Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1070 ID=scaffold_1070-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, 676
Length: 1128
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Found at i:239 original size:132 final size:132
Alignment explanation
Indices: 1--1126 Score: 1614
Period size: 132 Copynumber: 8.5 Consensus size: 132
* *
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATGCACCATCTTCGATCAGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * *
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCTCTACTGCTTATGGAGAT
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
*
131 TG
131 AG
* * * * * * *
133 GACTAATGGCTCAAATCTGCTTCTCCACTATCTTGAGAAGATAAGAATCACCATCTTTGATCCGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* ** * *
198 TCCACTACTGCTTAGGGTGACAGAACCTAAAATCTTTAACCTACTCCACTACTACTTAGGGTGAT
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
263 AG
131 AG
* * *
265 GACTAATGGCTTAAATCAGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTAC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * * * *
330 TCCAATACTGCATAGGGTGACAGAATCTGCAATCTTCAACCGACAT-CACTACTGCTGAGGGAGA
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTAC-TCCACTACTGCTTAGGGTGA
*
394 TTG
130 TAG
* * *
397 GACTAATGGCTTAAATCTTCTTCTCCACTGTATTTGGAAGATAAAGATTTCACCATGTTTCGATC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAT-AAGA-TTCACCAT-CTTCGATC
* * *
462 TACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCATCAACCTACTCCCACTACTACTTAGGG
63 TGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT-CCACTACTGCTTAGGG
527 TGATAG
127 TGATAG
* * * *
533 GACTAATGGCTTAAAT-TAGCTTCACCACTGTATTGGGAAAATAAGATTCATCATATTCGATCTG
1 GACTAATGGCTTAAATCT-GCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTG
* * * * * *
597 CTTCACTACTGTTTAGGGTGACAGAATATGCAATCTTCAACCAATTCCACTA-TGGCTTAGGGAG
65 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACT-GCTTAGGGTG
661 ATAG
129 ATAG
* * * *
665 GACAAATGGCATAAATCTGCTTCTCCACTGTATTGGGAAAATAAGATTCACCATCTTCGATCTAC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
* * *
730 TCCACTACAGCTTAGTGTGACAGAATCTGCAATCTTCAGCCTACTCCACTACTGCTTAGGGTGAT
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
795 AG
131 AG
* *
797 GACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATTCACCATATTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
*
862 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGTGTGAT
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGA-
927 TA-
130 TAG
* *
929 GACTAATGGCTTAAATCTGCTTCTCCACTGT-TTGGGAAGATAAGATTCACCATCATCGATCCGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
*
993 TCCACTACTGCCTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
66 TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
1058 AG
131 AG
* * *
1060 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTTATCATATTCGATCTGC
1 GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
1125 TC
66 TC
1127 AA
Statistics
Matches: 879, Mismatches: 102, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
130 2 0.00
131 124 0.14
132 572 0.65
133 57 0.06
134 16 0.02
135 55 0.06
136 53 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
GACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC
TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAT
AG
Found at i:1055 original size:44 final size:44
Alignment explanation
Indices: 717--1056 Score: 132
Period size: 44 Copynumber: 7.8 Consensus size: 44
707 AAGATTCACC
* * * *
717 ATCTTCGATCTACTCCACTACAGCTTAGTGTGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * *
761 ATCTTCAGCCTACTCCACTACTGCTTAGGGTGATAGGA-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* * * * * * * *
802 ATGGCTTAAATCTGCTTCTCCACTA-T-ATT-GGGAAGATAAGATTC-ACC
1 AT--CTTCAA-C--CTACTCCACTACTGCTTAGGG-TGA-CAGAATCTGCA
* * * *
849 ATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
* *
893 ATCTTCAACCTACTCCACTACTGCTTAGTGTGATTAG-A-CT--A
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA-CAGAATCTGCA
* * * * * * * * * * * *
934 ATGGCTTAAATCTGCTTCTCCACTG-TTTGGGAAGATAAGATTC-ACC
1 AT--CTTCAACCTACTCCACTACTGCTTAGGG-TGA-CAGAATCTGCA
* * * *
980 ATCATCGATCC-GCTCCACTACTGCCTAGGGTGACAGAATCTGCA
1 ATCTTC-AACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
1024 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGA
1057 TAGGACTAAT
Statistics
Matches: 207, Mismatches: 63, Indels: 52
0.64 0.20 0.16
Matches are distributed among these distances:
41 6 0.03
42 14 0.07
43 45 0.22
44 109 0.53
45 18 0.09
46 13 0.06
47 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCA
Done.