Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_852 ID=scaffold_852-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: 3112
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Found at i:579 original size:132 final size:132
Alignment explanation
Indices: 242--3111 Score: 3644
Period size: 132 Copynumber: 21.6 Consensus size: 132
232 GATTTCTTTC
*
242 CACCCTTAAGCCAGTTAGTGGAGCAGATTCGAAAGAATGGTGGAAATCTTATTCTTCCCAATAAT
1 CACCC-TAAG-CAG-TAGTGGAGCAGA-TCG-AAG-ATGGT-G-AATCTTA-TCTTCCCAAT-AC
* * *
307 AGGTGGAGAAAGCAAGATTTTAAGCCATTAGTCACTAT-AACCTAAAGCAGTAGTGGAGTAAGCT
56 A-GTGGAG-AAGC-AGA-TTTAAGCCATTAGTC-CTATCACCCT-AAGCAGTAGTGGAGTAGGTT
371 GAAGATTGCAGATTCTGT
115 GAAGATTGCAGATTCTGT
* *
389 CACCCTAAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAACACAGTGGAGTA
1 CACCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* * * * * * *
454 -CTAGATTAAAGCCATTAGTCCTATCTCCCTGAGTAGTAGTGGAGTAGGCTAAAGATAGCAGATT
65 GC-AGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
*
518 TTGT
129 CTGT
* * * * * *
522 CACCCTAAGCAGTAGTGGAGTAGGTCGAATATGATTAACCTTATCTTCCCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* ** * * *
587 -ATGAATTAAGCCATTAGTCCTATCTTCCTAAGCCA-TAGTGCAGCT-GGTAGAAGACTGCAGAT
66 CA-GATTTAAGCCATTAGTCCTATCACCCTAAG-CAGTAGTGGAG-TAGGTTGAAGATTGCAGAT
*
649 TCTAT
128 TCTGT
* * * * * *
654 CACCCTAAACAGTAGTGAAGCAGATCGAATATGATGAATCTTATTTTCCCAATTCAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * *
719 CAGATTTAAGCCATTACTCCTATCAACCTAAGCAGTAGTAGAGTAGGTTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
784 GT
131 GT
* *
786 CACCCTAA-CAGTAGTGGAACAAATCGAAGATGGTGAATCTTATCTT-CCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * * *
849 CAGATTTAAGTCATTAGTCCTATCACCCGAAGTAGTAGTAGAGTAGGTTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
*
914 AT
131 GT
* * *
916 TACCATAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* *
981 CAGATTTAAGCCATTAGT-CTAATCTCCCTAAGCAGTAGTGGAGTCA-GTTGAAGATTACAGATT
66 CAGATTTAAGCCATTAGTCCT-ATCACCCTAAGCAGTAGTGGAGT-AGGTTGAAGATTGCAGATT
1044 CTGT
129 CTGT
* * * * *
1048 CACCCTAAGCAGTAGTGTAGGAGAT-TAAGAATGATGAATCTTATTTTCCCAATACAGTGGAGAA
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAG-ATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* * * *
1112 GCAGATTTAAGCCATTAGTCCTATCACCCAAAGCAGTACTAGAGTAGGTTAAAGATTGCAGATTC
65 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
1177 TGT
130 TGT
* *
1180 CACCCTAAGCAGTAGTGGAGCAGATCGACGATGGTGAATCCTATCTTCCCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* *
1245 TAGATTTAAGCCATTAGTCCTATCACCCTAAGTAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
1310 GT
131 GT
* *
1312 CACCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCTAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * * *
1377 AAGATTTAAGCCATTAGTCCAATCATCCTAAGCAGTAGAGGAGTAGGTTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
1442 GT
131 GT
* * * * * * *
1444 CACCCTAAGAAGTATTGGAGTACATCGAAGATGGTGAATATTATTTTCCCAATACAGTGGAGAAA
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * * *
1509 CAGATTTAAGCCATTAGTCCTATCACCCAAAGCAGTACTAGAGTAGGTTAAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
1574 GT
131 GT
* *
1576 CACCCTAAGCAGTAGTGGAGCAGATCGACGATGGTGAATCCTATCTTCCCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * *
