Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_180 ID=scaffold_180-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: 10648
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.28
Warning! 759 characters in sequence are not A, C, G, or T
Found at i:6505 original size:44 final size:44
Alignment explanation
Indices: 6406--6506 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
6396 CTGACAGCGA
* *
6406 AGCAGATCGAAGA-CCCAGATCTTATCTCCCTTAGCAGCAGTGG
1 AGCAGATCGAAGATCACAGATCTTATCTCCCTAAGCAGCAGTGG
* * * * *
6449 AGTAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGCAGATCGAAGATCACAGATCTTATCTCCCTAAGCAGCAGTGG
6493 AGCAGATCGAAGAT
1 AGCAGATCGAAGAT
6507 GGCGAATCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 10 0.21
44 37 0.79
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
AGCAGATCGAAGATCACAGATCTTATCTCCCTAAGCAGCAGTGG
Found at i:6516 original size:44 final size:44
Alignment explanation
Indices: 6406--6520 Score: 126
Period size: 44 Copynumber: 2.6 Consensus size: 44
6396 CTGACAGCGA
** *
6406 AGCAGATCGAAGA-CCCAGATCTTATCTCCCTTAGCAGCAGTGG
1 AGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGCAGTGG
* * * * *
6449 AGTAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 AGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGCAGTGG
*
6493 AGCAGATCGAAGATGGC-GAATCTTATCT
1 AGCAGATCGAAGATGACAG-ATCTTATCT
6521 TCCCCAGGAG
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
43 11 0.19
44 47 0.81
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
AGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGCAGTGG
Found at i:6821 original size:100 final size:100
Alignment explanation
Indices: 6653--7038 Score: 434
Period size: 100 Copynumber: 3.9 Consensus size: 100
6643 TCCCAGGCAA
* * * * * ** * ** *
6653 TGCAGTTGAACAA-ATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 TGCAGTT-AAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGA
* **
6717 TTAAAGCCACAACGGTGAATCTTACTT-CCCAAGCGG
65 TTAAAGCCACAACGGCGAATCTTACTTCCCCAA-CAT
* ** * * ** *
6753 TGCAATGGAACAGATTAAAGCCACAACGGCGAATATTACTTCCCAAGCGGTGTAGTGGAACAGGT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGAT
*
6818 TAAAGCCACAACGGCGAATCTTACTTCCCCAAAAT
66 TAAAGCCACAACGGCGAATCTTACTTCCCCAACAT
* *
6853 TGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGATGTAGTGGAATAGAT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGAT
*
6918 TAAAGCCACAACGGCGAATCTTGCTTCCCCAACAT
66 TAAAGCCACAACGGCGAATCTTACTTCCCCAACAT
* * * *
6953 TGCAGTTAAAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGAT
1 TGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGAT
* * * *
7018 TGAAGCTACGACGGTGAATCT
66 TAAAGCCACAACGGCGAATCT
7039 CGTTTCCCTG
Statistics
Matches: 240, Mismatches: 44, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
99 2 0.01
100 233 0.97
101 5 0.02
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (100 bp):
TGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGAT
TAAAGCCACAACGGCGAATCTTACTTCCCCAACAT
Found at i:7007 original size:50 final size:50
Alignment explanation
Indices: 6642--7038 Score: 354
Period size: 50 Copynumber: 7.9 Consensus size: 50
6632 GAAACCAGTT
* * * * *
6642 TTCCCAGGCAATGCAGTTGAACAA-ATTAAAGCCACAATGGCGAATCTTGC
1 TTCCCAAGCAGTGCAG-TGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
* * * *
6692 TTCCC-CGACATTGCAGTTAAAAAGATTAAAGCCACAACGGTGAATCTTAC
1 TTCCCAAG-CAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
* * * * *
6742 TTCCCAAGCGGTGCAATGGAACAGATTAAAGCCACAACGGCGAATATTAC
1 TTCCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
* * * * *
6792 TTCCCAAGCGGTGTAGTGGAACAGGTTAAAGCCACAACGGCGAATCTTAC
1 TTCCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
* * *
6842 TTCCCCAA-AATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTAC
1 TT-CCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
** * * * *
6892 TTCCCTGGC-GATGTAGTGGAATAGATTAAAGCCACAACGGCGAATCTTGC
1 TTCCCAAGCAG-TGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
* * * *
6942 TTCCCCAA-CATTGCAGTTAAAAAGATTTAAGCCACAACGGTGAATCTTAC
1 TT-CCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
** * * * * * *
6992 TTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
1 TTCCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCT
7039 CGTTTCCCTG
Statistics
Matches: 282, Mismatches: 56, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
49 12 0.04
50 261 0.93
51 9 0.03
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (50 bp):
TTCCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTAC
Found at i:7018 original size:150 final size:150
Alignment explanation
Indices: 6642--7038 Score: 456
Period size: 150 Copynumber: 2.6 Consensus size: 150
6632 GAAACCAGTT
* * * * *
6642 TTCCCAGGCAATGCAGTTGAACAA-ATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGC
1 TTCCCAAGCAGTGCAGTT-AAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGC
*
