Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_741 ID=scaffold_741-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: 14217
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.08
Warning! 10077 characters in sequence are not A, C, G, or T
Found at i:162 original size:88 final size:88
Alignment explanation
Indices: 3--1477 Score: 2165
Period size: 88 Copynumber: 16.8 Consensus size: 88
1 TT
* * * * *
3 GATCTTTTGTCTTC-ACCAGCTCCATCACAACCGAGAGAGGCAAGGTTCGTGTCTTCGATCTGAT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
*
67 TCACTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* *
90 GATCTGTTGTCTTCAACCAGCTCTATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
155 TCGCTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * * *
178 GATCTTTTGTCTTCAACCAGCACCATCACAACCGAGAGAGGTAAGGTTTGTGCCTTCAACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
* * *
243 TCACTGTCAATCCAGGAACGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* *
266 GATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
**
331 TCTTTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * * *
354 GATCTGCTGTCTTTAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAATCTGAT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
*
419 TTGCTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * * * *
442 GATCTGTTGTCTTCAACCAGCTCTATCACAACCGAGGGAGGTAAGGTTTGTGTCTTCAATCTGCA
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
507 TCGCTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * * *
530 GATCTTTTGTCTTTAACCAGCTCCATCATAACCGAGAGAGGCAAGGTTTGTGTCTTTGAA-CTGC
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC-TTCAACCTGC
* * *
594 TACGCTGTCAATACAGGAAGGCAG
65 TTCGCTGTCAATGCAGGAAGGCAA
* * *
618 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAAGTTTGTGTCTTCGACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
* *
683 TCGCTGTCAATGCAGGTACGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
*
706 GATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG-ATAGGTTTGTGTCTTCAACCTGC
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCAACCTGC
* * *
770 CTCACTGTCAATGCACGAAGGC-A
65 TTCGCTGTCAATGCAGGAAGGCAA
793 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
*
858 TCGCTGTCAATGAAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * * **
881 GATCCGTTGTCTTCAACAAGCTCAATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
946 TCGCTGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* *
969 GATCTGTTGTCTTCAACCAGCTCCATCACAACTGAGAGAGGCAAGGTTTGTGTCTTTGAA-CTGC
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTC-TTCAACCTGC
* * *
1033 TACGCTGTCAATACAGGAAGGCAG
65 TTCGCTGTCAATGCAGGAAGGCAA
* * * *
1057 GATCTGTTGTCTTTAACCAGCTCCATCACAACCGAGGGAGGCAAAGTTTGTGTCTTCGACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
1122 TCGCTGTCAATGCAGGAACGG-AGA
66 TCGCTGTCAATGCAGGAA-GGCA-A
* *
1146 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG-ATAGGTTTGTGTATTCGACCTGC
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCAACCTGC
* *
1210 CTCGCTATCAATGCAGGAAGGCAA
65 TTCGCTGTCAATGCAGGAAGGCAA
*
1234 GATCTGTTGTCTTCAACCAGCTCCATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
1299 TCGCTGTCAATGCAAGGAAGGCAA
66 TCGCTGTCAATGC-AGGAAGGCAA
* * **
1323 GATCTGTTGTCTTCAACAAGCTCAATCACAACCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCT
1 GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
*
1388 TCGATGTCAATGCAGGAAGGCAA
66 TCGCTGTCAATGCAGGAAGGCAA
* * *
1411 GATCTGTTGTCTTC-ACTCAGCTTCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGC
1 GATCTGTTGTCTTCAAC-CAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGC
1475 TTC
65 TTC
1478 NNNNNNNNNN
Statistics
Matches: 1248, Mismatches: 125, Indels: 29
0.89 0.09 0.02
Matches are distributed among these distances:
