Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_949 ID=scaffold_949-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: 4560
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.14
Warning! 2417 characters in sequence are not A, C, G, or T
Found at i:243 original size:132 final size:132
Alignment explanation
Indices: 3--1059 Score: 1614
Period size: 132 Copynumber: 8.0 Consensus size: 132
1 GT
*
3 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATATGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* * * *
68 TGTATTGGGAAGATAAGAATCACCATCTTCGATCTGCAT-CACTATTGGTTAAGGTGACAGAATC
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC-TCCACTACTGATTAGGGTGACAGAATC
132 TGC
130 TGC
* * * *
135 AATCTTCAACCCACTCCACTACTGCTTAAGATGATAGGACTAATGGCTTAAACCTGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* **
200 TGTATTGGGAAAATAAGATTCACCATCTTCGATCTGCTCCACTACTCCTTAGGGTGACAGAATCT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
265 GC
131 GC
* * ** * * * *
267 AATTTTCAACCTACTCCAGTACTGCTTAAAGTGA-ATGGACAAATCGCTTAAACCTGTTTCTCCA
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCCA
* * *
331 CTGTATTGGGATGATAAGAGTCACCATCTTCGATCTGCTCCACTACTAATTAGGGTGACAGAATC
65 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATC
*
396 TGT
130 TGC
399 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* * * * * * *
464 TGTGTTAGCAAGATAAGATTCACCATTTTCGATCTGCTCCACTACTGCTTAGGGTGAAAGAATTT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
529 GC
131 GC
*
531 AATCTTCAACCTACTCCACTACTGCTTAGGGTAATAGGACTAATGGCTTAAATCTGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* * *
596 TGTATTAGGAAGATAAGATTAACCATCTTCGATCTGCTCCACAACTGATTAGGGTGACAGAATCT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
661 GC
131 GC
* * * *
663 AATCTTCGACCTACTCCACTACAGCTTAGGGTGATAGGACTAATTGCTTAAATCTGCTTCTCTAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* * *
728 TGTATTGGGAAGATAAGATTCACAATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAACCT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
793 GC
131 GC
*
795 AATCTTCAACCTACTGCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
* * * *
860 TATATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
925 GC
131 GC
* * * *
927 AATATTCAACCCACTCCACTACTGCTTAGGGTTATAGGACTCATGGCTTAAATCTGCTTCTCCAC
1 AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
*
992 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTAATTAGGGTGACAGAATCT
66 TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
1057 GC
131 GC
1059 A
1 A
1060 GGCAAATTGG
Statistics
Matches: 836, Mismatches: 86, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.00
132 833 1.00
133 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCAC
TGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
GC
Found at i:668 original size:44 final size:44
Alignment explanation
Indices: 620--828 Score: 149
Period size: 44 Copynumber: 4.8 Consensus size: 44
610 AAGATTAACC
* *
620 ATCTTCGATCTGCTCCACAACTGATTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * *
664 ATCTTCGACCTACTCCACTACAGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * * *
705 ATTGCTTAAATCTGCTTCTCTACTG-TATTGGGAAGATAAGATTC-ACA
1 A-T-CTTCGATCTGCTCCACTACTGCT-TAGGG-TGA-CAGAATCTGCA
*
752 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAACCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
796 ATCTTCAACCTACTGCACTACTGCTTAGGGTGA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
829 TAGGACTAAT
Statistics
Matches: 122, Mismatches: 33, Indels: 20
0.70 0.19 0.11
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 24 0.20
44 66 0.54
45 23 0.19
46 3 0.02
47 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:3763 original size:132 final size:132
Alignment explanation
Indices: 3538--4560 Score: 1751
Period size: 132 Copynumber: 7.7 Consensus size: 132
3528 CTTCGATCTG
* *
3538 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGGAAGG
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
3603 TAAGAGTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
3668 TA
131 TA
* * *
3670 CTCCACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTAGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* * * * * *
3735 TAAGATTAACCATCTTTGATCTGCTCCACTACTGATTTGGGTGACAGAATCTACAATATTTAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
3800 TA
131 TA
*
3802 CTCCACTACTGCTTAGGGTGATAGGACTAAATGGCTTAAATCTGCTTCTCCACCGTATTGGGAAG
1 CTCCACTACTGCTTAGGGTGATAGGACT-AATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAG
* *
3867 ATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTTGGGTGACAGAATCTGCAATCTTCGAC
