Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.009G095900.1-JGI_221_v2.1
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, 823
Length: 1373
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.24
Found at i:455 original size:39 final size:39
Alignment explanation
Indices: 397--625 Score: 244
Period size: 39 Copynumber: 5.8 Consensus size: 39
387 CAAGGTCGCA
* * *
397 CACCACCTACACAAGCTCATTCACCACCAACGCAATACC
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACC
* * * * * *
436 CGCCACCCACTCAAACTCATCCACCACCTACTCAAGGTTGCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAA---TACC
* * * *
478 CACCACCTACTCAAGCTCATCCACCACCAACACAATTCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACC
*
517 CACCACCCACTCAAGCTCATCCTCCACCAA-GACAATACC
1 CACCACCCACTCAAGCTCATCCACCACCAACG-CAATACC
* * *
556 CACCACCCATTCAAGCTCATCCACCACCAAGGCAATGCC
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACC
* *
595 CACCACCCACTCAAACACATCCACCACCAAC
1 CACCACCCACTCAAGCTCATCCACCACCAAC
626 TCAAACTCCT
Statistics
Matches: 158, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
39 125 0.79
40 1 0.01
42 32 0.20
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.13
Consensus pattern (39 bp):
CACCACCCACTCAAGCTCATCCACCACCAACGCAATACC
Found at i:461 original size:60 final size:60
Alignment explanation
Indices: 353--471 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
343 CTATTGAAAG
* * **
353 TCATCCACCACCAACGCAATACTCGCCACCCGCTCAAGGTCGCACACCACCTACACAAGC
1 TCATCCACCACCAACGCAATACCCGCCACCCACTCAAACTCGCACACCACCTACACAAGC
* * *
413 TCATTCACCACCAACGCAATACCCGCCACCCACTCAAACTCATC-CACCACCTACTCAAG
1 TCATCCACCACCAACGCAATACCCGCCACCCACTCAAACTC-GCACACCACCTACACAAG
472 GTTGCACACC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.31, C:0.47, G:0.08, T:0.13
Consensus pattern (60 bp):
TCATCCACCACCAACGCAATACCCGCCACCCACTCAAACTCGCACACCACCTACACAAGC
Found at i:462 original size:21 final size:21
Alignment explanation
Indices: 438--797 Score: 111
Period size: 21 Copynumber: 18.1 Consensus size: 21
428 GCAATACCCG
438 CCACCCACTCAAACTCATCCA
1 CCACCCACTCAAACTCATCCA
* **
459 CCACCTACTCAAGGT--TGCACA
1 CCACCCACTCAAACTCAT-C-CA
* *
480 CCACCTACTCAAGCTCATCCA
1 CCACCCACTCAAACTCATCCA
* * *
501 CCACCAACAC-AATTCA--CA
1 CCACCCACTCAAACTCATCCA
* *
519 CCACCCACTCAAGCTCATCCT
1 CCACCCACTCAAACTCATCCA
* ** *
540 CCACCAAGAC-AA-T-ACCCA
1 CCACCCACTCAAACTCATCCA
* *
558 CCACCCATTCAAGCTCATCCA
1 CCACCCACTCAAACTCATCCA
* **
579 CCACCAAGGC-AA-TGC--CCA
1 CCACCCACTCAAACT-CATCCA
*
597 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAACTCATCCA
* *
618 CCACCAACTCAAACTCCTCCA
1 CCACCCACTCAAACTCATCCA
** * *
639 CCA---AGGC-AA-T-ACCCG
1 CCACCCACTCAAACTCATCCA
* *
654 CCACCCACTCAAGCACATCCA
1 CCACCCACTCAAACTCATCCA
* ** * *
675 CCACCAAGGC-TA-T-ACCCA
