Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_485 ID=scaffold_485-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: 6611
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.31
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:574 original size:46 final size:46
Alignment explanation
Indices: 507--1035 Score: 743
Period size: 46 Copynumber: 11.5 Consensus size: 46
497 TCACTGTCAG
* * *
507 ATACAGGAAGACAATATCTGCTATCTTCGTTCTCCTCCGCTACCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* *
553 ATACAGGAAGACAAGAACTGCTATCTTCGATCTCATCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
599 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * * *
645 ATATAGGAAGATAAGATCTGCTATCTTCGATCTCCTCTGCTACCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
*
691 ATACAGGAAGACAAGATCCGCTATCTTCGATCTCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * * *
737 ATACATGAAGAGAAGATCCGCTATCTTCGATCTCCTTCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * * *
783 ATACAAGAAGATAAGATCCGCTGTCTTCGATCTCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
829 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * ** **
875 ATACAGAAAGATAAGATCCACTATCTTCGATCTCCTCCATTGCCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * *
921 ATACAGGAAGACAAGATCCGCTATCTTCGATCTCCTCTGCTACCAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
* * * *
967 ATACTGGAAGATAAGATCTGCTATCTTCGGTCTCCTCCACTGCCAAA
1 ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCC-AA
* **
1014 ATACAAGAAGATGAGATCTGCT
1 ATACAGGAAGACAAGATCTGCT
1036 GCTTCTGGTC
Statistics
Matches: 432, Mismatches: 50, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
46 411 0.95
47 21 0.05
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (46 bp):
ATACAGGAAGACAAGATCTGCTATCTTCGATCTCCTCCGCTGCCAA
Found at i:1832 original size:49 final size:49
Alignment explanation
Indices: 1779--1941 Score: 112
Period size: 49 Copynumber: 3.1 Consensus size: 49
1769 GATAAAATGG
1779 AATTTTATTGAGAATAAGGCTCAAAATGAATAAATTAATCAAGATATCA
1 AATTTTATTGAGAATAAGGCTCAAAATGAATAAATTAATCAAGATATCA
* * * * * * * *
1828 AATTTTGTTCAG-ATACGAACTGAATAAGATGAAAAATATTATTACAATGGATAAGATGA
1 AATTTTATTGAGAATAAG-GCT-CA-AA-ATGAATAA-ATTAAT-CAA--GAT---ATCA
* * * *
1887 AATTTTATTGAGAACAAAGCTCGAAATGAATAAATTAATCAAGATAGCA
1 AATTTTATTGAGAATAAGGCTCAAAATGAATAAATTAATCAAGATATCA
1936 AATTTT
1 AATTTT
1942 GCTAAGATAA
Statistics
Matches: 82, Mismatches: 20, Indels: 24
0.65 0.16 0.19
Matches are distributed among these distances:
48 4 0.05
49 20 0.24
50 1 0.01
51 2 0.02
52 10 0.12
53 5 0.06
54 6 0.07
55 5 0.06
56 10 0.12
57 2 0.02
59 15 0.18
60 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (49 bp):
AATTTTATTGAGAATAAGGCTCAAAATGAATAAATTAATCAAGATATCA
Found at i:1893 original size:108 final size:104
Alignment explanation
Indices: 1749--2067 Score: 375
Period size: 108 Copynumber: 3.1 Consensus size: 104
1739 GAAAAATGCT
* * * *
1749 TGAAAAAGATTATCAAAATGGATAAAATGGAATTTTATTGAGAATAAGGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAA-GCTCGAAATGAATAAAT
*
1814 TAATCAAGATATCAAATTTTGTTCAGATACGAACTGAATAAGA
65 TAATCAAGATAGCAAATTTTG-TCA-ATACGAA-TGAATAAGA
* * *
1857 TGAAAAATATTATTACAATGGATAAGATGAAATTTTATTGAGAACAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAAC-AAGCTCGAAATGAATAAAT
