Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_284 ID=scaffold_284-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: 8663
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Found at i:1922 original size:99 final size:99
Alignment explanation
Indices: 1684--2720 Score: 1605
Period size: 99 Copynumber: 10.5 Consensus size: 99
1674 CCAATTACAA
* * * * ** ** * * *
1684 TGTCGAGGAAACAAGATCTGCCGTCGTAACTTCAATCTATTCAACTGCACTGCTAAGGAGGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
* *
1749 ATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCGT
66 ATCCGCCGTTGTGGCTTCAATC-TTTTAATTGCGC
* *
1784 TGTCGAGGAAACCAGATCTGCCGTTGTGACTTCAATCTACTCCGCTGCACTGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
*
1849 ATCCGCTGTTGTGGCTTCAATCTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* * * * *
1883 TGTCAGGGAAACCAGATCTACCATTGTGACTTCAATCTACTCCACTGCA-TCGCCAGGGAAGTAA
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACT-GCCAGGGAAGTAA
*
1947 GATCCGCCGTTGTGGCTTTAATCTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
*
1982 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
*
2047 ATCCGCCATTGTGGCTTCAATCTTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATC-TTTTAATTGCGC
* *
2082 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCATTGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
*
2147 ATCCGCCCTTGTGGCTTCAATC-TTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
2180 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
2245 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* *
2279 TGTCGGGGAAACCAGATCTGCCATTGTGACTTCAATCTGCTCCACTGCA-TCGCCAGGGAAGTAA
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACT-GCCAGGGAAGTAA
*
2343 GATCCGCCGTTGTGGCTTCAATTTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* * *
2378 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTTCGCTGTACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
2443 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* * *
2477 TGTTGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTTCGCTGCACCGCCAGGGAAGTAAG
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
*
2542 ATCCGCCGTTGTGGCTTCAATCTTTTAATTACGC
66 ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* * *
2576 TGTCGGGGAAACCAGATCTACCGTTGTGACTTCAATCTGTTCCACTGCA-TCGCCAGGGAAGTAA
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACT-GCCAGGGAAGTAA
* *
2640 GATCTGCCATTGTGGCTTCAATCTTTTAATTGCGC
65 GATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
* *
2675 TGTCGGAGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCGCT
1 TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCT
2721 ACAACGTTAA
Statistics
Matches: 870, Mismatches: 60, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
98 97 0.11
99 602 0.69
100 171 0.20
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.29
Consensus pattern (99 bp):
TGTCGGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCGCTGCACTGCCAGGGAAGTAAG
ATCCGCCGTTGTGGCTTCAATCTTTTAATTGCGC
Found at i:4055 original size:7 final size:8
Alignment explanation
Indices: 4034--4066 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4024 CCTTAGCCTC
4034 TCCATTTTT
1 TCCA-TTTT
4043 TCCATTTT
1 TCCATTTT
4051 T-CATTTT
1 TCCATTTT
4058 TCCATTTT
1 TCCATTTT
4066 T
1 T
4067 ATTTTTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.30
8 12 0.52
9 4 0.17
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (8 bp):
TCCATTTT
Found at i:4073 original size:15 final size:16
Alignment explanation
Indices: 4036--4074 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4026 TTAGCCTCTC
4036 CATTTTTTCCATTTTT
1 CATTTTTTCCATTTTT
4052 CA-TTTTTCCATTTTT
1 CATTTTTTCCATTTTT
4067 -ATTTTTTC
1 CATTTTTTC
4075 ACATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.86
16 2 0.09
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (16 bp):
CATTTTTTCCATTTTT
Found at i:4086 original size:15 final size:15
Alignment explanation
Indices: 4037--4086 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
4027 TAGCCTCTCC
*
4037 ATTTTTTCCATTTTT
1 ATTTTTTCCATCTTT
*
4052 CA-TTTTTCCATTTTT
1 -ATTTTTTCCATCTTT
4067 ATTTTTTCACATCTTT
1 ATTTTTTC-CATCTTT
4083 -TTTT
1 ATTTT
4087 CTTCTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 23 0.74
16 7 0.23
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTCCATCTTT
Found at i:4576 original size:1 final size:1
Alignment explanation
Indices: 4570--4662 Score: 60
Period size: 1 Copynumber: 93.0 Consensus size: 1
4560 CCGGTAGAGG
* * * * * * * * * *
4570 TTTTTTTTATTTTTTTGTTTTTGTTTTTTGTTTTTTTCTCTTTCTTTTCTCTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
4635 TGTTTTTTGTTTTTTGTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
4663 GCATTAAATC
Statistics
Matches: 64, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.01, C:0.05, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:4584 original size:7 final size:7
Alignment explanation
Indices: 4580--4663 Score: 70
Period size: 7 Copynumber: 12.0 Consensus size: 7
4570 TTTTTTTTAT
4580 TTTTTTG
1 TTTTTTG
4587 -TTTTTG
1 TTTTTTG
4593 TTTTTTG
1 TTTTTTG
4600 TTTTTT-
1 TTTTTTG
4606 TCTCTTTCT-
1 T-T-TTT-TG
*
4615 TTTCTCTTT
1 TTT-T-TTG
4624 TTTTTTG
1 TTTTTTG
4631 -TTTTTG
1 TTTTTTG
4637 TTTTTTG
1 TTTTTTG
4644 TTTTTTG
1 TTTTTTG
*
4651 TTTTGT-
1 TTTTTTG
4657 TTTTTTG
1 TTTTTTG
4664 CATTAAATCT
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
6 18 0.28
7 34 0.52
8 7 0.11
9 6 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (7 bp):
TTTTTTG
Found at i:4596 original size:13 final size:13
Alignment explanation
Indices: 4580--4661 Score: 75
Period size: 13 Copynumber: 6.5 Consensus size: 13
4570 TTTTTTTTAT
4580 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
4593 TTTTTTGTTTTT-
1 TTTTTTGTTTTTG
* *
4605 TTCTCTTT-CTTTTC
1 TT-T-TTTGTTTTTG
*
4619 TCTTTT-TTTTTG
1 TTTTTTGTTTTTG
4631 -TTTTTGTTTTTTG
1 TTTTTTG-TTTTTG
4644 TTTTTTG-TTTTG
1 TTTTTTGTTTTTG
4656 TTTTTT
1 TTTTTT
4662 TGCATTAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.07
12 20 0.34
13 24 0.41
14 10 0.17
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:4662 original size:13 final size:13
Alignment explanation
Indices: 4570--4663 Score: 74
Period size: 13 Copynumber: 7.4 Consensus size: 13
4560 CCGGTAGAGG
*
4570 TTTT-TTTTATTT
1 TTTTGTTTTGTTT
4582 TTTTGTTTT-TGTT
1 TTTTGTTTTGT-TT
4595 TTTTGTTTT-TTT
1 TTTTGTTTTGTTT
* * *
4607 CTCTTTCTTTTCTCT
1 -T-TTTGTTTTGTTT
4622 TTTT-TTTTGTTT
1 TTTTGTTTTGTTT
4634 TTGTT-TTTTG-TT
1 TT-TTGTTTTGTTT
4646 TTTTGTTTTGTTT
1 TTTTGTTTTGTTT
4659 TTTTG
1 TTTTG
4664 CATTAAATCT
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
11 2 0.03
12 24 0.34
13 34 0.49
14 8 0.11
15 2 0.03
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTGTTTTGTTT
Done.