Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_175 ID=scaffold_175-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: 10010
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:4556 original size:14 final size:13
Alignment explanation
Indices: 4526--4562 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
4516 TTTGAGTCAA
4526 GAAAA-TGAAAAT
1 GAAAATTGAAAAT
4538 G-AAATTGAGAAAT
1 GAAAATTGA-AAAT
4551 GAAAATTGAAAA
1 GAAAATTGAAAA
4563 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.14
12 4 0.18
13 8 0.36
14 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (13 bp):
GAAAATTGAAAAT
Found at i:4741 original size:41 final size:42
Alignment explanation
Indices: 4658--4758 Score: 177
Period size: 41 Copynumber: 2.4 Consensus size: 42
4648 GCTCAAATAT
4658 TGATCAGAATGGGGCATGAAGTGATCAGAGCAACTCGTATCA
1 TGATCAGAATGGGGCATGAAGTGATCAGAGCAACTCGTATCA
4700 TGATCAGAATGGGGCATGAAGTGAT-AGAGCAACTCGTATCA
1 TGATCAGAATGGGGCATGAAGTGATCAGAGCAACTCGTATCA
* *
4741 TGATCAGATTGAGGCATG
1 TGATCAGAATGGGGCATG
4759 TGGTAATCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 32 0.56
42 25 0.44
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.23
Consensus pattern (42 bp):
TGATCAGAATGGGGCATGAAGTGATCAGAGCAACTCGTATCA
Found at i:6278 original size:88 final size:87
Alignment explanation
Indices: 5838--6408 Score: 804
Period size: 87 Copynumber: 6.5 Consensus size: 87
5828 CAGATCAGTG
* *
5838 AAGATAGCAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAGCAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
5903 TCGGTTGCAGTGGAGCGGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
*
5925 AAGATAGCAGATCTTGCCTTCCTGCTTTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
*
5990 TCAGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * *
6012 AAGATAGCAAATCTTGCCTTCTTGCATTGACAGCGAAGCAGATCGAAAATAAAGGCTCGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
6077 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* *
6099 AAGATAGCAAATCTTGCCTTCCTGCATTGACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
6164 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCTGGTTA
* * * * * * **
6186 AAGATAACAGATCTTGCCTTCCTACATAGATAGCGAAGTAGATCGAAGACCCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA-AACAAAGCCTTGCCTCC
*
6251 CTCGGTTGCAGTGGAG-TAGGTTA
65 ATCGGTTGCAGTGGAGCT-GGTTA
* * * * *
6274 AAGATAGCAGATCTTGCCTTCCTACATCGACGGCGAAGCAGATCGAAGACACAAGCCTTTCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCC
* *
6339 CTCGGTTGTAGTGGAG-TAGGTTA
65 ATCGGTTGCAGTGGAGCT-GGTTA
* ** *
6362 AAGATAGCAGATCTTACCTTCCTGCGCTGGCAGCGAAGCAGATCGAA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAA
6409 GATACCAGCC
Statistics
Matches: 435, Mismatches: 46, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
87 286 0.66
88 149 0.34
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCA
TCGGTTGCAGTGGAGCTGGTTA
Found at i:6619 original size:90 final size:90
Alignment explanation
Indices: 6505--7237 Score: 743
Period size: 90 Copynumber: 8.2 Consensus size: 90
6495 CATCAGGTCT
*
6505 TATCTCCCTGAGATTATAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
* * *
6570 CCGAGCATATTGAAGCTAATAATCC
66 CGGAGCAGATTGAAGCTAGTAATCC
* * *
6595 TATCTCACTGAGATTACAGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
*
6660 CGGAGCAGATTGAAGCTAGTAATTC
66 CGGAGCAGATTGAAGCTAGTAATCC
* * ** * ** * * *
6685 TATCTCCCTGAGATTACAGTGGAGTGGA-TTAAAACAATAAAGGATTTTATCTCTCT-AAAGTTA
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAA-ATTTCA-GATCTTATCTCCCTGAGA-TTA
** ** * * * * *
6748 CAGTAGAGTTGATCGCATC-AG--GTCT
63 CAGCGGAGCAGATTGAAGCTAGTAATCC
* *
6773 TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAA
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