6706 AGTTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTCCCAAGCGGTGCAATGGAACAGATTAA
65 AGTTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAATGGAACAGATTAA
6771 AGCCACAACGGCGAATATTAC
130 AGCCACAACGGCGAATATTAC
* * ** * * * *
6792 TTCCCAAGCGGTGTAGTGGAACAGGTTAAAGCCACAACGGCGAATCTTACTTCCCCAAAATTGCA
1 TTCCCAAGCAGTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCA
* ** * * *
6857 GTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGATGTAGTGGAATAGATTAAA
66 GTTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAATGGAACAGATTAAA
* *
6922 GCCACAACGGCGAATCTTGC
131 GCCACAACGGCGAATATTAC
* * * * * *
6942 TTCCCCAA-CATTGCAGTTAAAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGC
1 TT-CCCAAGCAGTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGC
** * * * *
7006 AGTGGAACAGATTGAAGCTACGACGGTGAATCT
65 AGTTAAAAAGATTAAAGCCACAACGGTGAATCT
7039 CGTTTCCCTG
Statistics
Matches: 202, Mismatches: 43, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
149 2 0.01
150 195 0.97
151 5 0.02
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (150 bp):
TTCCCAAGCAGTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCGACATTGCA
GTTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAATGGAACAGATTAAA
GCCACAACGGCGAATATTAC
Found at i:7046 original size:100 final size:100
Alignment explanation
Indices: 6764--7252 Score: 452
Period size: 100 Copynumber: 5.0 Consensus size: 100
6754 GCAATGGAAC
* ** * * * *
6764 AGATTAAAGCCACAACGGCGAATATTACTTCCCAAGCGGTGTAGTGGAACAGGTTAAAGCCACAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTAAAGCTACGA
** * *
6829 CGGCGAATCTTACTTCCCCAAAATTGCAGTTAAAA
66 CGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
* * *
6864 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGC-GATGTAGTGGAATAGATTAAAGCCACA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCAG-TGTAGTGGAACAGATTAAAGCTACG
* *
6928 ACGGCGAATCTTGCTTCCCCAACATTGCAGTTAAAA
65 ACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
* * * *
6964 AGATTTAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTACGA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTAAAGCTACGA
* * * *
7029 CGGTGAATCTCGTTTCCCTGACATTGC-----AAT
66 CGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
* ** ** * * *
7059 AGATTGAAGCC-CAACGGCGAATCTTACTTCTTTAACAGTGTAGAGGAACAGATTGAAGTTACGA
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTAAAGCTACGA
*
7123 CGGCGAATATTGTTTCCCCGACATT---G-T----
66 CGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
* * * * * * *
7150 AGATTGAAGCTACGACAGCGAATCTTACTTTCCTGAG-AGTGCAGTGGAATAGATTAAAGCTACG
1 AGATTAAAGCCACAACGGCGAATCTTACTTCCCTG-GCAGTGTAGTGGAACAGATTAAAGCTACG
* * * *
7214 ATGGCGAATCTTATTTCCCTGACATTGCAATTAAAA
65 ACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
7250 AGA
1 AGA
7253 GTGAAGCTGA
Statistics
Matches: 324, Mismatches: 51, Indels: 28
0.80 0.13 0.07
Matches are distributed among these distances:
91 10 0.03
92 61 0.19
94 66 0.20
95 12 0.04
96 1 0.00
99 1 0.00
100 172 0.53
101 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (100 bp):
AGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTAAAGCTACGA
CGGCGAATCTTGTTTCCCCGACATTGCAGTTAAAA
Found at i:7046 original size:150 final size:146
Alignment explanation
Indices: 6644--7088 Score: 369
Period size: 150 Copynumber: 3.0 Consensus size: 146
6634 AACCAGTTTT
* * * * * * * *
6644 CCCAGGCAATGCAGTTGAACAA-ATTAAAGCCACAATGGCGAATCTTGCTTCCCCGACATTGCAG
1 CCCAAGCAGTGCAG-TGAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCAAAAGTGCAG
* * * * *
6708 TTAAAAAGATTAAAGCCACAACGGTGAATCTTACTTCCCAAGCGGTG-CAATGGAACAGATTAAA
65 TGAAAAAGATTAAAGCCACAACGGCGAATCTCACTT-CC---C--TGACATTGGAATAGATTAAA
*
6772 GCCACAACGGCGAATATTACTT-
124 GCCACAACGGCGAATCTTACTTC
* * * * * *
6794 CCCAAGCGGTGTAGTGGAACAGGTTAAAGCCACAACGGCGAATCTTACTTCCCCAAAATTGCAGT
1 CCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCAAAAGTGCAGT
* * *
6859 TAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCTGGCGATGTAGTGGAATAGATTAAAGC
66 GAAAAAGATTAAAGCCACAACGGCGAATCTCACTTCCCTGAC-A--T--TGGAATAGATTAAAGC
*
6924 CACAACGGCGAATCTTGCTTC
126 CACAACGGCGAATCTTACTTC
* * * * ****
6945 CCCAA-CATTGCAGTTAAAAAGATTTAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTGCAGT
1 CCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCAAAAGTGCAGT
* * * * * * ** * *
7009 GGAACAGATTGAAGCTACGACGGTGAATCTCGTTTCCCTGACATTGCAATAGATTGAAGCC-CAA
66 GAAAAAGATTAAAGCCACAACGGCGAATCTCACTTCCCTGACATTGGAATAGATTAAAGCCACAA
7073 CGGCGAATCTTACTTC
131 CGGCGAATCTTACTTC
7089 TTTAACAGTG
Statistics
Matches: 242, Mismatches: 45, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
144 20 0.08
145 16 0.07
146 2 0.01
147 1 0.00
149 7 0.03
150 191 0.79
151 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (146 bp):
CCCAAGCAGTGCAGTGAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCCCCAAAAGTGCAGT
GAAAAAGATTAAAGCCACAACGGCGAATCTCACTTCCCTGACATTGGAATAGATTAAAGCCACAA
CGGCGAATCTTACTTC
Done.