGAGAGC
65 TGGTCGCGAAGTAGATCGAAGATAGC
* * * * * ** * * * * *
977 AAATATTATCTT--TAT-GTATTGGCGTAAAGCAGATTGAATAAAACAGATCTTGTCTTCATGTA
1 AGATCTTGTCTTCCCATACTGGTGGCG--AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATA
* * *
1039 TTGG-CGTGAAGTAGATTGAAGAAAGC
64 TTGGTCGCGAAGTAGATCGAAGATAGC
* * * *
1065 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATAA-CAGGTCCTG-CATTCCTATA
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATCTTGTC-TTCATATA
* * * *
1128 TCGGTAGCGAAGTGGATCGAATATA-C
64 TTGGTCGCGAAGTAGATCGAAGATAGC
* * *
1154 AGATCTTATCTTTCCATACTGGTGGTGAAGTAGATCGAAGA
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
1195 TACAAGTCTT
Statistics
Matches: 237, Mismatches: 60, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
86 1 0.00
87 4 0.02
88 32 0.14
89 147 0.62
90 47 0.20
91 6 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (90 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATT
GGTCGCGAAGTAGATCGAAGATAGC
Found at i:1208 original size:44 final size:45
Alignment explanation
Indices: 797--1204 Score: 209
Period size: 45 Copynumber: 9.2 Consensus size: 45
787 TTGAATACAA
* * * *
797 AAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGC
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATA-C
* *** * *
843 -AGATCTTTTCTTTATGTATTGG-CGTGAAGTAGATCGAAGATAC
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
* ** *
886 CAGATCTTGTCTCCCCATACTGGTGGTGGAA-TAGATCGAAGAAAGC
1 AAGATCTTGTCTTTCCATACTGGTGGT-GAAGTAGATCGAAGATA-C
* * *
932 -AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGC
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATA-C
* * *** * * * * * * *
977 AA-ATATTATCTTTATGTATTGG-CGTAAAGCAGATTGAATA-AA
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
* * * *
1019 ACAGATCTTGTC-TT-CATGTATTGG-CGTGAAGTAGATTGAAGAAAGC
1 A-AGATCTTGTCTTTCCA--TACTGGTGGTGAAGTAGATCGAAGATA-C
* * *
1065 -AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCAAAGATA-
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
* * * * * * *
1108 ACAGGTCCTG-CATTCCTATA-TCGGTAGCGAAGTGGATCGAATATAC
1 A-AGATCTTGTCTTTCC-ATACT-GGTGGTGAAGTAGATCGAAGATAC
*
1154 -AGATCTTATCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
1 AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
1198 AAG-TCTT
1 AAGATCTT
1205 ATCTCCCTGA
Statistics
Matches: 272, Mismatches: 67, Indels: 48
0.70 0.17 0.12
Matches are distributed among these distances:
42 1 0.00
43 5 0.02
44 125 0.46
45 134 0.49
46 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
AAGATCTTGTCTTTCCATACTGGTGGTGAAGTAGATCGAAGATAC
Found at i:5235 original size:20 final size:20
Alignment explanation
Indices: 5210--5249 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5200 TTCACCTCAT
5210 GCATCGCATCATATACATTA
1 GCATCGCATCATATACATTA
*
5230 GCATCGCATCATATGCATTA
1 GCATCGCATCATATACATTA
5250 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCGCATCATATACATTA
Found at i:8009 original size:48 final size:48
Alignment explanation
Indices: 7900--7991 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
7890 CTAAAAGGTG
*
7900 GGACCAAGGTGAAAGCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAA
1 GGACCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAA
*
7948 GGACCAGGGTGAAACCCTACAAAGGGAGC-C-TTGAGT-AAAAAAAA
1 GGACCAAGGTGAAACCCTACAAAGGG-GCGCTTTGAGTCAAAAAAAA
7992 GGAGAGGCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 8 0.20
47 6 0.15
48 25 0.61
49 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.27, T:0.12
Consensus pattern (48 bp):
GGACCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAA
Done.