Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1058 ID=scaffold_1058-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: 4783
ACGTcount: A:0.07, C:0.06, G:0.05, T:0.08
Warning! 3578 characters in sequence are not A, C, G, or T
Found at i:241 original size:132 final size:131
Alignment explanation
Indices: 5--343 Score: 561
Period size: 132 Copynumber: 2.6 Consensus size: 131
1 TCGT
*
5 TCTGCTCCACTACTGATTAGGGTGACAGAACCTGCAATCTTCACCTACTCCACTACTGCTTAGGG
1 TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCACCTACTCCACTACTGCTTAGGG
* * * *
70 TGATAGGACTAATTGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCG
66 TGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTCG
135 A
131 A
* *
136 TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCATCAACCTACTCCACTGCTGCTTAGG
1 TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTC-ACCTACTCCACTACTGCTTAGG
* * *
201 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACTATGTTT
65 GTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTC
266 GA
130 GA
*
268 TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACCACTGCTTAGG
1 TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTC-ACCTACTCCACTACTGCTTAGG
333 GTGATAGGACT
65 GTGATAGGACT
344 NNNNNNNNNN
Statistics
Matches: 193, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
131 40 0.21
132 153 0.79
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (131 bp):
TCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCACCTACTCCACTACTGCTTAGGG
TGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTCG
A
Found at i:4006 original size:44 final size:44
Alignment explanation
Indices: 3958--4432 Score: 134
Period size: 44 Copynumber: 10.8 Consensus size: 44
3948 AAGATTAACC
*
3958 ATCTTTGATCTACTCCACTACTGATTAGGGTGACAAAATCTGCA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
** * * * **
4002 ATCTTCAACCTACTCTACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
* * * * * * ** * * *
4043 ATGGTTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGAT-TAACC
1 AT-CTTT-GATCTACTCCACTACTG-ATTAGGGTGATAAAATCT-GCA
* * * * *
4090 ATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGTA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
* * * **
4134 ATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATA--A--AAT--CTGCA
* ** * * *
4184 ATC--TG--CTTCTCCACTA-T-ATTAGGAAGATAAGAT-TAACC
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCT-GCA
* * *
4222 ATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
** * * **
4266 ATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
* * * * * * ** * * *
4307 ATGGTTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGAT-TAACC
1 AT-CTTT-GATCTACTCCACTACTG-ATTAGGGTGATAAAATCT-GCA
* * * *
4354 ATCTTTGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
** * * *
4398 ATCTTCAACCTACTTCACTACTGCTTAGGGTGATA
1 ATCTTTGATCTACTCCACTACTGATTAGGGTGATA
4433 GGACTAATGG
Statistics
Matches: 304, Mismatches: 97, Indels: 60
0.66 0.21 0.13
Matches are distributed among these distances:
37 1 0.00
38 3 0.01
40 4 0.01
41 6 0.02
42 15 0.05
43 28 0.09
44 187 0.62
45 30 0.10
46 16 0.05
47 4 0.01
48 4 0.01
50 6 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
ATCTTTGATCTACTCCACTACTGATTAGGGTGATAAAATCTGCA
Found at i:4159 original size:132 final size:132
Alignment explanation
Indices: 3922--4783 Score: 1400
Period size: 132 Copynumber: 6.4 Consensus size: 132
3912 NNNNNNNNNN
*
3922 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTACTCCACTACTGATTAGG
1 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
* * *
3987 GTGACAAAATCTGCAATCTTCAACCTACTCTACTACTGCTTAGGGTGATAGGACTAATGGTTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
4052 AT
131 AT
*
4054 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGCTTAGG
1 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
* *
4119 GTGACAGAATCTGTAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
4184 AT
131 AT
*
4186 CTGCTTCTCCACTATATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
1 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
*
4251 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGTTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
4316 AT
131 AT
*
4318 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGCTTAGG
1 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
*
4383 GTGACAGAATCTGCAATCTTCAACCTACTTCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
4448 AT
131 AT
* * * *
4450 CTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACGGATTAGG
1 CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
*
4515 GTGACAGAATCTGCAATCTTCAACCTACTCCACTGCTGCTTAGGGTGATAGGACTAATGGCTTAA
66 GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
4580 AT
131 AT
*
4582 CTGCTTCTCCACTGTATTAGGGAAGATAAGATTAACCATGTTTGATCTGCTCCACTACTGATTAG
1 CTGCTTCTCCACTGTATTA-GGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTA-
*
4647 GGGGGACAGAAAATCTGCAATCTTTCAAACCTACTCCACTACTGCTTAGGAGTGATAAGGACCTA
64 GGGTGACAG--AATCTGCAATC-TTC-AACCTACTCCACTACTGCTTAGG-GTGAT-AGGA-CTA
*
4712 ATGGTTTAAAT
122 ATGGCTTAAAT
* * * *
4723 CCTGCTTCTCCACTGTATTTGGGAAGAATAAGATTCACTATCTTCGATCTGGCTCCACTAC
1 -CTGCTTCTCCACTGTA-TTAGGAAG-ATAAGATTAACCATCTTTGATCT-GCTCCACTAC
Statistics
Matches: 681, Mismatches: 36, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
132 523 0.77
133 40 0.06
134 8 0.01
136 11 0.02
137 3 0.00
138 22 0.03
139 5 0.01
140 4 0.01
141 13 0.02
142 21 0.03
143 21 0.03
144 10 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
CTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGG
GTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAA
AT
Done.