1 CCACCCACTCAAACTCATCCA
* * *
693 CCACCTATTCAAGCTCATCCA
1 CCACCCACTCAAACTCATCCA
*
714 CCACCCACTCAAACACATCCA
1 CCACCCACTCAAACTCATCCA
* * * * *
735 CCGCCAACGC-AA-T-ACCCG
1 CCACCCACTCAAACTCATCCA
* * *
753 CCACCCACACAAGCTCATCCG
1 CCACCCACTCAAACTCATCCA
*
774 CCACCCACTCAAACCCATCCA
1 CCACCCACTCAAACTCATCCA
795 CCA
1 CCA
798 TCAAGGCAAT
Statistics
Matches: 234, Mismatches: 78, Indels: 54
0.64 0.21 0.15
Matches are distributed among these distances:
15 5 0.02
16 1 0.00
17 2 0.01
18 55 0.24
19 13 0.06
20 13 0.06
21 143 0.61
22 1 0.00
23 1 0.00
ACGTcount: A:0.33, C:0.49, G:0.06, T:0.12
Consensus pattern (21 bp):
CCACCCACTCAAACTCATCCA
Found at i:580 original size:78 final size:79
Alignment explanation
Indices: 395--625 Score: 266
Period size: 81 Copynumber: 2.9 Consensus size: 79
385 CTCAAGGTCG
* * * *
395 CACACCACCTACACAAGCTCATTCACCACCAACGCAATACCCGCCACCCACTCAAACTCATCCAC
1 CACACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCAC
* * *
460 CACCTACTCAAGGTTG
66 CACCAACACAA-G-TA
* * * * * *
476 CACACCACCTACTCAAGCTCATCCACCACCAACACAATTCACACCACCCACTCAAGCTCATCCTC
1 CACACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCAC
*
541 CACCAAGACAA-TA
66 CACCAACACAAGTA
* * * * *
554 CCCACCACCCATTCAAGCTCATCCACCACCAAGGCAATGCCCACCACCCACTCAAACACATCCAC
1 CACACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCAC
619 CACCAAC
66 CACCAAC
626 TCAAACTCCT
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
78 62 0.49
81 65 0.51
ACGTcount: A:0.34, C:0.48, G:0.06, T:0.13
Consensus pattern (79 bp):
CACACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCAC
CACCAACACAAGTA
Found at i:619 original size:57 final size:57
Alignment explanation
Indices: 575--736 Score: 161
Period size: 57 Copynumber: 2.8 Consensus size: 57
565 TTCAAGCTCA
*
575 TCCACCACCAAGGCAATGCCCACCACCCACTCAAACACATCCA-CCACCAACTCAAAC
1 TCCACCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCCACCAACTC-AAC
* * *
632 TCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCACATCCA-CCACCAAGGCT-ATAC
1 TCCACCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCCACCAA--CTCA-AC
* ** *
690 -CCACCACCTATTCAAGCTCATCCACCACCCACTCAAACACATCCACC
1 TCCACCACCAAGGCAA--T-ACCCACCACCCACTCAAACACATCCACC
737 GCCAACGCAA
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
57 58 0.67
58 2 0.02
59 3 0.03
60 23 0.26
61 1 0.01
ACGTcount: A:0.33, C:0.49, G:0.06, T:0.12
Consensus pattern (57 bp):
TCCACCACCAAGGCAATACCCACCACCCACTCAAACACATCCACCCACCAACTCAAC
Found at i:640 original size:78 final size:79
Alignment explanation
Indices: 397--1009 Score: 269
Period size: 78 Copynumber: 7.8 Consensus size: 79
387 CAAGGTCGCA
* * * *
397 CACCACCTACACAAGCTCATTCACCACCAACGCAATACCCGCCACCCACTCAAACTCATCCACCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACCA
* **
