Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4000
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: 16411
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1151 original size:15 final size:14
Alignment explanation
Indices: 1130--1172 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1120 TTAAATCAAA
1130 ATAATTTTATTTTT
1 ATAATTTTATTTTT
*
1144 ATTAATTTAAATTTTT
1 A-TAATTT-TATTTTT
*
1160 AAAATTTTATTTT
1 ATAATTTTATTTT
1173 GGTGAGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATAATTTTATTTTT
Found at i:7201 original size:31 final size:31
Alignment explanation
Indices: 7132--7201 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
7122 TTTGGCCTAC
7132 TTCAATCCCTAATGTTATCAGACATTCTCAA
1 TTCAATCCCTAATGTTATCAGACATTCTCAA
* * *
7163 TTTAATCCCTAATGTTATTAGACATT-TCTAG
1 TTCAATCCCTAATGTTATCAGACATTCTC-AA
7194 TTCAATCC
1 TTCAATCC
7202 TTTGGATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
TTCAATCCCTAATGTTATCAGACATTCTCAA
Found at i:7305 original size:12 final size:12
Alignment explanation
Indices: 7288--7312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7278 CTTTGAAATC
7288 TTTAAAAATTAT
1 TTTAAAAATTAT
7300 TTTAAAAATTAT
1 TTTAAAAATTAT
7312 T
1 T
7313 AAAATTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAAATTAT
Found at i:7364 original size:22 final size:21
Alignment explanation
Indices: 7339--7379 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
7329 GAAAAAATAT
7339 ATATAAATTTATAAAAATTACA
1 ATATAAATTTA-AAAAATTACA
**
7361 ATATTTATTTAAAAAATTA
1 ATATAAATTTAAAAAATTA
7380 AAAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAATTTAAAAAATTACA
Found at i:7538 original size:26 final size:25
Alignment explanation
Indices: 7509--7566 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
7499 TGTTTTATAA
*
7509 AATTTTAATAAAATTTATTTCTTTTT
1 AATTTTAATAAAATTTAGTT-TTTTT
* *
7535 AATTTTAGTAAATTTTAGTTTTTTT
1 AATTTTAATAAAATTTAGTTTTTTT
7560 ATATTTT
1 A-ATTTT
7567 TAAAATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 6 0.21
26 22 0.79
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
AATTTTAATAAAATTTAGTTTTTTT
Found at i:7631 original size:24 final size:23
Alignment explanation
Indices: 7601--7648 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
7591 ATTTTTTAAA
7601 ATAATTTCAATAATTTAATTTTAT
1 ATAATTT-AATAATTTAATTTTAT
* * *
7625 ATAATTTTATAGTTTTATTTTAT
1 ATAATTTAATAATTTAATTTTAT
7648 A
1 A
7649 ACAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
ATAATTTAATAATTTAATTTTAT
Found at i:7664 original size:24 final size:23
Alignment explanation
Indices: 7610--7664 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
7600 AATAATTTCA
* *
7610 ATAATTTAATTTTATATAATTTT
1 ATAATTTTATTTTATACAATTTT
*
7633 ATAGTTTTATTTTATAACAATTTT
1 ATAATTTTATTTTAT-ACAATTTT
*
7657 TTAATTTT
1 ATAATTTT
7665 TTAAATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
ATAATTTTATTTTATACAATTTT
Found at i:9181 original size:21 final size:21
Alignment explanation
Indices: 9152--9243 Score: 130
Period size: 21 Copynumber: 4.4 Consensus size: 21
9142 TTTTGCTCTG
* *
9152 CTCTGCTTCTCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
9173 CTTTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
9194 CTCTGCTTCCCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
* *
9215 CGCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
9236 CTCTGCTT
1 CTCTGCTT
9244 TAAGTTGTAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.04, C:0.45, G:0.18, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:12875 original size:9 final size:9
Alignment explanation
Indices: 12638--12906 Score: 191
Period size: 9 Copynumber: 28.4 Consensus size: 9
12628 TTAAAATGCC
*
12638 AGTTATTTA
1 AGTTATGTA
*
12647 ATTTATGTA
1 AGTTATGTA
*
12656 ATTTATGTA
1 AGTTATGTA
12665 AGTTATGTA
1 AGTTATGTA
*
12674 AGATATTATGTT
1 AG---TTATGTA
12686 A-TTATGTA
1 AGTTATGTA
*
12694 AGTTATGCA
1 AGTTATGTA
*
12703 AGTTTATATATA
1 AG--T-TATGTA
*
12715 AGCTTGTAGATA
1 AG-TTAT-G-TA
*
12727 ACTTATGTA
1 AGTTATGTA
12736 AGTTAATATGTA
1 AG-T--TATGTA
* *
12748 AGTTTTTTA
1 AGTTATGTA
*
12757 ATTTATGTA
1 AGTTATGTA
12766 AGTTATGTA
1 AGTTATGTA
*
12775 AGTTATTTA
1 AGTTATGTA
*
12784 ATTTATGTA
1 AGTTATGTA
12793 AGTTATGTA
1 AGTTATGTA
*
12802 AGTTATTTA
1 AGTTATGTA
*
12811 AGTTATTTA
1 AGTTATGTA
*
12820 ATTTATGTA
1 AGTTATGTA
12829 AGTTATGTA
1 AGTTATGTA
*
12838 AGTTATTTA
1 AGTTATGTA
*
12847 ATTTATGTA
1 AGTTATGTA
*
12856 ATTTATGTA
1 AGTTATGTA
12865 AGTTATGTA
1 AGTTATGTA
*
12874 AGATAT-TA
1 AGTTATGTA
*
12882 CGTTACTGAGTA
1 AGTTA-T--GTA
*
12894 AGTTATGCA
1 AGTTATGTA
12903 AGTT
1 AGTT
12907 TATATATAAG
Statistics
Matches: 207, Mismatches: 37, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
8 12 0.06
9 154 0.74
10 4 0.02
11 7 0.03
12 30 0.14
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Done.