*
6838 CGGAGTAGATTGAAGCTAGTAATCC
66 CGGAGCAGATTGAAGCTAGTAATCC
* * * * *
6863 TATCTCACTGAGATTACAGTGGAATAGATCGAAGAATTTCAGATCTTGTCCCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
* *
6928 CGAAGCAGATTGAAGCTAGTAATTC
66 CGGAGCAGATTGAAGCTAGTAATCC
* *** ** * ** * *
6953 TATCTCCCTGAAATTACAGTGGAGCGGA-TTAAAACAATAAAGGATCTTACCTCTCTGA-AGTTA
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAA-ATTTCA-GATCTTATCTCCCTGAGA-TTA
** * * * * * * *
7016 CAGTAGAGTATATCGCATC-AG--CTCT
63 CAGCGGAGCAGATTGAAGCTAGTAATCC
* *
7041 TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCTCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
* *
7106 CGGAGCATATTAAAGCTAGTAATCC
66 CGGAGCAGATTGAAGCTAGTAATCC
*
7131 TATCTCCCTGAGATTATAGTGGAATAGACC-AAAGAATTTCAGATCTTATCTCCCTGAGATTACA
1 TATCTCCCTGAGATTACAGTGGAATAGACCGAAA-AATTTCAGATCTTATCTCCCTGAGATTACA
*
7195 TCGGAGCAGATTGAAGCTAGTAATCC
65 GCGGAGCAGATTGAAGCTAGTAATCC
7221 TATCT-CCTCGAGATTAC
1 TATCTCCCT-GAGATTAC
7238 GATGGAGTGG
Statistics
Matches: 514, Mismatches: 111, Indels: 36
0.78 0.17 0.05
Matches are distributed among these distances:
87 57 0.11
88 65 0.13
89 17 0.03
90 322 0.63
91 53 0.10
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (90 bp):
TATCTCCCTGAGATTACAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
CGGAGCAGATTGAAGCTAGTAATCC
Found at i:6852 original size:268 final size:268
Alignment explanation
Indices: 6420--7307 Score: 1339
Period size: 268 Copynumber: 3.3 Consensus size: 268
6410 ATACCAGCCT
* * *
6420 TATCTCCTTGAGATTACAGTAGAGCGGATT--AA-AATAAAAGATCTTATCTCTCTGAAGTTACA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAATAAAGGATCTTATCTCTCTGAAGTTACA
* * * * *
6482 GTAGAATAGATCACATCAGGTCTTATCTCCCTGAGATTATAGTGGAATAGACCGAAAAATTTCAG
66 GTAGAGTTGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG
* *
6547 ATCTTATCTCCCTGAGATTACAGCCGAGCATATTGAAGCTAATAATCCTATCTCACTGAGATTAC
131 ATCTTATCTCCCTGAGATTACAGCGGAGCATATTGAAGCTAGTAATCCTATCTCACTGAGATTAC
6612 AGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
196 AGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
6677 AGTAATTC
261 AGTAATTC
* * *
6685 TATCTCCCTGAGATTACAGTGGAGTGGATTAAAACAATAAAGGATTTTATCTCTCTAAAGTTACA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAATAAAGGATCTTATCTCTCTGAAGTTACA
6750 GTAGAGTTGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG
66 GTAGAGTTGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG
* * *
6815 ATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAGCTAGTAATCCTATCTCACTGAGATTAC
131 ATCTTATCTCCCTGAGATTACAGCGGAGCATATTGAAGCTAGTAATCCTATCTCACTGAGATTAC
* * *
6880 AGTGGAATAGATCGAAGAATTTCAGATCTTGTCCCCCTGAGATTACAGCGAAGCAGATTGAAGCT
196 AGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
6945 AGTAATTC
261 AGTAATTC
* *
6953 TATCTCCCTGAAATTACAGTGGAGCGGATTAAAACAATAAAGGATCTTACCTCTCTGAAGTTACA
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAATAAAGGATCTTATCTCTCTGAAGTTACA
*
7018 GTAGAGTAT-ATCGCATCAGCTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
66 GTAGAGT-TGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCA
* * *
7082 GATCTTATCTCTCTGAGATTACAGCGGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTA
130 GATCTTATCTCCCTGAGATTACAGCGGAGCATATTGAAGCTAGTAATCCTATCTCACTGAGATTA
* * * *
7147 TAGTGGAATAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGC
195 CAGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC
*
7212 TAGTAATCC
260 TAGTAATTC
* * *
7221 TATCT-CCTCGAGATTAC-GATGGAGTGGATTAAAA-AA-ATA-GATCTTATCTCTCTGAGGTAG
1 TATCTCCCT-GAGATTACAG-TGGAGCGGATTAAAACAATAAAGGATCTTATCTCTCTGAAGT--
* *
7281 TA-A-TAGAGTAGGTCGCATCAGGTCTTA
62 TACAGTAGAGTTGATCGCATCAGGTCTTA
7308 CTTCTCTGGC
Statistics
Matches: 567, Mismatches: 47, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
