Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_444 ID=scaffold_444-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: 7321
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.31
Warning! 384 characters in sequence are not A, C, G, or T
Found at i:344 original size:24 final size:24
Alignment explanation
Indices: 324--371 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
314 AAGATTTAGT
*
324 ATTTATGAGTATAATATATTTAAC
1 ATTTATGAGCATAATATATTTAAC
*
348 ATTTATTAGCATAATATATTTAAC
1 ATTTATGAGCATAATATATTTAAC
372 TTCGATTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTTATGAGCATAATATATTTAAC
Found at i:379 original size:24 final size:24
Alignment explanation
Indices: 334--380 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
324 ATTTATGAGT
*
334 ATAATATATTTAACATTTATTAGC
1 ATAATATATTTAACATTGATTAGC
358 ATAATATATTTAAC-TTCGATTAG
1 ATAATATATTTAACATT-GATTAG
381 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAACATTGATTAGC
Found at i:2117 original size:17 final size:18
Alignment explanation
Indices: 2095--2138 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
2085 CTAATGAGCG
*
2095 ACAAATAATCAATA-AAT
1 ACAAATAAGCAATACAAT
2112 ACAAATAAGCAATACAAT
1 ACAAATAAGCAATACAAT
*
2130 ACACATAAG
1 ACAAATAAG
2139 AGCAATAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (18 bp):
ACAAATAAGCAATACAAT
Found at i:2542 original size:12 final size:12
Alignment explanation
Indices: 2525--2556 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2515 TGAAAAGTTT
2525 AATAATAATATA
1 AATAATAATATA
2537 AATAATAATATA
1 AATAATAATATA
*
2549 TATAATAA
1 AATAATAA
2557 ATTGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAATAATATA
Found at i:2556 original size:15 final size:15
Alignment explanation
Indices: 2524--2553 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2514 ATGAAAAGTT
2524 TAATAATAATATAAA
1 TAATAATAATATAAA
2539 TAATAATATATATAA
1 TAATAATA-ATATAA
2554 TAAATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAATAATATAAA
Found at i:2942 original size:24 final size:23
Alignment explanation
Indices: 2852--3042 Score: 156
Period size: 24 Copynumber: 8.1 Consensus size: 23
2842 GTATAAAACG
* * *
2852 ATACATGGTAACTTTAAATAATA
1 ATACATGATAAATTAAAATAATA
* *
2875 ATAAATGATAAGTTAAAAAATAATA
1 ATACATGATAAATT--AAAATAATA
* *
2900 ATACTTGATAGATTCAAAATGAA-A
1 ATACATGATAAATT-AAAAT-AATA
*
2924 ATACGTGATAAACTTAAAATAATA
1 ATACATGATAAA-TTAAAATAATA
* *
2948 ATACATGATAAATTTAAATAACAA
1 ATACATGATAAATTAAAATAA-TA
*
2972 ATACAAGATAAATTTAAAATAATA
1 ATACATGATAAA-TTAAAATAATA
2996 ATACATTG-TAAATTAAAATAAT-
1 ATACA-TGATAAATTAAAATAATA
** *
3018 ATTGATGATAAATTTAAA-AATA
1 ATACATGATAAATTAAAATAATA
3040 ATA
1 ATA
3043 TTAAGCTTAA
Statistics
Matches: 136, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.04
22 14 0.10
23 31 0.23
24 55 0.40
25 31 0.23
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.31
Consensus pattern (23 bp):
ATACATGATAAATTAAAATAATA
Found at i:3083 original size:24 final size:24
Alignment explanation
Indices: 2981--3093 Score: 83
Period size: 24 Copynumber: 4.7 Consensus size: 24
2971 AATACAAGAT
* * *
2981 AAATTTAAAATAATAATACATTGT-
1 AAATTAAAAATAATATTAGATT-TA
*
3005 AAATT-AAAATAATATT-GATGATA
1 AAATTAAAAATAATATTAGAT-TTA
* *
3028 AATTTAAAAATAATATTA-AGCTTA
1 AAATTAAAAATAATATTAGA-TTTA
3052 AACA-TAAAAATAATATTAGATTTA
1 AA-ATTAAAAATAATATTAGATTTA
*
3076 AAATTAAATATATATATT
1 AAATTAAAAATA-ATATT
3094 TTTAAAAACA
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
22 3 0.04
23 15 0.21
24 47 0.66
25 6 0.08
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATTAAAAATAATATTAGATTTA
Found at i:4468 original size:2 final size:2
Alignment explanation
Indices: 4461--4500 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4451 AATACTACCC
4461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4501 GTAAACTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.