Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_923 ID=scaffold_923-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: 3981
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.19
Warning! 1586 characters in sequence are not A, C, G, or T
Found at i:105 original size:44 final size:44
Alignment explanation
Indices: 55--528 Score: 186
Period size: 44 Copynumber: 10.8 Consensus size: 44
45 AAGATTCACC
*
55 ATCTTCGATCTGCTCCACTACTGCCTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * *
99 ATCTTCGACCTACTCCACTACTGCTTAGGGTGACAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * ** * * * *
140 ATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTC-ACC
1 AT--CTTCGATCTGCTCCACTACTG-CTTAGGGTGA-CAGAATCTGCA
*
187 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
231 ATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * ** * ** *
272 ATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGAAT-AACC
1 AT--CTTCGATCTGCTCCACTACTG-CTTAGGGTGA-CAGAATCTGCA
* * * * *
319 ATCTTTGATCTGCTCCACTACTGATTAGGGTTACAAAATCAGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * *
363 ATCTTCAACCTACTCCACTACTGATTAGGGTGATAGGA-CT--A
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
** * * * * * *
404 ATGGGCTTAAATCTGCTTCTCCACTA-T-ATT-GGGAAGATAAGATTC-ACC
1 AT---CTTCGATCTG---CTCCACTACTGCTTAGGG-TGA-CAGAATCTGCA
*
452 ATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * *
496 ATCTTCGACCTACTCCACTATTGCTTAGAGTGA
1 ATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
529 TAGGACTAAT
Statistics
Matches: 310, Mismatches: 89, Indels: 62
0.67 0.19 0.13
Matches are distributed among these distances:
41 9 0.03
42 8 0.03
43 48 0.15
44 173 0.56
45 53 0.17
46 4 0.01
47 13 0.04
48 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
Found at i:240 original size:132 final size:132
Alignment explanation
Indices: 3--1668 Score: 1742
Period size: 132 Copynumber: 12.6 Consensus size: 132
1 AA
3 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
** * *
68 TCCACTACTGCCTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGGGTGAC
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
133 AG
131 AG
*
135 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTCACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
*
200 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTACTGCTTAGGGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
265 AG
131 AG
* * * *
267 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGAATAACCATCTTTGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * * *
332 TCCACTACTGATTAGGGTTACAAAATCAGCAATCTTCAACCTACTCCACTACTGATTAGGGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
397 AG
131 AG
*
399 GACTAATGGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCATCTTCGATCTG
1 GACTAAT-GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTG
* * *
464 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTACTCCACTATTGCTTAGAGTGA
65 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
529 TAG
130 TAG
* * *
532 GACTAATGGCTTAAATATGCTTCCCCACTGTAGTTGGGAAGATAAGATTCACCATCTTCGTTCTG
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTA-TTGGGAAGATAAGATTCACCATCTTCGATCTG
** *
597 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTGGACCTACTCCACTACTGTTTAGGGTGA
65 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
662 TAGG
130 TA-G
*******************************************
666 GACTAATGGCTTAAATCTGCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
***************************************************************
731 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
796 AG
131 AG
* *
798 GACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGTTCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* *
863 TCCACTACTGATTAGGGTGACAGAACCTGTAATCTTC-ACCTACT---C--CTGCTTAGGGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
922 AG
131 AG
*
924 GACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
*
989 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTGCTGCTTAGGGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
1054 AG
131 AG
* * * * * *
1056 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAATATAAGATTAACTATGTTTGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
1121 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
1186 AG
131 AG
* * *
1188 GACTAATGGCTTAAATCTGCTTCTCCACTGTGTTGGAAAGATAAGATGCACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * * * * *
1253 TCCGCTACTGATTACGCTGACAGAATCTGCAATCTTCAACGTACTCTACTACTGCTTAGAGTGAT
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
1318 AG
131 AG
* *
1320 GAGTAATGTCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * * * * *
1385 TCCACTACTGCTTAGGCTGACAGAATTTGCAATCTTCAACCTACTCTACTACTGCTTAGGATGAG
66 TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
1450 AG
131 AG
* *** *
1452 GACTAATGGGTTAAATCTGCTTCTCCACTGTATTACAAAAGATAAAATTCACCATCTTCGATCTG
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATT-GGGAAGATAAGATTCACCATCTTCGATCTG
*
1517 CTCCACTACTGATTAGGGTGACAAAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
65 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1582 TAG
130 TAG
* *
1585 GACTAATGGCTGAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTTACCATCTTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
*
1650 TCCACTAGTGATTAGGGTG
66 TCCACTACTGATTAGGGTG
1669 NNNNNNNNNN
Statistics
Matches: 1223, Mismatches: 301, Indels: 20
0.79 0.19 0.01
Matches are distributed among these distances:
126 103 0.08
127 7 0.01
130 1 0.00
132 754 0.62
133 336 0.27
134 22 0.02
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.29
Consensus pattern (132 bp):
GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
TCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
AG
Found at i:3386 original size:132 final size:132
Alignment explanation
Indices: 3149--3981 Score: 1441
Period size: 132 Copynumber: 6.3 Consensus size: 132
3139 NNNNNNNNNN
* * *
3149 CACTACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTGTTGGAAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
*
3214 GATTCACCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCGACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3279 TC
131 TC
*
3281 CACTACTGCTTAGAGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* *
3346 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATTTTCAATCTTCGACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3411 TC
131 TC
*
3413 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* * * *
3478 GATTAACCATCTTTGATCTGCTCCACTACTGGTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3543 TC
131 TC
*
3545 CACTACTGCTTAGGGTGATAGGACTAATGGTTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* *
3610 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCGAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3675 TC
131 TC
3677 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* *
3742 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGATAGAATTTGCAATCTTCGACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3807 TC
131 TC
* * *
3809 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATTTCCTTCTCCACTGTATTAGGAAGATAA
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* * * *
3874 GATTAACCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAAAATCTGCAATCTTCGACCTAC
66 GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
3939 TC
131 TC
*
3941 CACTACTGCTTAGGGTGATAGGACTAATGGTTTAAATCTGC
1 CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGC
Statistics
Matches: 663, Mismatches: 38, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 663 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (132 bp):
CACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
GATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCGACCTAC
TC
Done.