Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_816 ID=scaffold_816-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: 6300
ACGTcount: A:0.17, C:0.11, G:0.10, T:0.17
Warning! 2851 characters in sequence are not A, C, G, or T
Found at i:108 original size:17 final size:18
Alignment explanation
Indices: 65--111 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
55 ATATGTGTAT
*
65 ATATATAAATATGAGAAAA
1 ATATAT-AATATGAAAAAA
84 ATAT-TAAT-TGAAAAAA
1 ATATATAATATGAAAAAA
100 ATATATAATATG
1 ATATATAATATG
112 TACATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.44
17 7 0.28
18 3 0.12
19 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
ATATATAATATGAAAAAA
Found at i:348 original size:3 final size:3
Alignment explanation
Indices: 340--377 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
330 TGTACATGAA
*
340 AAT AAT AAT TA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
378 GATGATGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:634 original size:14 final size:14
Alignment explanation
Indices: 614--645 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
604 TGCAGCATAG
614 AAAAAAAAAGAAAAC
1 AAAAAAAAA-AAAAC
629 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
643 AAA
1 AAA
646 GGCTCTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:1226 original size:17 final size:17
Alignment explanation
Indices: 1199--1242 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1189 TTTGAGCCAC
1199 TAAATTTGGGCCA-TTTT
1 TAAA-TTGGGCCACTTTT
1216 TGAAATTGGGCCACCTTTT
1 T-AAATTGGGCCA-CTTTT
1235 TAAATTGG
1 TAAATTGG
1243 TTTTGGGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (17 bp):
TAAATTGGGCCACTTTT
Found at i:1501 original size:45 final size:44
Alignment explanation
Indices: 1450--1556 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 44
1440 GGAGCTAGTG
* * *
1450 CTTCAATCTATTTCACTGCGACTGC-AGGGAGATAAGA-CTTACAAT
1 CTTCAATCTATTCCACT--GAATGCTAGGGAGATAAGATCTGA-AAT
1495 CTTCAATCTATTCCACT-AATGCTTAGGGAGATAAGATCTGAAAT
1 CTTCAATCTATTCCACTGAATGC-TAGGGAGATAAGATCTGAAAT
1539 CTTCAATCTATTCCACTG
1 CTTCAATCTATTCCACTG
1557 TTGTCCAGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
42 4 0.07
44 32 0.58
45 19 0.35
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (44 bp):
CTTCAATCTATTCCACTGAATGCTAGGGAGATAAGATCTGAAAT
Found at i:1686 original size:132 final size:132
Alignment explanation
Indices: 1506--1819 Score: 540
Period size: 132 Copynumber: 2.4 Consensus size: 132
1496 TTCAATCTAT
* *
1506 TCCACTAATGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGGAGT
1 TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
* * *
1571 AGAATTACTGGCTTCCATGTAC-TCTATTATAACCACAGGGAGGTAAAATCTGACATCTTCGATC
66 AGAATTACTGGCTTCAATGTACTTC-ACTATAACCACAGGGAGGTAAAATCCGACATCTTCGATC
1635 TGC
130 TGC
* *
1638 TCCAGTACTGCTTAGGGAGATAAGATCTTAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
1 TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
*
1703 AGAATTACTGGCTTCAATGTACTTCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCT
66 AGAATTACTGGCTTCAATGTACTTCACTATAACCACAGGGAGGTAAAATCCGACATCTTCGATCT
1768 GC
131 GC
1770 TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
1 TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
1820 TTNNNNNNNN
Statistics
Matches: 171, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
132 169 0.99
133 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (132 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
AGAATTACTGGCTTCAATGTACTTCACTATAACCACAGGGAGGTAAAATCCGACATCTTCGATCT
GC
Found at i:2464 original size:132 final size:132
Alignment explanation
Indices: 2227--2521 Score: 527
Period size: 132 Copynumber: 2.2 Consensus size: 132
2217 NNNNNNNNNN
*
2227 AAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTACCATCTTTG
1 AAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTACCATCTTCG
2292 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAG
66 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAG
2357 GA
131 GA
* *
2359 AAGTAGAATTACTGGCTTCAATGTACTCCTCTATAACCACAGGGAGGTAAAATCTGCCATCTTCG
1 AAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTACCATCTTCG
*
2424 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCGG
66 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAG
*
2489 GG
131 GA
* *
2491 AAGTAGAATTACTAGCTTCAATATACTCCAC
1 AAGTAGAATTACTGGCTTCAATGTACTCCAC
2522 AGGGAAGTAA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 155 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
AAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTACCATCTTCG
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAG
GA
Done.