Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_955 ID=scaffold_955-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: 3809
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.14
Warning! 1772 characters in sequence are not A, C, G, or T
Found at i:161 original size:88 final size:88
Alignment explanation
Indices: 4--1538 Score: 2256
Period size: 88 Copynumber: 17.4 Consensus size: 88
1 TTT
* *
4 TTGTCTTC-ACCAGCTCCATCACAACCGAGAGAGG-ATAGGTTTGTGTATTCGACCTGCCTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCGACCTGCTTCGCT
*
67 ATCAATGCAGGAAGGCAAGATCTG
65 GTCAATGCAGGAAGGCAAGATCTG
* *
91 TTGTCTTCAACCAGCTCCATCACACCCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
*
156 TCAATGCAGGAAAGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* * * *
179 TTGTCTTCAACCAGCTCAATCACAACCAAGAGAGGCAAGGTTTGTGGCTTTGACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
*
244 TCAATGCAGGAAGGCAAAATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* * * * *
267 TTGTCTTAAACCAGCTCCATCACAACCGAGGGAGGCAGGGCTTT-TGTCTTCGATCTGATTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGCT
*
331 GTCAATGCAGGAAGGCAAGATCTT
65 GTCAATGCAGGAAGGCAAGATCTG
355 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGG-ATAGGTTTGTGTCTTCGACCTGCTTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTTTGTGTCTTCGACCTGCTTCGCT
* *
419 GTCAATACAGGAAGGCAGGATCTG
65 GTCAATGCAGGAAGGCAAGATCTG
*
443 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCAACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* *
508 TCAATGCAAGAAAGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTG
531 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTTCTTCGACCTGCTTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTG-TCTTCGACCTGCTTCGCT
*
596 GTCAATGCAAGAAAGGCAAGATCTG
65 GTCAATGC-AGGAAGGCAAGATCTG
* * *
621 TTGTC-TCACCCAGCTCCATCACAACCGAGAGA-GCAAGGGTTTGTGTCTTCGATCTGATTCGCT
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA-GGTTTGTGTCTTCGACCTGCTTCGCT
*
684 GTCAATGCAGGAAGGCAAGATTTTG
65 GTCAATGCAGGAAGGCAAGA-TCTG
* * * *
709 TTGTCTTCATCCAGCTCCATCACAGCCGAGAGAGACAAGGTTTGTGTCTTTGACCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* *
774 TCAATGCAGGAAGGCAGGATCTT
66 TCAATGCAGGAAGGCAAGATCTG
* *
797 TTGTCTTCAATCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
*
862 TCAATGCAGGATGGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* * * *
885 TTGTCTTCAACCAGCTCTATCATAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTACTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
*
950 TCAATGCAGGAAGGCAAGATCTT
66 TCAATGCAGGAAGGCAAGATCTG
* * * *
973 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGTAAGGTTTGTGCCTTCGACATGCTTCACTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* * * *
1038 TCAATCCAGGAACGCACGATCTT
66 TCAATGCAGGAAGGCAAGATCTG
* * * * *
1061 TTGTCTTCGACCAGCTCCATCACAACCGAGAGAGGTAAGGCTTGTGTCTTCGACTTGCTTCGTTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* *
1126 TCAATGCAGGAAGGTAATATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* * * *
1149 CTGTCTTCAACCAGCCCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGATTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
1214 TCAATGCAGGAAGGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* ** * * * * *
1237 TTGTCTGCAACCAGCTTTATCACAACCGAGGGAGGTAAGATTTGTGTTTTCGATCTGCTTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
* *
1302 TCAACGCAGGAAGGCAAGATCTT
66 TCAATGCAGGAAGGCAAGATCTG
*
1325 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTA
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
1390 TCAATGCAGGAAGGCAAGATCTG
66 TCAATGCAGGAAGGCAAGATCTG
* * * *
1413 CTGTCTTCAACCAACTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGATTCGCTG
1 TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
*
1478 TCAATGCATGAAGGCAAGATCT-
66 TCAATGCAGGAAGGCAAGATCTG
*
1500 TATGTCTTCAACCAGCTCCATCAGAACCGAGAGAGGCAA
1 T-TGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAA
1539 NNNNNNNNNN
Statistics
Matches: 1296, Mismatches: 139, Indels: 25
0.89 0.10 0.02
Matches are distributed among these distances:
87 23 0.02
88 1121 0.86
89 131 0.10
90 21 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (88 bp):
TTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTG
TCAATGCAGGAAGGCAAGATCTG
Found at i:3462 original size:88 final size:88
Alignment explanation
Indices: 3313--3809 Score: 742
Period size: 88 Copynumber: 5.6 Consensus size: 88
3303 NNNNNNNNCA
* * * *
3313 ACCTGCTTCGCTGTCAATGAAGGAAGGCAAGATCTGTTGTCTTCAACAAGCTCAATCACAACCGA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
*
3378 GAGAGTCAAGGTTTGTGTCTTTG
66 GAGAGGCAAGGTTTGTGTCTTTG
*
3401 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTATCTTCAACCAGCTCCATCACAACCGA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
**
3466 GAGAGGCAAGGTTTGTGTCTTCA
66 GAGAGGCAAGGTTTGTGTCTTTG
* * * *
3489 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCAACAAGCTCAATCACAACCGA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
*
3554 GAGAGGCAAGGTTTTTGTCTTTG
66 GAGAGGCAAGGTTTGTGTCTTTG
* *
3577 ACCTGCTTCGCTGTCAATGCAAGATGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
* * *
3642 GGGAGGCAGGGCTTGTGTCTTTG
66 GAGAGGCAAGGTTTGTGTCTTTG
* * * * *
3665 ATCTGATTCGCTGTCAATGTAGGAAGGTAAGATATATTGTCTTCAACCAGCTCCATCACAACCGA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
* *
3730 GGGAGGCAAGGTTTGTGTCTTCG
66 GAGAGGCAAGGTTTGTGTCTTTG
* * *
3753 ACCTGCTTCGCTGTCAATGCAGGAAGGCAGGATCTTTTGTCTTCAATCAGCTCCATC
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATC
Statistics
Matches: 367, Mismatches: 42, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 367 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGA
GAGAGGCAAGGTTTGTGTCTTTG
Found at i:3534 original size:45 final size:45
Alignment explanation
Indices: 3401--3535 Score: 136
Period size: 44 Copynumber: 3.0 Consensus size: 45
3391 TGTGTCTTTG
*
3401 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTATCTTCA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCA
* * * * * * *
3446 ACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGGTTTG-TGTCTTCA
1 ACCTGCTTCGCTGTCA-ATGCAG-GA-AGGCAAGATCTGTTATCTTCA
3489 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCA
1 ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCA
3534 AC
1 AC
3536 AAGCTCAATC
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
42 5 0.07
43 16 0.24
44 23 0.34
45 18 0.27
46 5 0.07
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (45 bp):
ACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTATCTTCA
Done.