462 CCTACTCAAGGTTGC
66 CCAACTCAAGACT-C
* * * * * *
477 ACACCACCTACTCAAGCTCATCCACCACCAACACAATTCACACCACCCACTCAAGCTCATCCTCC
1 -CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACC
** *
542 ACCAAGACAATAC-C
65 ACCAACTCAAGACTC
* * * *
556 CACCACCCATTCAAGCTCATCCACCACCAAGGCAATGCCCACCACCCACTCAAACACATCCACCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACCA
621 CCAACTCAA-ACTC
66 CCAACTCAAGACTC
* * ** * * * * * * *
634 CTCCACCAAGGCAA--T-ACCCGCCACCCACTCAA-GCACATCCA-CCAC-CAAGGCT-ATACCC
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCA-CCACCCACTCAA-ACTCAT--CC
* * *
692 ACCACCTATTCAAGCTCATC
62 ACCACCAACTCAAG-AC-TC
* * * * * * *
712 CACCACCCACTCAAACACATCCACCGCCAACGCAATACCCGCCACCCACACAAGCTCATCCGCCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACCA
*
777 CCCACTCAA-AC-C
66 CCAACTCAAGACTC
* * ** *
789 CATCCA-CCA-TCAAGGC-AATACTCACCACCCATTCAA-ACACATCCA-CCAC-C-AA-TGCAA
1 CA-CCACCCACTCAA-GCTCAT-C-CACCACCAACGCAATACCCA-CCACCCACTCAAACT-C-A
* * * ** *
846 TACACGCCACCCACTAAAGGTTGTG
59 T-C-CACCACCAACTCAA-G-ACTC
* * * * * * * *
871 AACCACCTACTCAAGCTCATCCTCCACCGAGGCAATACTCACCTCCAACTCAAACTCATCCACCA
1 CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACCA
* *
936 CCAACCCAATACT-
66 CCAACTCAAGACTC
* * * * * * *
949 CGCCGCCCACTCAAAG-TCATCCACCACCAATGCAGTACTCACCACCTACTCAAATTCATCC
1 CACCACCCACTC-AAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCC
1010 GCAGCCTCCT
Statistics
Matches: 397, Mismatches: 98, Indels: 77
0.69 0.17 0.13
Matches are distributed among these distances:
73 5 0.01
74 10 0.03
75 30 0.08
76 10 0.03
77 19 0.05
78 161 0.41
79 6 0.02
81 115 0.29
82 23 0.06
83 14 0.04
84 3 0.01
85 1 0.00
ACGTcount: A:0.33, C:0.46, G:0.07, T:0.14
Consensus pattern (79 bp):
CACCACCCACTCAAGCTCATCCACCACCAACGCAATACCCACCACCCACTCAAACTCATCCACCA
CCAACTCAAGACTC
Found at i:649 original size:96 final size:99
Alignment explanation
Indices: 517--860 Score: 351
Period size: 99 Copynumber: 3.5 Consensus size: 99
507 ACACAATTCA
* * * * * *
517 CACCACCCACTCAAGCTCATCCTCCACCAAGACAATACCCACCACCCATTCAAGCTCATCCACCA
1 CACCACCAACTCAAACACATCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCA
*
582 CCAAGGCAATGCCCACCACCCACTCAAACACATC
66 CCAAGGCAATACCCACCACCCACTCAAACACATC
*
616 CACCACCAACTC-AA-AC-TCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCACATCCACCA
1 CACCACCAACTCAAACACATCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCA
* * * * *
678 CCAAGGCTATACCCACCACCTATTCAAGCTCATC
66 CCAAGGCAATACCCACCACCCACTCAAACACATC
* * * * * *
712 CACCACCCACTCAAACACATCCACCGCCAACGCAATACCCGCCACCCACACAAGCTCATCCGCCA
1 CACCACCAACTCAAACACATCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCA
* ** *
777 CCCACTCAA-ACCCATCCA-CCA-TCAAGGCA-ATAC
66 CCAAGGCAATACCCA-CCACCCACTCAA-ACACAT-C
* * * * *
