Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_174 ID=scaffold_174-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: 10060
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Found at i:5548 original size:15 final size:16
Alignment explanation
Indices: 5510--5549 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5500 AATATTTAAA
*
5510 AAAATGATG-AAAATG
1 AAAATGATGAAAAAAG
5525 AAAATGATGAAAAAAG
1 AAAATGATGAAAAAAG
5541 AAAA-GATGA
1 AAAATGATGA
5550 GAGAAGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (16 bp):
AAAATGATGAAAAAAG
Found at i:7923 original size:44 final size:44
Alignment explanation
Indices: 7862--8605 Score: 370
Period size: 44 Copynumber: 16.7 Consensus size: 44
7852 GAAGATGGAA
* * *
7862 AATCTTATCTCCCTAAAGTTACAGTGGAGTAAATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
* * * * * **
7906 AATCCTATCTCCCTAAAGTTGCAATGGAACGAATTAAAGTTACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-AT
* * * * * * *
7950 AGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAG-AAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA-T
* * * * * * * *
7994 AAGTCTTATC-CCTCTGAAATTACAGTGGGGTAGACTGAAGATGGC--G
1 AA-TCTTATCTCC-CTGAAGTTGCAGTGGAGCA-AATTAA-A-GCCAAT
* * * *
8040 AATCTTATCTCCCTAAAGTTGCAGTGTAGCAGATTAAATCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
* * * **
8084 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGAATTAAAGTTACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-AT
* * * *
8128 AATCTTGTCTCCTTGAAGTTACAGTGAAG-AAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAA-ATTAAAGCCAAT
* * * * * *
8172 AGTCTTATCCCCCTGAAGTTGCAGTAGG-GCAGACTGAAGATGGC--G
1 AATCTTATCTCCCTGAAGTTGCAGT-GGAGCA-AATTAA-A-GCCAAT
*
8217 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
* * * **
8261 AATCTTATCTCCTTGAAGTTGCAATGGAGCGAATTAAAGTTACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-AT
* * * ** **
8305 AATCTTATCTCCCTGAAGTTACAGTGGAGCAAACTAATGATACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
*** * *
8349 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA-ACGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
* * * * * * *
8392 GAATCCTATAC-CTCTGAAGTTACAGTAGG-TCAGATTAAATCTACTATAAC
1 -AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAAATTAAAGC--C---AAT
* * * * * *
8442 AAGTCTTATCTCCTTGAGGTTGCAGTGGAGTAGACTGAAGATGGC-A-
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCA-AATTAA-A-GCCAAT
8488 AATCTTATCTCCCTGAAGTTGCAGTGGAG-AAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAA-ATTAAAGCCAAT
* * * * * * *
8532 AGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
* *
8576 AATCCTATCTCCCTAAAGTTGCAGTGGAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC
8606 TGATTAAAAC
Statistics
Matches: 517, Mismatches: 139, Indels: 88
0.69 0.19 0.12
Matches are distributed among these distances:
42 6 0.01
43 9 0.02
44 355 0.69
45 104 0.20
46 9 0.02
47 5 0.01
48 1 0.00
49 5 0.01
50 18 0.03
51 4 0.01
52 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAAT
Found at i:8147 original size:88 final size:88
Alignment explanation
Indices: 7861--8613 Score: 511
Period size: 88 Copynumber: 8.4 Consensus size: 88
7851 AGAAGATGGA
* * * *
7861 AAATCTTATCTCCCTAAAGTTACAGTGGAGTAAATTAAAGCCAATAATCCTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
* *
7926 GCAATGGAACGAATTAAAGTTAC
66 GCAGTGGAGCGAATTAAAGTTAC
* * * * * * *
7949 AAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAAG-AAAGCAAGTCTTATC-CCTCTGAA