265 64 0.11
266 3 0.01
267 10 0.02
268 489 0.86
269 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (268 bp):
TATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAATAAAGGATCTTATCTCTCTGAAGTTACA
GTAGAGTTGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAG
ATCTTATCTCCCTGAGATTACAGCGGAGCATATTGAAGCTAGTAATCCTATCTCACTGAGATTAC
AGTGGAATAGATCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT
AGTAATTC
Found at i:7265 original size:178 final size:179
Alignment explanation
Indices: 6505--7276 Score: 701
Period size: 178 Copynumber: 4.3 Consensus size: 179
6495 CATCAGGTCT
* * ** *
6505 TATCTCCCTGAGATTATAGTGGAATAGACCGAAAAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGA-TGAAAAAAATCAGATCTTATCTCTCTGAGATTACAG
* * * * * *
6570 CCGAGCATATTGAAGCTAATAATCCTATCTCACTGAGATTACAGTGGAATAGATCGAAGAATTTC
65 CGGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTC
* *
6635 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATTC
130 AGATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCC
* * * * * * *
6685 TATCTCCCTGAGATTACAGTGGAGTGGATTAAAACAATAAAGGATTTTATCTCTCT-AAAGTTAC
1 TATCTCCCTGAGATTACAGTGGAATAGATGAAAAAAAT-CA-GATCTTATCTCTCTGAGA-TTAC
** * ** * * *
6749 AGTAGAG--T-TGATCGC-A-TCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAA
63 AGCGGAGCATATTAAAGCTAGT-A-ATCCTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAA
* *
6809 TTTCAGATCTTATCTCCCTGAGATTACAACGGAGTAGATTGAAGCTAGTAATCC
126 TTTCAGATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCC
* * ** * * *
6863 TATCTCACTGAGATTACAGTGGAATAGATCGAAGAATTTCAGATCTTGTCCCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGAT-GAAAAAAATCAGATCTTATCTCTCTGAGATTACAG
* * * * * *** ** * *
6928 CGAAGCAGATTGAAGCTAGTAATTCTATCTCCCTGAAATTACAGTGGAGCGGATTAAA-ACAATA
65 CGGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCAAAGA-ATTT
* * * * * * * * * * *
6992 AAGGATCTTACCTCTCTGA-AGTTACAGT-AGAGTATATCGCATC-AG--CTCT
129 CA-GATCTTATCTCCCTGAGA-TTACA-TCGGAGCAGATTGAAGCTAGTAATCC
* * **
7041 TATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAGATCTTATCTCTCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAATAGA-TGAAAAAAATCAGATCTTATCTCTCTGAGATTACAG
*
7106 CGGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTATAGTGGAATAGACCAAAGAATTTC
65 CGGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTC
7171 AGATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCC
130 AGATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCC
* * *
7221 TATCT-CCTCGAGATTAC-GATGGAGTGGATTAAAAAAAT-AGATCTTATCTCTCTGAG
1 TATCTCCCT-GAGATTACAG-TGGAATAGATGAAAAAAATCAGATCTTATCTCTCTGAG
7277 GTAGTAATAG
Statistics
Matches: 461, Mismatches: 106, Indels: 52
0.74 0.17 0.08
Matches are distributed among these distances:
176 2 0.00
177 48 0.10
178 251 0.54
179 21 0.05
180 86 0.19
181 52 0.11
182 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (179 bp):
TATCTCCCTGAGATTACAGTGGAATAGATGAAAAAAATCAGATCTTATCTCTCTGAGATTACAGC
GGAGCATATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCA
GATCTTATCTCCCTGAGATTACATCGGAGCAGATTGAAGCTAGTAATCC
Found at i:9195 original size:27 final size:25
Alignment explanation
Indices: 9133--9226 Score: 98
Period size: 25 Copynumber: 3.6 Consensus size: 25
9123 ATTAAATTCG
* * *
9133 TATATGATTATTTTAACTTGCTTTA
1 TATATTATTATTTTAAGTTACTTTA
*
9158 TAGATTATTATTTTAAGTTACTTTA
1 TATATTATTATTTTAAGTTACTTTA
* *
9183 TATATCATTTTATTTTAAGTTATTTTA
1 TATAT--TATTATTTTAAGTTACTTTA
*
9210 CATATTACTTATTTTAA
1 TATATTA-TTATTTTAA
9227 AATTAACCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
25 26 0.46
26 9 0.16
27 22 0.39
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.57
Consensus pattern (25 bp):
TATATTATTATTTTAAGTTACTTTA
Done.