Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_565 ID=scaffold_565-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: 5964
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.31
Warning! 307 characters in sequence are not A, C, G, or T
Found at i:766 original size:14 final size:14
Alignment explanation
Indices: 747--775 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
737 GAGTTGCTGC
747 GACGTGGGAGCAAT
1 GACGTGGGAGCAAT
761 GACGTGGGAGCAAT
1 GACGTGGGAGCAAT
775 G
1 G
776 GGGGTGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.45, T:0.14
Consensus pattern (14 bp):
GACGTGGGAGCAAT
Found at i:1692 original size:132 final size:132
Alignment explanation
Indices: 1484--1953 Score: 728
Period size: 132 Copynumber: 3.6 Consensus size: 132
1474 CATCAGTCTA
* * * * * * * *
1484 CTCCACTACTGCTTAGGGAGATAAAATCTGCTATTCTTCGATCGATTCCACTGTCGACCAAGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTG-AAATCTTCAATCTATTCCACTGCCAACCAGGGAG
*
1549 ATAGAATTACTGGCTTCAATGTACTCCACTGTAACCCTAGGGAGGTAAAATCTGCCATCTTCAAT
65 ATAGAATTACTGGCTTCAATGTACTCCACTGTAACCCTAGGGAGGTAAAATCTGCCATCTTCGAT
1614 CTG
130 CTG
* * *
1617 CTCCACTACTGCTTAGGGAAATAAGATCTAAAATCTTCAATCTATTCCACTGCCAACCAGGGGGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
* *
1682 TAGAGTTACTGGCTTCAATGTACTCCACTGTAACCCCAGGGAGGTAAAAT-TCGCCATCTTCGAT
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCCTAGGGAGGTAAAATCT-GCCATCTTCGAT
1746 CTG
130 CTG
* *
1749 CTCCACTACCGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
*
1814 TAGAATTACTGGCTTCAATGTACTCCACTGTAA-CCTCGGGGAGGTAAAATCTGCCATCTTCGAT
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCCT-AGGGAGGTAAAATCTGCCATCTTCGAT
1878 CTG
130 CTG
* *
1881 CTCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
1946 TAGAATTA
66 TAGAATTA
1954 GTATCTTCGA
Statistics
Matches: 308, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
131 3 0.01
132 277 0.90
133 28 0.09
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGA
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCCTAGGGAGGTAAAATCTGCCATCTTCGATC
TG
Found at i:1813 original size:44 final size:44
Alignment explanation
Indices: 1631--1947 Score: 140
Period size: 44 Copynumber: 7.2 Consensus size: 44
1621 ACTACTGCTT
* * *
1631 AGGGAAATAAGATCTAAAATCTTCAATCTATTCCACTGCCAACC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCCAACC
* * * * *
1675 AGGGGGATAGAGTTACTG---GCTTCAATGTACTCCACTG-TAACCCC
1 AGGGAGATA-AGAT-CTGAAATCTTCAATCTACTCCACTGCCAA--CC
* * ** * * * * *
1719 AGGGAGGTAAAAT-TCGCCATCTTCGATCTGCTCCACTACC-GCTT
1 AGGGAGATAAGATCT-GAAATCTTCAATCTACTCCACTGCCAAC-C
* *
1763 AAGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCCAACC
* * *
1807 AGGGAGAT-AGAATTACTG---GCTTCAATGTACTCCACTG-TAACCTC
1 AGGGAGATAAG-A-T-CTGAAATCTTCAATCTACTCCACTGCCAA-C-C
* * * ** * *
1851 GGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACT---AATGCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCCAA--CC
*
1894 TAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACC
1 -AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCCAACC
1939 AGGGAGATA
1 AGGGAGATA
1948 GAATTAGTAT
Statistics
Matches: 195, Mismatches: 52, Indels: 52
0.65 0.17 0.17
Matches are distributed among these distances:
41 1 0.01
42 8 0.04
43 42 0.22
44 100 0.51
45 37 0.19
46 5 0.03
47 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (44 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGCCAACC
Found at i:3254 original size:23 final size:24
Alignment explanation
Indices: 3226--3282 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
3216 AGCCTCTCCA
3226 TTTTTACTTTTTC-CAT-TTTTTAT
1 TTTTTACTTTTTCACATCTTTTT-T
3249 TTTTTA-TTTTTCACATCTTTTTT
1 TTTTTACTTTTTCACATCTTTTTT
*
3272 TTCTT-CTTTTT
1 TTTTTACTTTTT
3283 TTTTGTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 19 0.63
24 5 0.17
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTACTTTTTCACATCTTTTTT
Found at i:3753 original size:6 final size:6
Alignment explanation
Indices: 3742--3779 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
3732 CCCAGCAGGG
3742 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT TTCTTT T
3780 CCCCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:3804 original size:15 final size:15
Alignment explanation
Indices: 3784--3826 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3774 TCTTTTCCCC
*
3784 CTTTTTTTATTTTTTT
1 CTTTTTTT-TTGTTTT
3800 CTTTTTTTTTGTTTT
1 CTTTTTTTTTGTTTT
3815 CTCTCTTTTTTT
1 CT-T-TTTTTTT
3827 TTGGATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (15 bp):
CTTTTTTTTTGTTTT
Found at i:3808 original size:35 final size:36
Alignment explanation
Indices: 3751--3826 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 36
3741 GTTCTTTTTC
*
3751 TTTTTCTTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
1 TTTTTATTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
* * *
3787 TTTTTATTTTT-TTCTTT-TTTTTTGTTTTCTCTCTT
1 TTTTTATTTTTCTT-TTTCTTTTTTCTTTTCCCCCTT
3822 TTTTT
1 TTTTT
3827 TTGGATTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (36 bp):
TTTTTATTTTTCTTTTTCTTTTTTCTTTTCCCCCTT
Found at i:3829 original size:19 final size:18
Alignment explanation
Indices: 3742--3828 Score: 72
Period size: 19 Copynumber: 4.8 Consensus size: 18
3732 CCCAGCAGGG
3742 TTCT-TTTTCTTTTTCTTT
1 TTCTCTTTT-TTTTTCTTT
*
3760 TTCTTTTTCTTTTTTCTTT
1 TTCTCTTT-TTTTTTCTTT
* * *
3779 TCCCCCTTTTTTTAT-TTT
1 T-TCTCTTTTTTTTTCTTT
*
3797 TT-TCTTTTTTTTTGTTT
1 TTCTCTTTTTTTTTCTTT
3814 TCTCTCTTTTTTTTT
1 T-TCTCTTTTTTTTT
3829 GGATTGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.16
17 4 0.07
18 9 0.16
19 29 0.52
20 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (18 bp):
TTCTCTTTTTTTTTCTTT
Done.