1922 TAATCAAGATAGCAAATTTTG-C--T---AA-G-ATAAGA
65 TAATCAAGATAGCAAATTTTGTCAATACGAATGAATAAGA
* * *
1954 TGAAAAAGATTATCACAATGGATAAAATGAAACTTTATTGAGAGCACAGCTCGAAATGTATAAAT
1 TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACA-AGCTCGAAATGAATAAAT
* * *
2019 TAATCAATATAGAAAATTTTGCTAATATACGAAATGAATAAGA
65 TAATCAAGATAGCAAATTTTG-TCA-ATACG-AATGAATAAGA
2062 TGAAAA
1 TGAAAA
2068 CAGGTGCCCC
Statistics
Matches: 181, Mismatches: 17, Indels: 26
0.81 0.08 0.12
Matches are distributed among these distances:
96 1 0.01
97 82 0.45
98 1 0.01
100 2 0.01
102 1 0.01
103 1 0.01
106 3 0.02
107 1 0.01
108 87 0.48
109 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (104 bp):
TGAAAAAGATTATCACAATGGATAAAATGAAATTTTATTGAGAACAAGCTCGAAATGAATAAATT
AATCAAGATAGCAAATTTTGTCAATACGAATGAATAAGA
Found at i:2017 original size:97 final size:97
Alignment explanation
Indices: 1851--2043 Score: 305
Period size: 97 Copynumber: 2.0 Consensus size: 97
1841 TACGAACTGA
* * * *
1851 ATAAGATGAAAAATATTATTACAATGGATAAGATGAAATTTTATTGAGAACAAAGCTCGAAATGA
1 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAACTTTATTGAGAACAAAGCTCGAAATGA
*
1916 ATAAATTAATCAAGATAGCAAATTTTGCTAAG
66 ATAAATTAATCAAGATAGAAAATTTTGCTAAG
* * *
1948 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAACTTTATTGAGAGCACAGCTCGAAATGT
1 ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAACTTTATTGAGAACAAAGCTCGAAATGA
*
2013 ATAAATTAATCAATATAGAAAATTTTGCTAA
66 ATAAATTAATCAAGATAGAAAATTTTGCTAA
2044 TATACGAAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.28
Consensus pattern (97 bp):
ATAAGATGAAAAAGATTATCACAATGGATAAAATGAAACTTTATTGAGAACAAAGCTCGAAATGA
ATAAATTAATCAAGATAGAAAATTTTGCTAAG
Found at i:2340 original size:6 final size:6
Alignment explanation
Indices: 2331--2420 Score: 71
Period size: 6 Copynumber: 14.8 Consensus size: 6
2321 TGACCTCTCA
* *
2331 TTTTTC TTTTTC TTTTT- ATTTTC TTTTTC TTCTTT- TATTTTA TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC T-TTTTC TTTTTC
* *
2379 TTCTGTTC TTTTTTC CTTTTC TTTTTC -TCTTC TTTTT- TTTTT
1 TT-T-TTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2421 TGGACATTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
5 13 0.19
6 41 0.59
7 9 0.13
8 4 0.06
9 2 0.03
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:2406 original size:19 final size:19
Alignment explanation
Indices: 2332--2401 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
2322 GACCTCTCAT
2332 TTTTCTTTTTC-T-TTTTA
1 TTTTCTTTTTCTTCTTTTA
2349 TTTTCTTTTTCTTCTTTTA
1 TTTTCTTTTTCTTCTTTTA
* *
2368 TTTTATTTTTCTTCTGTTCTT
1 TTTTCTTTTTCTTCT-TT-TA
*
2389 TTTTCCTTTTCTT
1 TTTTCTTTTTCTT
2402 TTTCTCTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.24
18 1 0.02
19 19 0.42
20 2 0.04
21 12 0.27
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTTCTTCTTTTA
Found at i:3839 original size:26 final size:26
Alignment explanation
Indices: 3799--3851 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
3789 CGTAACTCCC
*
3799 GCATGATAGTTACATTGCGCATTCAT
1 GCATGATAGTCACATTGCGCATTCAT
*
3825 GCATGATAGTCACATTGTGCATTCAT
1 GCATGATAGTCACATTGCGCATTCAT
3851 G
1 G
3852 TCGTACCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
GCATGATAGTCACATTGCGCATTCAT
Done.