810 TCACCACCCATTCAAACACATCCACCACCAATGCAATACACGCCACCCACT
1 -CACCACCAACTCAAACACATCCTCCACCAAGGCAATACCCGCCACCCACT
861 AAAGGTTGTG
Statistics
Matches: 207, Mismatches: 31, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
96 81 0.39
97 9 0.04
98 13 0.06
99 104 0.50
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.12
Consensus pattern (99 bp):
CACCACCAACTCAAACACATCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCTCATCCACCA
CCAAGGCAATACCCACCACCCACTCAAACACATC
Found at i:664 original size:36 final size:36
Alignment explanation
Indices: 615--716 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 36
605 TCAAACACAT
615 CCACCACCAACTCAAACTCCTCCACCAAGGCAATAC
1 CCACCACCAACTCAAACTCCTCCACCAAGGCAATAC
* * * *
651 CCGCCACCCACTCAAGCACATCCACCACCAAGGCTATAC
1 CCACCACCAACTCAA--AC-TCCTCCACCAAGGCAATAC
* * * *
690 CCACCACCTATTCAAGCTCATCCACCA
1 CCACCACCAACTCAAACTCCTCCACCA
717 CCCACTCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 21 0.40
37 1 0.02
38 2 0.04
39 29 0.55
ACGTcount: A:0.32, C:0.48, G:0.07, T:0.13
Consensus pattern (36 bp):
CCACCACCAACTCAAACTCCTCCACCAAGGCAATAC
Found at i:731 original size:60 final size:60
Alignment explanation
Indices: 594--838 Score: 255
Period size: 60 Copynumber: 4.1 Consensus size: 60
584 AAGGCAATGC
** * * ** *
594 CCACCACCCACTCAAACACATCCACCACCAACTCAA-ACTCCTCCACCAAGGCAA--T-AC
1 CCACCACCCACTCAAACACATCCACCACCAAGGCAATAC-CCACCACCCATTCAAGCTCAT
* * * *
651 CCGCCACCCACTCAAGCACATCCACCACCAAGGCTATACCCACCACCTATTCAAGCTCAT
1 CCACCACCCACTCAAACACATCCACCACCAAGGCAATACCCACCACCCATTCAAGCTCAT
* * * **
711 CCACCACCCACTCAAACACATCCACCGCCAACGCAATACCCGCCACCCACACAAGCTCAT
1 CCACCACCCACTCAAACACATCCACCACCAAGGCAATACCCACCACCCATTCAAGCTCAT
* * * * * *
771 CCGCCACCCACTCAAACCCATCCACCATCAAGGCAATACTCACCACCCATTCAAACACAT
1 CCACCACCCACTCAAACACATCCACCACCAAGGCAATACCCACCACCCATTCAAGCTCAT
831 CCACCACC
1 CCACCACC
839 AATGCAATAC
Statistics
Matches: 153, Mismatches: 31, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
57 42 0.27
58 2 0.01
59 1 0.01
60 108 0.71
ACGTcount: A:0.33, C:0.49, G:0.06, T:0.11
Consensus pattern (60 bp):
CCACCACCCACTCAAACACATCCACCACCAAGGCAATACCCACCACCCATTCAAGCTCAT
Found at i:796 original size:99 final size:94
Alignment explanation
Indices: 517--978 Score: 331
Period size: 99 Copynumber: 4.7 Consensus size: 94
507 ACACAATTCA
* * * * *
517 CACCACCCACTCAAGCTCATCCTCCACCAAGACAATACCCACCACCCATTCAAGCTCATCCACCA
1 CACCACCCACTCAAACACATCCACCACCAAG-CAATACCCGCCACCCACTCAAGCTCATCCACCA
** * *
582 CCAAGGCAATGCCCACCACCCACTCAAACACATC
65 CCAACTCAA-ACCCACCA-CCA-TCAAGC-CATC
* * *
616 CACCACCAACTC-AA-AC-TCCTCCACCAAGGCAATACCCGCCACCCACTCAAGCACATCCACCA
1 CACCACCCACTCAAACACATCCACCACCAA-GCAATACCCGCCACCCACTCAAGCTCATCCACCA
*
678 CCAAGGCT-ATACCCACCACCTATTCAAGCTCATC
65 CCAA--CTCAAACCCACCACC-A-TCAAGC-CATC