87 102 0.08
88 978 0.78
89 168 0.13
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
GATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCT
TCGCTGTCAATGCAGGAAGGCAA
Found at i:6373 original size:88 final size:88
Alignment explanation
Indices: 6142--6950 Score: 1172
Period size: 88 Copynumber: 9.2 Consensus size: 88
6132 NNNNNNNNNN
* * *
6142 CAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGAAGGAAGGCAAGATCC
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* *
6207 GTTGTCTTCAACAAGCTCAATCA
66 GTTGTCTTCAACCAGCTCCATCA
*
6230 CAACCCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
1 CAA-CCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
6295 TGTTGTCTTCAACCAGCTCCATCA
65 TGTTGTCTTCAACCAGCTCCATCA
* *
6319 CAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGAAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* *
6384 GTTGTCTTCAACAAGCTCAATCA
66 GTTGTCTTCAACCAGCTCCATCA
* ** * *
6407 CAACCGAGAGAGGCAAGGTTTGTCTCTTTAACCTGCTTCGCTGTCAATACAGGAAGGCAGGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
6472 GTTGTCTTCAACCAGCTCCGTCA
66 GTTGTCTTCAACCAGCTCCATCA
* * * * *
6495 CAACCGAGGGAGGGAAAGTTTGTGTCTTCGACCTGCATCGCTGTCAATGCAGGAACGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
6560 TTTGTCTTCAACCAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
***** * * *
6583 CAACCGAGAGAGG-ATAGGTCCCCCTCTTCGACCTGCCTCACTGTCAATCCAGGAAGGCAAGATC
1 CAACCGAGAGAGGCA-AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATC
* *
6647 TGTTGTCTTCAACCTGCTTCATCA
65 TGTTGTCTTCAACCAGCTCCATCA
*
6671 CAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* *
6736 GTTGTCTTCAACAAGCTCAATCA
66 GTTGTCTTCAACCAGCTCCATCA
* * *
6759 CAATCGAGAGAGGCAAGGTTTGTGTCTTTGACCTGCTTCGCTGTCAATGCAGGAAGGTAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
6824 GTTGTCTTCAACTAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
* * * * *
6847 CAACCGAGGGAGGCAGGGCTTGTGTCTTCGATCTGATTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
**
6912 ACTGTCTTCAACCAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
6935 CAACCGAGAGA-GCAAG
1 CAACCGAGAGAGGCAAG
6951 TTGATCGNNN
Statistics
Matches: 641, Mismatches: 77, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
87 5 0.01
88 553 0.86
89 83 0.13
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (88 bp):
CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
GTTGTCTTCAACCAGCTCCATCA
Found at i:10384 original size:88 final size:88
Alignment explanation
Indices: 10234--11243 Score: 1459
Period size: 88 Copynumber: 11.5 Consensus size: 88
10224 CTGTCAATGC
* * * * *
10234 AGATCTTTTGTCTTCAACCAGCTCCATCACAAGCGAGAGAGGCAAGGTTAGTGTCTTTGACCTAC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
*
10299 TTCGCTGTCAATACAGGAAGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * *
10322 GGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAAGTTTGTGTCTTCGACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
*
10387 TTCGCTGTCAATGCAGGAACGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * * *
10410 AGATCTTTTGTCTTCAACCATCTCCATCACAACCGAGAGAGG-ATAGGTTTGTGTATTCGACTTG
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCGACCTG
*
10474 CCTCGCTGTCAATGCAGGAAGGCA
65 CTTCGCTGTCAATGCAGGAAGGCA
* *
10498 AGATCTGTTGTCTTCAACCTGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
*
10563 TTCACTGTCAATGCAGGAAGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * * * * *
10586 AGATCTGTTCTCTTCAACAAGCTCAATCACAACCGAGAGAGGTAAGGTTTGTGTCTTTGACGTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
* *
10651 TTAGTTGTCAATGCAGGAAGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * *
10674 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAG-GAAGGCAGGGCTTGTGTCTTCGATCTG