1641 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTCGGTTGAAGATTACAGATACT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
1706 GT
131 GT
* *
1708 CACCCTAAGCAGTAGT-GATGCAGATCGAAGATGGTGAATCTTATTTTCCCCATACAGTGGAGAA
1 CACCCTAAGCAGTAGTGGA-GCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1772 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
65 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
1837 TGT
130 TGT
* * * * *
1840 CACCCTAAGCAGTAGTGGAGCGGATCGAAGATGGTGATTCTTATCTTCTCAAGATAGTGGA-AAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA-
* * * *
1904 GCAGATTTCAGCCATTAGT-CTAATCTCCCTAAGCAGTGGTGGAGTAGGTTGAAGATTACAGATT
65 GCAGATTTAAGCCATTAGTCCT-ATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1968 CTGT
129 CTGT
* * * * ** ** * * * * * * * *
1972 CACCCTAAGCAGTATTGGTGTAGGTTAAAGATTGCAGATTC-TGTC-ACCCTAA-GCATTAGTGG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAATCTTATCTTCCC-AATACAGTGGAGA
* ** ** * * * * *
2034 AGTAGATCGAAGATAGTGAATCTTATCTTCCC-AATACAGTAGTGGAGTAGGTTGAAGATT-CTA
64 AGCAGATTTAAGCCA-TTAGTCCTATC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAGATTGC-A
*
2097 GTTTCTGT
125 GATTCTGT
* * * *
2105 CACTCTAAGCAGTAGTGGAGCAGATCGAATATAGTGAATCTTATCTTCCCAATATAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * *
2170 CAGATTTAAGCCATTAGTCCTATCACCCTAAGTAGAAGTGGAGTAGGCTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
2235 GT
131 GT
* * * * *
2237 CACCCTGAA-CAGTAGTGAAGCAGATCGAATATGATGAATCTTATTTTCCCAATTCAGTGGAGAA
1 CACCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* *
2301 GCAGATTTAAGCCATCAGTCCTATCACCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTC
65 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
2366 TGT
130 TGT
* * *
2369 CACCCTAAGCATTAGTGAAGCAAATCGAAGATGGTGAATCTTATCTT-CCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
** * * * *
2433 TGGATTTAAGTCATTAGTCCTATCACCCTAAGTAGTCGTGGAGTAGGTTGAAGATTGCATATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
2498 GT
131 GT
* * *
2500 CACCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAATACGGTGGAGATG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * * * *
2565 CAGATTTAAGCCATTAGTCCAATCACCCTAAGTATTAGTGGAATAGGCTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
2630 GT
131 GT
* * * * *
2632 CACCCTAAGCAGTAGTGGAGTAGGTCGAATATGATGAACCTTATCTTCCCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* ** *
2697 CAGAATTAAGCCATTAGTCCTATCTTCCTAAGCCA-TAGTGGAGTTGGTTGAAGATTGCAGATTC
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAG-CAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
2761 TGT
130 TGT
* * * * *
2764 CACCCTGAA-CAGTAGTGAAGCAGATCGAATATGATGAATCTTATTTTCCCAATTCAGTGGAGAA
1 CACCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* *
2828 GCAGATTTAAGCCATTAATCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGACTGCAGATTC
65 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC
2893 TGT
130 TGT
*
2896 CACCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGAATCTTATCTT-CCAATACAGTGGAGAAG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
* * * * * *
2960 CATATTTAAGTCGTTAGTCGTATCACCCTAAGTAGTAGTTGAGTAGGTTGAAGATTGCAGATTCT
66 CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
3025 GT
131 GT
* * * *
3027 AACCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAATACGGTGGAGATG
1 CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
