Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_719 ID=scaffold_719-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: 4333
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Found at i:451 original size:132 final size:132
Alignment explanation
Indices: 213--513 Score: 439
Period size: 132 Copynumber: 2.3 Consensus size: 132
203 GCAACTGGAA
* *
213 GGAGATAAGACTT-ACAATCTTCAACCTATTCCACTGTTGACCAGGGAGATAGGATTACTGACTT
1 GGAGATAAGATTTGA-AATCTTCAACCTATTCCACTGTTGACCAGGGAGATAGAATTACTGACTT
*
277 CAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCT
65 CAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCT
342 TAG
130 TAG
* *
345 GGAGATAAGATTTGAAATCTTCAATCTATTCCACTGTTG-CTTAGGGA-AGTAGAATTACT-AGC
1 GGAGATAAGATTTGAAATCTTCAACCTATTCCACTGTTGAC-CAGGGAGA-TAGAATTACTGA-C
* * * *
407 TTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTT
63 TTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTG
472 CTTAG
128 CTTAG
* *
477 GGAGATAAGATCTGAGATCTTCAACCTATTCCACTGT
1 GGAGATAAGATTTGAAATCTTCAACCTATTCCACTGT
514 AAAGCCAAAG
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
131 3 0.02
132 149 0.97
133 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
GGAGATAAGATTTGAAATCTTCAACCTATTCCACTGTTGACCAGGGAGATAGAATTACTGACTTC
AATGTACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCTT
AG
Found at i:732 original size:44 final size:44
Alignment explanation
Indices: 681--1184 Score: 361
Period size: 44 Copynumber: 11.5 Consensus size: 44
671 CTGTCGGTGC
* * *
681 AGGAAGACAGGA-CTTGCTATTTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATC-TGCTATTTTCGATCTACTTCACACCAATAT
* * *
725 ATGAAGACAAGATCTGCT-TTCTTCGATCTACTTCGCTACCAGTAT
1 AGGAAGACAAGATCTGCTATT-TTCGATCTACTTCAC-ACCAATAT
* * * * * * *
770 GGGAAGATAAGATCT-CCATCTTCGATCCACTTC-CTTCCAATTT
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCAC-ACCAATAT
* * * *
813 AGGAAGACAGGACCTGCTATCTTT-GATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTAT-TTTCGATCTACTTCACACCAATAT
* * * *
857 ATGAAGACAAGATCTTCT-TTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATT-TTCGATCTACTTC-ACACCAATAT
* * *
902 AGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCAC-ACCAATAT
* * * *
946 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
*
990 ATGAAGACAAGATCTGC-ATCTTT-GATGC-ACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTAT-TTTCGAT-CTACTTCAC-ACCAATAT
* * * * * *
1033 AGGAAGACAGGACCTACTATCTTCGATCTACTTCACGCCAATAA
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
* * * *
1077 ATGAAGACAAGATCTG-TTTTCTTCGATCTACTCCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATT-TTCGATCTACTTC-ACACCAATAT
* * * * * *
1122 GGGAAGACATGATCTGC-ATCTTAGATCCACTTC-CTATCAATAT
1 AGGAAGACAAGATCTGCTATTTTCGATCTACTTCAC-ACCAATAT
* *
1165 AGGAAGACAGGACCTGCTAT
1 AGGAAGACAAGATCTGCTAT
1185 CTTCACTAAT
Statistics
Matches: 357, Mismatches: 78, Indels: 50
0.74 0.16 0.10
Matches are distributed among these distances:
42 3 0.01
43 79 0.22
44 193 0.54
45 82 0.23
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATTTTCGATCTACTTCACACCAATAT
Found at i:842 original size:132 final size:133
Alignment explanation
Indices: 681--1066 Score: 557
Period size: 132 Copynumber: 2.9 Consensus size: 133
671 CTGTCGGTGC
*
681 AGGAAGACAGGACTTGCTAT-TTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
1 AGGAAGACAGGACCTGCTATCTTT-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
* * *
745 CTTCGATCTACTTCGCTACCAGTATGGGAAGATAAGATCTCCATCTTCGATCCACTTC-CTTCCA
65 CTTCGATCTACTTCGCTACCAGTATAGGAAGACAAGATCTCCATCTTCGATCCACTTCGCTACCA
*
809 ATTT
130 ATAT
*
813 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTTTC
1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
* *
878 TTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTCGCTACCAGTATAGGAAGACAAGATCTCCATCTTCGATCCACTTCGCTACCAA
943 TAT
131 TAT
* * *
946 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-ATC
1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
