Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_145 ID=scaffold_145-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: 10953
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:3371 original size:50 final size:50
Alignment explanation
Indices: 3300--3847 Score: 239
Period size: 50 Copynumber: 11.0 Consensus size: 50
3290 AGCAATGTCG
* * * *
3300 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCTA
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
* * * * ** ** *
3350 GGGAGGTGAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATG-TCG
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCT-A
* * *
3400 GGGAAGTGAGATTCACTGATGTGGCTTTAATCTGTTCCACTGCACCGCCA
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
* * * ** * ** *
3450 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATG-TC
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
** * * * * * * * * *
3499 GGGTAAGCAAAATTCACCGATGTGGCTTTAATCTGTTGCAATACACTGCCA
1 GGG-AAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
* * * * * ** ***
3550 GGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCA-ATTTCA
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCT-A
** ** * *
3600 GGGAAGCAAGATTCACCATTGTGGCTTTAATCTGTTCCACTGCACCGCCA
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
* * * * ** * ** *
3650 GGGAAATAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTTCAATG-TCG
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCT-A
** * * *
3700 GGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCAC-CT-
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCA-C-CGCTA
* ** * ** **
3750 GAGG-AGTAAGATTTGCTGTTGTAGCTTTAATCTTTTTAACTGCAATG-TCA
1 G-GGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCT-A
** * * * *
3800 GGGAAGCAAGGTTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGC
1 GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGC
3848 CAGGAAAATA
Statistics
Matches: 361, Mismatches: 121, Indels: 31
0.70 0.24 0.06
Matches are distributed among these distances:
48 1 0.00
49 6 0.02
50 348 0.96
51 5 0.01
52 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
GGGAAGTGAGATTCACTGTTGTAGCTTTAATCTGTTCCACTGCACCGCTA
Found at i:3863 original size:100 final size:100
Alignment explanation
Indices: 3274--3862 Score: 786
Period size: 100 Copynumber: 5.9 Consensus size: 100
3264 TAACTCGTAA
* * * * * * * * *
3274 CTTTAATCTATTGAACAGCAATGTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * * * * *
3339 CTACACCGCTAGGGAGGTGAGATTCACCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
** *
3374 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTGAGATTCACTGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
3439 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
* * * *
3474 CTTTAATCTTTTTAATTGCAATGTCGGGTAAGCAAAATTCACCGATGTGGCTTTAATCTGTTGCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * * *
3539 ATACACTGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
* *
3574 CTTTAATCTTTTTAACTGCAATTTCAGGGAAGCAAGATTCACC-ATTGTGGCTTTAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGTTCC
*
3638 ACTGCACCGCCAGGGAAATAAGATTCGCTGTTGTAG
65 ACTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
*
3674 CTTTAATCTTTTTAACTTCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * *
3739 CTGCATCACCTGAGG-AGTAAGATTTGCTGTTGTAG
66 CTGCACCGCCAG-GGAAGTAAGATTCGCTGTTGTAG
* *
3774 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGGTTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
3839 CTGCACCGCCAGGAAAATAAGATT
66 CTGCACCGCCAGGGAAGTAAGATT
3863 TAATGCGATC
Statistics
Matches: 430, Mismatches: 55, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
99 2 0.00
100 425 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCACCGCCAGGGAAGTAAGATTCGCTGTTGTAG
Found at i:5371 original size:14 final size:14
Alignment explanation
Indices: 5352--5400 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
5342 TTAGCCTCTC
5352 CATTTTTACTTTTT
1 CATTTTTACTTTTT
*
5366 CATTTTTCCATTTTT
1 CATTTTTAC-TTTTT
*
5381 CATTTTCA-TTTTT
1 CATTTTTACTTTTT
*
5394 TATTTTT
1 CATTTTT
5401 TTCTGACTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 11 0.38
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
CATTTTTACTTTTT
Found at i:5394 original size:22 final size:22
Alignment explanation
Indices: 5350--5393 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5340 CTTTAGCCTC
*
5350 TCCATTTTTACTTTTTCATTTT
1 TCCATTTTTACATTTTCATTTT
5372 TCCATTTTT-CATTTTCATTTT
1 TCCATTTTTACATTTTCATTTT
5393 T
1 T
5394 TATTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (22 bp):
TCCATTTTTACATTTTCATTTT
Found at i:5401 original size:7 final size:7
Alignment explanation
Indices: 5352--5400 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
5342 TTAGCCTCTC
5352 CATTTTT
1 CATTTTT
5359 -ACTTTTT
1 CA-TTTTT
5366 CATTTTT
1 CATTTTT
5373 CCATTTTT
1 -CATTTTT
5381 CA-TTTT
1 CATTTTT
5387 CATTTTT
1 CATTTTT
*
5394 TATTTTT
1 CATTTTT
5401 TTCTGACTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
6 7 0.19
7 22 0.59
8 8 0.22
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Done.