3092 CAGATTTAAGCCATTAGTCC
66 CAGATTTAAGCCATTAGTCC
3112 A
Statistics
Matches: 2367, Mismatches: 314, Indels: 99
0.85 0.11 0.04
Matches are distributed among these distances:
130 83 0.04
131 339 0.14
132 1707 0.72
133 139 0.06
134 34 0.01
135 4 0.00
136 1 0.00
137 6 0.00
138 2 0.00
139 9 0.00
140 7 0.00
141 1 0.00
142 5 0.00
143 3 0.00
144 3 0.00
145 12 0.01
146 4 0.00
147 8 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
CACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAG
CAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCT
GT
Found at i:1845 original size:44 final size:44
Alignment explanation
Indices: 1795--2124 Score: 209
Period size: 44 Copynumber: 7.5 Consensus size: 44
1785 ATTAGTCCTA
1795 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * **
1839 TCACCCTAAGCAGTAGTGGAG-CGGATCGAAGA-TGGTGATTCT-
1 TCACCCTAAGCAGTAGTGGAGTAGG-TTGAAGATTGCAGATTCTG
* * * * *
1881 T-ATCTTCTCAAG-A-TAGTGGA--AAG--GCAGATTTCAGCCATTAGTCTAA
1 TCA-C-CCT-AAGCAGTAGTGGAGTAGGTTGAAGATTGCAG--A-T--TCT-G
* * *
1927 TCTCCCTAAGCAGTGGTGGAGTAGGTTGAAGATTACAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * *
1971 TCACCCTAAGCAGTATTGGTGTAGGTTAAAGATTGCAGATTCTG
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
* * * * * * *
2015 TCACCCTAAGCATTAGTGGAGTAGATCGAAGATAG-TGAATCTTA
1 TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTC-TG
* * *
2059 TCTTCCC-AATACAGTAGTGGAGTAGGTTGAAGATT-CTAGTTTCTG
1 TC-ACCCTAA-GCAGTAGTGGAGTAGGTTGAAGATTGC-AGATTCTG
*
2104 TCACTCTAAGCAGTAGTGGAG
1 TCACCCTAAGCAGTAGTGGAG
2125 CAGATCGAAT
Statistics
Matches: 214, Mismatches: 47, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
38 4 0.02
39 2 0.01
41 3 0.01
42 10 0.05
43 17 0.08
44 120 0.56
45 34 0.16
46 11 0.05
47 1 0.00
48 3 0.01
50 9 0.04
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
TCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTG
Found at i:2104 original size:89 final size:89
Alignment explanation
Indices: 1805--2158 Score: 289
Period size: 89 Copynumber: 4.0 Consensus size: 89
1795 TCACCCTAAG
* *
1805 CAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCGGATCGAAG
1 CAGTAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAG
* * *
1870 ATGGTGATTCTTATCTTCTC-A-A
66 ATAGTGAATCTTATCTTCCCAATA
* * * * * * * * *
1892 GA-TAGTGGA-AAGG---CAGATTTCAGCCATTAGTCTAATCTCCCTAAGCAGTGGTGGAGTAGG
1 CAGTAGTGGAGTAGGTTAAAGATTGCAG--A-T--TCT-GTCACCCTAAGCAGTAGTGGAGCAGA
* ** * * * *
1952 TTGAAGATTACAGATTC-TGTC-ACCCTAA-G
60 TCGAAGA-TAGTGAATCTTATCTTCCC-AATA
* * * *
1981 CAGTATTGGTGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCATTAGTGGAGTAGATCGAAG
1 CAGTAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAG
2046 ATAGTGAATCTTATCTTCCCAATA
66 ATAGTGAATCTTATCTTCCCAATA
* * *
2070 CAGTAGTGGAGTAGGTTGAAGATT-CTAGTTTCTGTCACTCTAAGCAGTAGTGGAGCAGATCGAA
1 CAGTAGTGGAGTAGGTTAAAGATTGC-AGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAA
*
2134 TATAGTGAATCTTATCTTCCCAATA
65 GATAGTGAATCTTATCTTCCCAATA
2159 TAGTGGAGAA
Statistics
Matches: 205, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
82 8 0.04
84 1 0.00
85 4 0.02
86 7 0.03
87 12 0.06
88 62 0.30
89 93 0.45
90 5 0.02
91 4 0.02
92 1 0.00
94 8 0.04
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (89 bp):
CAGTAGTGGAGTAGGTTAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAG
ATAGTGAATCTTATCTTCCCAATA
Done.