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAA-TAA-TCTTATCTCC-CT-AA
* * * **
8012 A-TTACAGTGG-G-GTAGACTGAAGATGGC
62 AGTTGCAGTGGAGCG-A-ATTAAAG-TTAC
* * * * * *
8039 GAATCTTATCTCCCTAAAGTTGCAGTGTAGCAGATTAAATCCAATAATCCTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
8104 GCAGTGGAGCGAATTAAAGTTAC
66 GCAGTGGAGCGAATTAAAGTTAC
* * * * * * *
8127 AAATCTTGTCTCCTTGAAGTTACAGTGAAGAAGATTAAAGCCAATAGTCTTATCCCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
* * **
8192 GCAGTAGG-GC-AGACTGAAGATGGC
66 GCAGT-GGAGCGA-ATTAAAG-TTAC
* * * *
8216 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCTTGAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
*
8281 GCAATGGAGCGAATTAAAGTTAC
66 GCAGTGGAGCGAATTAAAGTTAC
* * * ** ** *
8304 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAAACTAATGATACCAATCTTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
* * *** *
8369 GCAGTGGAGTGGATTAAAACGAT
66 GCAGTGGAGCGAATTAAAGTTAC
* * * * * *
8392 GAATCCTATAC-CTCTGAAGTTACAGTAGG-TCAGATTAAATCTACTATAACAAGTCTTATCTCC
1 AAATCTTAT-CTCCCTGAAGTTACAGT-GGAGCAGATTAAAGC--C---AATAA-TCTTATCTCC
* * * * * * **
8455 TTGAGGTTGCAGTGGAG-TAGACTGAAGATGGC
58 CTAAAGTTGCAGTGGAGCGA-ATTAAAG-TTAC
* * * * * *
8487 AAATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAATAGTCTTATCTTCTTGAAGTT
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
* *
8552 GCAGTGGAGC-AGATTGAAGCTAC
66 GCAGTGGAGCGA-ATTAAAGTTAC
* * * * *
8575 TAATCCTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAA
1 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA
8614 ACGATGAATC
Statistics
Matches: 513, Mismatches: 122, Indels: 60
0.74 0.18 0.09
Matches are distributed among these distances:
87 4 0.01
88 244 0.48
89 148 0.29
90 47 0.09
91 3 0.01
93 5 0.01
94 32 0.06
95 30 0.06
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTT
GCAGTGGAGCGAATTAAAGTTAC
Found at i:8236 original size:133 final size:130
Alignment explanation
Indices: 7860--8605 Score: 423
Period size: 133 Copynumber: 5.6 Consensus size: 130
7850 AAGAAGATGG
* * * * * * *
7860 AAAATCTTATCTCCCTAAAGTTACAGTGGAGTAAATTAAAGCCAATAATCCTATCTCCCTAAAGT
1 AAAATCTTATCTCCTTGAAGTTACAGTGAAG-AGATTAAAGCCAA-AGTCTTATCTCCCTGAAGT
* * * * ** *
7925 TGCAATGGAAC-GAATTAA-AGTTACAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACTGAA
64 TGCAGTGGAGCAGACTGAAGA-TGGCAAATCTTATCTCCCTGAAGTTGCAGT-G-G-AG-C-GAA
*
7988 -GAAAG-C
123 TTAAAGCC
* * ** * * * *
7994 -AAGTCTTATC-CCTCTGAAATTACAGTGGGGTAGACTGAAGATGGCGAA-TCTTATCTCCCTAA
1 AAAATCTTATCTCCT-TGAAGTTACAGTGAAG-AGA-TTAA-A-GCCAAAGTCTTATCTCCCTGA
* * * * *
8056 AGTTGCAGTGTAGCAGA-TTAA-AT-CCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGAAT
61 AGTTGCAGTGGAGCAGACTGAAGATGGC-A-AATCTTATCTCCCTGAAGTTGCAGTGGAGCGAAT
**
8118 TAAAGTT
124 TAAAGCC
* *
8125 ACAAATCTTGTCTCCTTGAAGTTACAGTGAAGAAGATTAAAGCCAATAGTCTTATCCCCCTGAAG
1 A-AAATCTTATCTCCTTGAAGTTACAGTGAAG-AGATTAAAGCCAA-AGTCTTATCTCCCTGAAG
*
8190 TTGCAGTAGG-GCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTA
63 TTGCAGT-GGAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGA-ATTA
8253 AAGCC
126 AAGCC
* * * * *
8258 AATAATCTTATCTCCTTGAAGTTGCAATGGAGCGAATTAAAGTTACAAA-TCTTATCTCCCTGAA
1 AA-AATCTTATCTCCTTGAAGTTACAGTGAAGAG-ATTAAAG--CCAAAGTCTTATCTCCCTGAA
* * * * * *
8322 GTTACAGTGGAGCAAACT-AATGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTA
62 GTTGCAGTGGAGCAGACTGAA-GATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTA
* *
8385 AAACG
126 AAGCC
* * * * *
8390 ATGAATCCTAT-ACCTCTGAAGTTACAGT-AGGTCAGATTAAATCTACTATAACAAGTCTTATCT
