Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga07g00606.P1
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: 6261
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2032 original size:64 final size:65
Alignment explanation
Indices: 1959--2094 Score: 240
Period size: 64 Copynumber: 2.1 Consensus size: 65
1949 AGTGACATTC
1959 TTTAAATAGTAAATGTTAATTCTATT-TCAATTTAGTTTTATTTAATTC-TTTTAATAGTATAAT
1 TTTAAATAGTAAATGTTAATTCTATTCT-AATTTAGTTTTATTTAATTCTTTTTAATAGTATAAT
2022 G
65 G
2023 TTTAAATAGTAAATGTTAATTCTATTCTAATTTAGTTTTATTTAATTCTTTTTAATAGTATAATG
1 TTTAAATAGTAAATGTTAATTCTATTCTAATTTAGTTTTATTTAATTCTTTTTAATAGTATAATG
*
2088 GTTAAAT
1 TTTAAAT
2095 TAATCCATTT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
64 46 0.67
65 23 0.33
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (65 bp):
TTTAAATAGTAAATGTTAATTCTATTCTAATTTAGTTTTATTTAATTCTTTTTAATAGTATAATG
Found at i:2746 original size:19 final size:18
Alignment explanation
Indices: 2716--2776 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
2706 TTCATTTTAA
2716 TAAAATTTATAAAAATTAT
1 TAAAA-TTATAAAAATTAT
* *
2735 TAAGAATTATAAAAATCAA
1 TAA-AATTATAAAAATTAT
*
2754 TAAAAATATTAAAAATTA-
1 TAAAATTA-TAAAAATTAT
2772 TAAAA
1 TAAAA
2777 AAATTACAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.25
19 25 0.69
20 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAAATTATAAAAATTAT
Found at i:2777 original size:9 final size:9
Alignment explanation
Indices: 2715--2777 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
2705 ATTCATTTTA
*
2715 ATAAAATTT
1 ATAAAAATT
2724 ATAAAAATT
1 ATAAAAATT
*
2733 ATTAAGAATT
1 A-TAAAAATT
*
2743 ATAAAAATCA
1 ATAAAAAT-T
2753 ATAAAAA-T
1 ATAAAAATT
2761 ATTAAAAATT
1 A-TAAAAATT
2771 ATAAAAA
1 ATAAAAA
2778 AATTACAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
8 1 0.02
9 27 0.60
10 17 0.38
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2777 original size:19 final size:19
Alignment explanation
Indices: 2725--2782 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
2715 ATAAAATTTA
* *
2725 TAAAAATTATTAAGAAT-T
1 TAAAAATTATAAAAAATAT
*
2743 ATAAAAATCA-ATAAAAATAT
1 -TAAAAATTATA-AAAAATAT
2763 TAAAAATTATAAAAAA-AT
1 TAAAAATTATAAAAAATAT
2781 TA
1 TA
2783 CAAGTCATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 4 0.12
19 26 0.81
20 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAAAATAT
Found at i:2842 original size:26 final size:27
Alignment explanation
Indices: 2804--2868 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
2794 AATAATATTT
*
2804 AAATTTTATAAAAATAAGAAAA-TTATA
1 AAATATTATAAAAAT-AGAAAATTTATA
*
2831 AAATATTA-AAAAGTAGAAAATTTATAA
1 AAATATTATAAAAATAGAAAATTTAT-A
*
2858 AAACATTATAA
1 AAATATTATAA
2869 TTATGCCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 6 0.19
26 9 0.28
27 15 0.47
28 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (27 bp):
AAATATTATAAAAATAGAAAATTTATA
Found at i:3534 original size:2 final size:2
Alignment explanation
Indices: 3527--3554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3517 TCAACATCAC
3527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3555 AATAACATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6053 original size:3 final size:3
Alignment explanation
Indices: 6045--6069 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6035 CCTAACATAC
6045 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
6070 GATGTGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.