65 ATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAAC
3932 CTA
130 CTA
* *
3935 CTCCACTACTGCTTAGGGTGATAGGTCTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
* *
4000 TAAGAGTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGTAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
4065 TA
131 TA
4067 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
4132 TAAGATTCACCATGTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
4197 TA
131 TA
4199 CTCCACTACTGCTTAGGGTGATAGGACTAATGG-TTCAAATCTGCTTCTCCACTGTATTGGGAAG
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTT-AAATCTGCTTCTCCACTGTATTGGGAAG
* * * *
4263 ATAAGATTCACTATCTTCGATCTGCACCACTACTGATTAGGGTGACAGAATCTACAATCTTCGAC
65 ATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAAC
4328 CTA
130 CTA
* *
4331 CTCCACTACTACTTAGGGTGATAGGACTAACGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
*
4396 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACC
66 TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
4461 TA
131 TA
* * *
4463 CTCCACTACTCCTTAGGGTGATAGGACTAATGGCTTAAATCTACTTCTCCACTGTATTAGGAAGA
1 CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
4528 TAAGATTCACCATCTTCGATCTGCTCCACTACT
66 TAAGATTCACCATCTTCGATCTGCTCCACTACT
Statistics
Matches: 841, Mismatches: 47, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.00
132 715 0.85
133 124 0.15
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
CTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGA
TAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACC
TA
Found at i:4174 original size:88 final size:88
Alignment explanation
Indices: 3512--4439 Score: 262
Period size: 88 Copynumber: 10.5 Consensus size: 88
3502 NNNNNNNNNN
*
3512 AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGATAGGACT-AATGGCTTAA
1 AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGACTCAATGGCTTAA
* * *
3576 ATCTGCTTCTCCACTGTATTTGGA
66 ATCTGCTCCACCACTGTA-TTGGG
* * * *
3600 AGGTAAGAGTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CTT
1 AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGA-CT-CAATGGCTT
* * * *
3663 CAACCTACTCCACTAC--TACTTAGGG
64 AAATCTGCTCCACCACTGTA-TT-GGG
* * * ** ** * * *
3688 TGATAGGACT-A--ATGGCTTAAATCTGCTTCTCCACTA-T-ATTAGGAAGATAAGATTAACCAT
1 AGATAAGATTCACCAT--CTTCGATCTG---CTCCACTACTGATTAGGGTGATAGGACT--CAAT
** *
3748 --CTTTGATCTGCTCCACTACTG-ATTTGGG
59 GGCTTAAATCTGCTCCACCACTGTA-TTGGG
* * * * * ** * * * *
3776 TGA-CAGAATCTACAATATTTAACCTACTCCACTACTGCTTAGGGTGATAGGACTAAATGGCTTA
1 AGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGACTCAATGGCTTA
* * *
3840 AATCTGCTTCTCCACCGTATTGGG
65 AATCTGCTCCACCACTGTATTGGG
* * *
3864 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTTGGGTGACAGAATCTGCAAT--CT
1 -AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGA-CT-CAATGGCT
** * * * *
3927 TCGACCTACTCCACTACTGCT-TAGGG
63 TAAATCTGCTCCACCACTG-TATTGGG
* * ** * * *
3953 TGAT-AG-GTCTA--ATGGCTTAAATCTGCTTCTCCACTA-T-ATT-GGGAAGATAAGAGTCACC
1 AGATAAGATTC-ACCAT--CTTCGATCTG---CTCCACTACTGATTAGGG-TGATAGGACTCA--
** *
4011 AT--CTTCGATCTGCTCCACTACTG-ATTAGGG
57 ATGGCTTAAATCTGCTCCACCACTGTATT-GGG
* * * *** * * * *
4041 TGA-CAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACT-AATGGCTTA
1 AGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGACTCAATGGCTTA
* *
4104 AATCTGCTTCTCCACTGTATTGGG
65 AATCTGCTCCACCACTGTATTGGG
* * *
4128 AAGATAAGATTCACCATGTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAAT--CT
1 -AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGA-CT-CAATGGCT
* * * * *
4191 TCAACCTACTCCACTACTGCT-TAGGG
63 TAAATCTGCTCCACCACTG-TATTGGG
* * * * * * * * * * * * **
4217 TGATAGGACT-A--ATGGTTCAAATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTCACTATC
1 AGATAAGATTCACCAT-CTTC-GATCTGCTCCACTACTG-ATTAGGG-TGATAGGACTCAATGGC
** * *
4278 TTCGATCTGCACCACTACTG-ATTAGGG
62 TTAAATCTGCTCCACCACTGTATT-GGG
* * * * * * *
4305 TGA-CAGAATCTACAATCTTCGACCTACTCCACTACT-ACTTAGGGTGATAGGACT-AACGGCTT
1 AGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGA-TTAGGGTGATAGGACTCAATGGCTT
* *
4367 AAATCTGCTTCTCCACTGTATTGGG
64 AAATCTGCTCCACCACTGTATTGGG
4392 AAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGA
1 -AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGA
4440 CAGAATCTGC
Statistics
Matches: 601, Mismatches: 168, Indels: 142
0.66 0.18 0.16
Matches are distributed among these distances:
85 8 0.01
86 29 0.05
87 97 0.16
88 287 0.48
89 137 0.23
90 28 0.05
91 15 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (88 bp):
AGATAAGATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGATAGGACTCAATGGCTTAA
ATCTGCTCCACCACTGTATTGGG
Done.