Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_250 ID=scaffold_250-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: 8969
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1861 original size:18 final size:18
Alignment explanation
Indices: 1838--1879 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1828 AGGCTGCTGA
1838 ACGTGGGCGGTTGCTGCG
1 ACGTGGGCGGTTGCTGCG
1856 ACGTGGGCGGTTGCTGCG
1 ACGTGGGCGGTTGCTGCG
1874 ACGTGG
1 ACGTGG
1880 AGTACGCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (18 bp):
ACGTGGGCGGTTGCTGCG
Found at i:2563 original size:128 final size:127
Alignment explanation
Indices: 2374--2717 Score: 483
Period size: 128 Copynumber: 2.7 Consensus size: 127
2364 GTCTGATGAG
* * * *** * *
2374 ATCTGCTCTACTGCAAC-TCATAGAGATAAGATCCGTTTTTAATCCGCTCCACTGCATCTTCAGG
1 ATCTACTCTTCTGCAACTTCAGAGAGATAAGATCTAATGTTAATCCGCTCCACTGCAACTTCAGG
*
2438 GAGATAGGATTATTTTCTTCAATTTACTCCACTGCAACTTCAGGGAGATAAGATTGGATACA
66 GAGATAGGATTATTTTCTTCAATTTACTCCACTGCAACTTCAGGGAGATAAGACTGGATACA
* * *
2500 ATCTGCTCTTCTGTAACTTCAGAGAAGCTAAGATCTAATGTTAATCCGCTCCACTGCAACTTCAG
1 ATCTACTCTTCTGCAACTTCAGAG-AGATAAGATCTAATGTTAATCCGCTCCACTGCAACTTCAG
* * * * *
2565 GGAGATAGGATTATTTTCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGCG
65 GGAGATAGGATTATTTTCTTCAATTTACTCCACTGCAACTTCAGGGAGATAAGACTGGATACA
* * * *
2628 ATCTACTCTTCTGCAACTTTAGAGAGATAAGATTTGATTTTAATCCGCTCCACTGCAACTTCAGG
1 ATCTACTCTTCTGCAACTTCAGAGAGATAAGATCTAATGTTAATCCGCTCCACTGCAACTTCAGG
2693 GAGATAGGATTATTTTCTTCAATTT
66 GAGATAGGATTATTTTCTTCAATTT
2718 GTTTAACTGC
Statistics
Matches: 193, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
126 15 0.08
127 66 0.34
128 112 0.58
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (127 bp):
ATCTACTCTTCTGCAACTTCAGAGAGATAAGATCTAATGTTAATCCGCTCCACTGCAACTTCAGG
GAGATAGGATTATTTTCTTCAATTTACTCCACTGCAACTTCAGGGAGATAAGACTGGATACA
Found at i:2598 original size:44 final size:44
Alignment explanation
Indices: 2414--2715 Score: 187
Period size: 44 Copynumber: 7.1 Consensus size: 44
2404 ATCCGTTTTT
* *
2414 AATCCGCTCCACTGCATCTTCAGGGAGATAGGATTATTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
* * * *** *
2458 AATTTACTCCACTGCAACTTCAGGGAGATA--A-GATTGGATAC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
** * * * * * *
2499 AATCTGCTCTTCTGTAACTTCAGAGAAGCTAAGATCTA--ATGTT-
1 AATCTGCTCCACTGCAACTTCAG-GGAGATAGGAT-TATTTTCTTC
*
2542 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
* * * *** *
2586 AATCTGCTCCACTGCAACTTTAGGGAGATA--A-GACTGGATGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
* * ** * * * *
2627 GATCTACTCTTCTGCAACTTTAGAGAGATAAGATT-TGATT-TT-
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAT-TTTCTTC
*
2669 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
2713 AAT
1 AAT
2716 TTGTTTAACT
Statistics
Matches: 185, Mismatches: 58, Indels: 30
0.68 0.21 0.11
Matches are distributed among these distances:
41 54 0.29
42 44 0.24
43 27 0.15
44 59 0.32
46 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATTTTCTTC
Found at i:2763 original size:50 final size:50
Alignment explanation
Indices: 2709--3067 Score: 183
Period size: 50 Copynumber: 7.2 Consensus size: 50
2699 GGATTATTTT
* *
2709 CTTCAATTTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGA
1 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGG
** *** *** ** * * *
2759 CTTCAATCTGTTCCACTGC-ACCACCAAGAAGGTAAAATTCGTCGTTGTGG
1 CTTCAATCTGTTTAACTGCAATGTCGGGGAA-ACAAGATTCGCCGTCGTGG
* * * * *
2809 CTTCAATATATTTAACTACAATGTCAGGGG-AACAAGATTCGCCATCGTGA
1 CTTCAATCTGTTTAACTGCAATGTC-GGGGAAACAAGATTCGCCGTCGTGG
* *** ** * ** * * *
2859 CTTCAATCTATTCCCCT--ACCG-CTAGGGAAGTAAGATTCACTGTTGTGG
1 CTTCAATCTGTTTAACTGCAATGTC-GGGGAAACAAGATTCGCCGTCGTGG
* * * * *
2907 CTTCAATCTTTTTAATTGCAATGT-TGGGAAACAAGATACGCCGTCGTAG
1 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGG
** * ** * * ** *
2956 CTTCAATCTGTTCCACTACACCGCCGAGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGG
* * *
3006 CTTCAATCTTTTTAATTGCAATGTCGAGGAAACAAGA-TCTGCCGTCGTGG
1 CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTC-GCCGTCGTGG
3056 CTTCAATCTGTT
1 CTTCAATCTGTT
3068 ACACTGTAAT
Statistics
Matches: 210, Mismatches: 90, Indels: 18
0.66 0.28 0.06
Matches are distributed among these distances:
47 4 0.02
48 27 0.13
49 40 0.19
50 135 0.64
51 3 0.01
52 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (50 bp):
CTTCAATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGG
Found at i:2843 original size:100 final size:98
Alignment explanation
Indices: 2709--3073 Score: 418
Period size: 100 Copynumber: 3.7 Consensus size: 98
2699 GGATTATTTT
2709 CTTCAAT-TTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTGACTTCAATCTGTTCC
1 CTTCAATCTT-TTTAACTGCAATGTC-GGGAAACAAGATTCGCCGTCGTGACTTCAATCTGTTCC
* * * *
2773 ACTGCACCACCAAGAAGGTAAAATTCGTCGTTGTGG
64 ACTGCACCGCCAGGAA-GTAAGATTCGACGTTGTGG
* * * * * * *
2809 CTTCAATATATTTAACTACAATGTCAGGGGAACAAGATTCGCCATCGTGACTTCAATCTATTCCC
1 CTTCAATCTTTTTAACTGCAATGTC-GGGAAACAAGATTCGCCGTCGTGACTTCAATCTGTTCCA
*
2874 CT--ACCGCTAGGGAAGTAAGATTC-ACTGTTGTGG
65 CTGCACCGCCA-GGAAGTAAGATTCGAC-GTTGTGG
* * *
2907 CTTCAATCTTTTTAATTGCAATGTTGGGAAACAAGATACGCCGTCGT-AGCTTCAATCTGTTCCA
1 CTTCAATCTTTTTAACTGCAATGTCGGGAAACAAGATTCGCCGTCGTGA-CTTCAATCTGTTCCA
* *
2971 CTACACCGCCGAGGAAGTAAGATTCGCCGTTGTGG
65 CTGCACCGCC-AGGAAGTAAGATTCGACGTTGTGG
* * *
3006 CTTCAATCTTTTTAATTGCAATGTCGAGGAAACAAGA-TCTGCCGTCGTGGCTTCAATCTGTTAC
1 CTTCAATCTTTTTAACTGCAATGTCG-GGAAACAAGATTC-GCCGTCGTGACTTCAATCTGTTCC
3070 ACTG
64 ACTG
3074 TAATGCCAAA
Statistics
Matches: 225, Mismatches: 29, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
96 1 0.00
97 35 0.16
98 40 0.18
99 54 0.24
100 94 0.42
101 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (98 bp):
CTTCAATCTTTTTAACTGCAATGTCGGGAAACAAGATTCGCCGTCGTGACTTCAATCTGTTCCAC
TGCACCGCCAGGAAGTAAGATTCGACGTTGTGG
Found at i:4480 original size:21 final size:20
Alignment explanation
Indices: 4456--4524 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 20