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAG-AGGCAAGGTTTGTGTCTTCGACCTG
*
10738 ATTCGCTGTCAATGCAGGAAGGCA
65 CTTCGCTGTCAATGCAGGAAGGCA
* * *
10762 AGATTTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAGGTTTGTGTCTTCGACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
*
10827 TTCGCTGTCAATACAGGAAGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * * *
10850 GGATCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
* *
10915 TTCGCTGTCAAAGCAGGATGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * * * *
10938 AGATCTGTTATCTTCAACCAGCTCTATCATAACCGAGGGAGGCAAGGTTTGTGTCCTT-GATCTG
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGT-CTTCGACCTG
11002 CTTCGCTGTCAATGCAGGAAGGCA
65 CTTCGCTGTCAATGCAGGAAGGCA
* * *
11026 AGATCTGTTGTCTTCAACCAGCTCTATCACAATCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
11091 TTCGCTGTCAATGCAGGAAGGCA
66 TTCGCTGTCAATGCAGGAAGGCA
* * * * *
11114 AGATCTTTTGTCTTCAACCGGCACCATCACAACCGAGAGAGGTAAGGTTTGTGCCTTCGACCTGC
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
* * *
11179 TTCACTGTCAATCCAGGAACGCA
66 TTCGCTGTCAATGCAGGAAGGCA
*
11202 AGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
1 AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG
11244 NNNNNNNNNN
Statistics
Matches: 821, Mismatches: 95, Indels: 12
0.88 0.10 0.01
Matches are distributed among these distances:
87 5 0.01
88 811 0.99
89 5 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
AGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGC
TTCGCTGTCAATGCAGGAAGGCA
Found at i:13748 original size:88 final size:88
Alignment explanation
Indices: 13477--14214 Score: 1101
Period size: 88 Copynumber: 8.3 Consensus size: 88
13467 NNNNNNNNNN
13477 GCTGTCCAATGCAGGAAGGCAAGATCT-TTCGTCTTCAACCAGCTCCATCACAACCGAGAGAGGC
1 GCTGT-CAATGCAGGAAGGCAAGATCTGTT-GTCTTCAACCAGCTCCATCACAACCGAGAGAGGC
*
13541 ATAGGTTTGTGTCATTCGATCTGCTTC
64 A-AGGTTTGTGTC-TTCGACCTGCTTC
*
13568 GCTGTCAATGCAAGCAAGGCAAGATCTTGTTGTCTTTCAACCAGCCTCCATCCACAA-CGAAGAG
1 GCTGTCAATGC-AGGAAGGCAAGATC-TGTTGTC-TTCAACCAG-CTCCAT-CACAACCG-AGAG
13632 AGGC-AGG-TTGTGTCTTCGA-CTGCTTC
60 AGGCAAGGTTTGTGTCTTCGACCTGCTTC
*
13658 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCAATCACAACCGAGAGAGGCAA
1 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
*
13723 GGTTTGTGTCTTTGACCTGCTTC
66 GGTTTGTGTCTTCGACCTGCTTC
* *
13746 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAG
1 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
* * *
13811 GGCTTGTGTCTTCGATCTGATTC
66 GGTTTGTGTCTTCGACCTGCTTC
* * * * * *
13834 GTTGTCAATGTAAGG-AGGTAAGATTTTTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCA
1 GCTGTCAATG-CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA
13898 AGGTTTGTGTCTTCGACCTGCTTC
65 AGGTTTGTGTCTTCGACCTGCTTC
* *
13922 GCTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
1 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
*
13987 GGTTTGTGTCTTCGACCTACTTC
66 GGTTTGTGTCTTCGACCTGCTTC
* * *
14010 GCTGTCAATGCAGGAAGGCAAGATCTGTTCTCTTCAACCAGCTCCATCATAACCGAGGGAGGCAA
1 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
*
14075 GGTTTGTGTCTTCGATCTGCTTC
66 GGTTTGTGTCTTCGACCTGCTTC
* * *
14098 GCTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAA
1 GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
14163 GGTTTGTGTCTTCGACCTGCTTC
66 GGTTTGTGTCTTCGACCTGCTTC
*
14186 GCTGTCAATGCAGGATGGCAAGATCTGTT
1 GCTGTCAATGCAGGAAGGCAAGATCTGTT
14215 CTC
Statistics
Matches: 590, Mismatches: 44, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
85 13 0.02
86 10 0.02
87 23 0.04
88 435 0.74
89 16 0.03
90 24 0.04
91 23 0.04
92 11 0.02
93 14 0.02
94 8 0.01
95 13 0.02
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
GCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
GGTTTGTGTCTTCGACCTGCTTC
Done.