* * * * * *
1010 TTTGATGC-ACTTC-CTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTC
66 TTCGAT-CTACTTCGCTACCAGTATAGGAAGACAAGATCT-CCATCTTCGATCCACTTC
1067 ACGCCAATAA
Statistics
Matches: 230, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
131 21 0.09
132 139 0.60
133 70 0.30
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (133 bp):
AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCGCTACCAGTATAGGAAGACAAGATCTCCATCTTCGATCCACTTCGCTACCAA
TAT
Found at i:1063 original size:220 final size:220
Alignment explanation
Indices: 718--1188 Score: 676
Period size: 220 Copynumber: 2.1 Consensus size: 220
708 CTACTTCACG
* * * * * * ** *
718 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCTACCAGTATGGGAAGATAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGAT
* * * *
783 CTCCATCTTCGATCCACTTCCTTCCAATTTAGGAAGACAGGACCTGCTATCTTTGATCTACTTCA
66 CTCCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCA
* * *
848 CGCCAATACATGAAGACAAGATCT-TCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAA
131 CGCCAATAAATGAAGACAAGATCTGT-TTTCTTCGATCTACTCCGCCACCAATATAGGAAGACAA
*
912 GATCTGCATCTTCGATCCACTTCGCTA
195 GATCTGCATCTTAGATCCACTTC-CTA
* *
939 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGAT
* * *
1003 CTGCATCTTTGATGCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCA
66 CTCCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCA
* *
1068 CGCCAATAAATGAAGACAAGATCTGTTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACATG
131 CGCCAATAAATGAAGACAAGATCTGTTTTCTTCGATCTACTCCGCCACCAATATAGGAAGACAAG
1133 ATCTGCATCTTAGATCCACTTCCTA
196 ATCTGCATCTTAGATCCACTTCCTA
* *
1158 TCAATATAGGAAGACAGGACCTGCTATCTTC
1 CCAATATAGGAAGACAGGATCTGCTATCTTC
1189 ACTAATCTGC
Statistics
Matches: 223, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
219 32 0.14
220 152 0.68
221 39 0.17
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (220 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGAT
CTCCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCA
CGCCAATAAATGAAGACAAGATCTGTTTTCTTCGATCTACTCCGCCACCAATATAGGAAGACAAG
ATCTGCATCTTAGATCCACTTCCTA
Found at i:1142 original size:132 final size:132
Alignment explanation
Indices: 681--1188 Score: 477
Period size: 132 Copynumber: 3.8 Consensus size: 132
671 CTGTCGGTGC
* * * * * *
681 AGGAAGACAGGA-CTTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
1 AGGAAGACAAGATC-TGCTATCTTCGATCTACTCCACACCAATACAGGAAGACAAGATCTGC-AT
* * * * * * * * *
745 CTTCGATCTACTTCGCTACCAGTATGGGAAGATAAGATCT-CCATCTTCGATCCACTTC-CTTCC
64 CTTAGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCCACTTCACTACC
**
808 AATTT
128 AATAA
* * * * * * * *
813 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTTCTTTC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCACACCAATACAGGAAGACAAGATCTGC-ATC
* * * * * * *
878 TTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCA
65 TTAGATCCACTTC-CTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCCACTTCACTACCA
*
942 ATAT
129 ATAA
* * * *
946 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCATCT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCCACACCAATACAGGAAGACAAGATCTGCATCT
* * * * *
1011 TTGATGCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCAC-GCCAAT
66 TAGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCCACTTCACTACCAAT
1075 AA
131 AA
* * * * ** *
1077 ATGAAGACAAGATCTGTTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACATGATCTGCATC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTCC-ACACCAATACAGGAAGACAAGATCTGCATC
*
1142 TTAGATCCACTTCCTATCAATATAGGAAGACAGGACCTGCTATCTTC
65 TTAGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTC
1189 ACTAATCTGC
Statistics
Matches: 332, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
131 57 0.17
132 207 0.62
133 68 0.20
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTCCACACCAATACAGGAAGACAAGATCTGCATCT
TAGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCCACTTCACTACCAAT
AA
Done.