4446 TGAGCTCCTC
4456 TGATCACCTCATGCCCTATTT
1 TGATCACCTCATGCCC-ATTT
* * *
4477 TGATCA-AT-ATTTGAGCCATTC
1 TGATCACCTCA--TG-CCCATTT
4498 TGATCACCTCATGCCCCATTT
1 TGATCACCTCATG-CCCATTT
4519 TGATCA
1 TGATCA
4525 ATATTTGAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 30 0.83
22 3 0.08
23 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (20 bp):
TGATCACCTCATGCCCATTT
Found at i:4483 original size:42 final size:42
Alignment explanation
Indices: 4415--4535 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 42
4405 AGTATAGCAA
* * *
4415 GATCACCGCATG-CCTCATTCTAATCAATATTTGAGCTC-CTCT
1 GATCACCTCATGCCCT-ATTTTGATCAATATTTGAGC-CACTCT
*
4457 GATCACCTCATGCCCTATTTTGATCAATATTTGAGCCATTCT
1 GATCACCTCATGCCCTATTTTGATCAATATTTGAGCCACTCT
*
4499 GATCACCTCATGCCCCATTTTGATCAATATTTGAGCC
1 GATCACCTCATGCCCTATTTTGATCAATATTTGAGCC
4536 GCCCTTTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (42 bp):
GATCACCTCATGCCCTATTTTGATCAATATTTGAGCCACTCT
Found at i:4697 original size:23 final size:22
Alignment explanation
Indices: 4666--4732 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 22
4656 TTATTTTTTA
*
4666 TTTTGATTTTGATTTTTCCTGAT
1 TTTTTATTTTGATTTTT-CTGAT
4689 TTTTTATTTTTTGATTTTT-TGAT
1 TTTTTA--TTTTGATTTTTCTGAT
4712 TTTATT-TTTTCAGATTTTTCT
1 TTT-TTATTTT--GATTTTTCT
4733 TTGATTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 4 0.11
23 19 0.51
24 3 0.08
25 11 0.30
ACGTcount: A:0.13, C:0.06, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTTTATTTTGATTTTTCTGAT
Found at i:4698 original size:16 final size:16
Alignment explanation
Indices: 4672--4714 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
4662 TTTATTTTGA
4672 TTTTGATTTTTCCTGATT
1 TTTTGA-TTTT-CTGATT
*
4690 TTTT-ATTTTTTGATT
1 TTTTGATTTTCTGATT
4705 TTTTGATTTT
1 TTTTGATTTT
4715 ATTTTTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 1 0.04
18 4 0.17
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTTGATTTTCTGATT
Found at i:4705 original size:8 final size:8
Alignment explanation
Indices: 4672--4714 Score: 61
Period size: 8 Copynumber: 5.2 Consensus size: 8
4662 TTTATTTTGA
4672 TTTTGATT
1 TTTTGATT
4680 TTTCCTGATT
1 TTT--TGATT
4690 TTTT-ATT
1 TTTTGATT
4697 TTTTGATT
1 TTTTGATT
4705 TTTTGATT
1 TTTTGATT
4713 TT
1 TT
4715 ATTTTTTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.22
8 17 0.53
10 8 0.25
ACGTcount: A:0.12, C:0.05, G:0.09, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:4721 original size:7 final size:7
Alignment explanation
Indices: 4649--4714 Score: 55
Period size: 7 Copynumber: 9.0 Consensus size: 7
4639 TTTATCATTC
4649 TTATTTT
1 TTATTTT
4656 TTATTTT
1 TTATTTT
4663 TTA-TTT
1 TTATTTT
*
4669 TGA-TTT
1 TTATTTT
*
4675 TGATTTT
1 TTATTTT
4682 TCCTGATTTT
1 T--T-ATTTT
4692 TTATTTT
1 TTATTTT
4699 TTGATTTT
1 TT-ATTTT
4707 TTGATTTT
1 TT-ATTTT
4715 ATTTTTTCAG
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
6 11 0.21
7 21 0.40
8 14 0.27
10 6 0.12
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (7 bp):
TTATTTT
Done.