* * *
712 CACCACCCACTCAAACACATCCACCGCCAACGCAATACCCGCCACCCACACAAGCTCATCCGCCA
1 CACCACCCACTCAAACACATCCACCACCAA-GCAATACCCGCCACCCACTCAAGCTCATCCACCA
* *
777 CCCACTCAAACCCATCCACCATCAAGGCAATAC
65 CCAACTCAAACCCA-CCACCATCAA-GCCAT-C
* * * * ** **
810 TCACCACCCATTCAAACACATCCACCACCAATGCAATACACGCCACCCACTAAAGGTTGTGAACC
1 -CACCACCCACTCAAACACATCCACCACCAA-GCAATACCCGCCACCCACTCAAGCTCATCCACC
* * * * * * *
875 ACCTACTCAAGCTCATCCTCCACCGAGGCAATAC
64 ACCAACTCAAACCCA-CCACCATC-AAGCCAT-C
* * * * * *
909 TCACCTCCAACTCAAACTCATCCACCACCAACCCAATACTCGCCGCCCACTCAAAG-TCATCCAC
1 -CACCACCCACTCAAACACATCCACCACCAA-GCAATACCCGCCACCCACTC-AAGCTCATCCAC
973 CACCAA
63 CACCAA
979 TGCAGTACTC
Statistics
Matches: 294, Mismatches: 55, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
95 2 0.01
96 73 0.25
97 13 0.04
98 13 0.04
99 189 0.64
100 4 0.01
ACGTcount: A:0.33, C:0.47, G:0.07, T:0.13
Consensus pattern (94 bp):
CACCACCCACTCAAACACATCCACCACCAAGCAATACCCGCCACCCACTCAAGCTCATCCACCAC
CAACTCAAACCCACCACCATCAAGCCATC
Found at i:858 original size:39 final size:39
Alignment explanation
Indices: 636--860 Score: 136
Period size: 39 Copynumber: 5.7 Consensus size: 39
626 TCAAACTCCT
* *
636 CCACCAAGGCAATACCCGCCACCCACTCAAGCACATCCA
1 CCACCAAGGCAATACACGCCACCCACTCAAACACATCCA
* * * * * * *
675 CCACCAAGGCTATACCCACCACCTATTCAAGCTCATCCA
1 CCACCAAGGCAATACACGCCACCCACTCAAACACATCCA
* ** * * **
714 CCACCCACTCAA-ACACATCCACCGCCAACGCAATAC-CCGCCA
1 CCACCAAGGCAATACAC-GCCA-C-CC-ACTCAA-ACACATCCA
* *
756 CCCACACAA-GCTCAT-C-CGCCACCCACTCAAACCCATCCA
1 -CCAC-CAAGGC-AATACACGCCACCCACTCAAACACATCCA
* * * *
795 CCATCAAGGCAATACTCACCACCCATTCAAACACATCCA
1 CCACCAAGGCAATACACGCCACCCACTCAAACACATCCA
*
834 CCACCAATGCAATACACGCCACCCACT
1 CCACCAAGGCAATACACGCCACCCACT
861 AAAGGTTGTG
Statistics
Matches: 139, Mismatches: 34, Indels: 26
0.70 0.17 0.13
Matches are distributed among these distances:
37 5 0.04
38 11 0.08
39 96 0.69
40 3 0.02
41 2 0.01
42 11 0.08
43 7 0.05
44 4 0.03
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (39 bp):
CCACCAAGGCAATACACGCCACCCACTCAAACACATCCA
Found at i:1002 original size:39 final size:39
Alignment explanation
Indices: 872--1009 Score: 143
Period size: 39 Copynumber: 3.5 Consensus size: 39
862 AAGGTTGTGA
* * *
872 ACCACCTACTC-AAGCTCATCCTCCACCGAGGCAATACTC
1 ACCACCTACTCAAAG-TCATCCACCACCAACGCAATACTC
* * * *
911 ACCTCCAACTCAAACTCATCCACCACCAACCCAATACTC
1 ACCACCTACTCAAAGTCATCCACCACCAACGCAATACTC
* * * * *
950 GCCGCCCACTCAAAGTCATCCACCACCAATGCAGTACTC
1 ACCACCTACTCAAAGTCATCCACCACCAACGCAATACTC
*
989 ACCACCTACTCAAATTCATCC
1 ACCACCTACTCAAAGTCATCC
1010 GCAGCCTCCT
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 78 0.98
40 2 0.03
ACGTcount: A:0.31, C:0.45, G:0.07, T:0.17
Consensus pattern (39 bp):
ACCACCTACTCAAAGTCATCCACCACCAACGCAATACTC
Done.