1 A-AAATCTTATCTCCT-TGAAGTTACAGTGAAG--AGATTAAAGC--C----A-AAGTCTTATCT
* * *
8453 CCTTGAGGTTGCAGTGGAGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAG-
55 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
*
8517 AAGATTAAAGCC
120 GA-ATTAAAGCC
* * * * * * * *
8529 AATAGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAA-TCCTATCTCCCTAAA
1 AA-AATCTTATCTCCTTGAAGTTACAGTGAAG-AGATTAAAGC--CAAAGTCTTATCTCCCTGAA
8593 GTTGCAGTGGAGC
62 GTTGCAGTGGAGC
8606 TGATTAAAAC
Statistics
Matches: 478, Mismatches: 90, Indels: 89
0.73 0.14 0.14
Matches are distributed among these distances:
129 3 0.01
130 8 0.02
131 8 0.02
132 102 0.21
133 178 0.37
134 62 0.13
135 8 0.02
136 4 0.01
137 2 0.00
138 31 0.06
139 69 0.14
140 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (130 bp):
AAAATCTTATCTCCTTGAAGTTACAGTGAAGAGATTAAAGCCAAAGTCTTATCTCCCTGAAGTTG
CAGTGGAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAGCC
Found at i:8357 original size:177 final size:176
Alignment explanation
Indices: 7852--8373 Score: 686
Period size: 177 Copynumber: 2.9 Consensus size: 176
7842 GTGGATTGAA
** * * *
7852 GAAGATGGAAAATCTTATCTCCCTAAAGTTACAGTGGAGTAAATTAAAGCCAATAATCCTATCTC
1 GAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
* * * * *
7917 CCTAAAGTTGCAATGGAACGAATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAG
66 CCTAAAGTTGCAATGGAGCGAATTAAAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAA
* * * * * *
7982 ACTGAAGAAAGCAAGTCTTATCCCTCTGAAATTACAGTGGGGTAGACT
131 ACT-AAGAAAACAA-TCTTATCCCCCTGAAGTTGCAGTAGGGCAGACT
* *
8030 GAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGTAGCAGATTAAATCCAATAATCCTATCTC
1 GAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
* * * *
8095 CCTAAAGTTGCAGTGGAGCGAATTAAAGTTACAAATCTTGTCTCCTTGAAGTTACAGTGAAG-AA
66 CCTAAAGTTGCAATGGAGCGAATTAAAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAA
* ** * *
8159 GATTAAAGCCAATAGTCTTATCCCCCTGAAGTTGCAGTAGGGCAGACT
131 -ACT-AAGAAAACAATCTTATCCCCCTGAAGTTGCAGTAGGGCAGACT
* *
8207 GAAGATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTC
1 GAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
* *
8272 CTTGAAGTTGCAATGGAGCGAATTAAAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAA
66 CCTAAAGTTGCAATGGAGCGAATTAAAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAA
* * *
8337 ACTAATGATACCAATCTTATCTCCCTGAAGTTGCAGT
131 ACTAA-GAAAACAATCTTATCCCCCTGAAGTTGCAGT
8374 GGAGTGGATT
Statistics
Matches: 296, Mismatches: 45, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
176 2 0.01
177 173 0.58
178 121 0.41
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (176 bp):
GAAGATGGCGAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTC
CCTAAAGTTGCAATGGAGCGAATTAAAGTTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCAA
ACTAAGAAAACAATCTTATCCCCCTGAAGTTGCAGTAGGGCAGACT
Found at i:8624 original size:44 final size:43
Alignment explanation
Indices: 8488--8644 Score: 136
Period size: 44 Copynumber: 3.6 Consensus size: 43
8478 GAAGATGGCA
* * *
8488 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ACAAT
* * * * * * *
8532 AGTCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC-AAT
* * *
8576 AATCCTATCTCCCTAAAGTTGCAGTGGAGCTGATTAAAACGAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAAT
**
8619 GAATCCTATAC-CTTTGAAGTTGCAGT
1 -AATCCTAT-CTCCCTGAAGTTGCAGT
8645 AGGTCGGATT
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
43 2 0.02
44 87 0.97
45 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACAAT
Done.