Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold880
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: 17111
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Found at i:7708 original size:40 final size:40
Alignment explanation
Indices: 7608--7828 Score: 356
Period size: 40 Copynumber: 5.5 Consensus size: 40
7598 CGGATGATAA
7608 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATGAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
7649 AACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 --CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
7691 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7731 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7771 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
7811 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
7829 TACTTGGTTT
Statistics
Matches: 172, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
39 17 0.10
40 115 0.67
42 2 0.01
43 38 0.22
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:9559 original size:39 final size:39
Alignment explanation
Indices: 9447--9715 Score: 368
Period size: 39 Copynumber: 7.0 Consensus size: 39
9437 AAGACACTGA
* *
9447 AAATGTATCCGGGCTAAAGTCCCGCACGCTTCGTGCTGG
1 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
9486 AAATGTATC-CGGCTAAAGT-CCGCAGGCTTCGTGCTGG
1 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
9523 AAATATATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* **
9562 AAATATAT-TCGGGCTAAAGTCCCGCAGGCTTCGTGCTTT
1 AAATGTATCT-GGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
9601 AAATGTATCCT-GGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTAT-CTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
9640 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
9679 AAATGTATC-CGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTG
9716 ATAATATAAT
Statistics
Matches: 209, Mismatches: 15, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
37 25 0.12
38 44 0.21
39 139 0.67
41 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (39 bp):
AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:9669 original size:117 final size:115
Alignment explanation
Indices: 9447--9715 Score: 405
Period size: 117 Copynumber: 2.3 Consensus size: 115
9437 AAGACACTGA
* * *
9447 AAATGTATCCGGGCTAAAGTCCCGCACGCTTCGTGCTGGAAATGTATCCGGCTAAAGTCCGCAGG
1 AAATGTATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGCCAAAGTCCGCAGG
* *
9512 CTTCGTGCTGGAAATATATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
66 CTTCGTGCTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* **
9562 AAATATATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTTTAAATGTATCCTGGCCAAAGTCCCGCA
1 AAATGTATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCC-GGCCAAAGT-CCGCA
*
9627 GGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
64 GGCTTCGTGCTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* * *
9679 AAATGTA-TCCGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
9716 ATAATATAAT
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
115 44 0.32
116 34 0.25
117 60 0.43
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.25
Consensus pattern (115 bp):
AAATGTATTCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGCCAAAGTCCGCAGG
CTTCGTGCTGGAAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:15548 original size:114 final size:111
Alignment explanation
Indices: 15320--15581 Score: 397
Period size: 114 Copynumber: 2.3 Consensus size: 111
15310 AAGACACTGA
*
15320 AAATGTATCCGGGCTAAAGTCCCG-AGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTACAGGC
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTACAGGC
15384 TTCGTGCTGAAATATACGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
66 TTCGTGCTGAAATATACGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
*
15430 AAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTAT-C-GGCCAAAGTCCCGCA
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGT---ACA
*
15492 GGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
63 GGCTTCGTGCT-GAAA--TATACGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
* *
15544 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
15582 ATAATATATT
Statistics
Matches: 139, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
108 8 0.06
109 14 0.10
110 32 0.23
111 13 0.09
112 4 0.03
114 43 0.31
115 25 0.18
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (111 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTACAGGC
TTCGTGCTGAAATATACGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:15597 original size:39 final size:39
Alignment explanation
Indices: 15320--15581 Score: 391
Period size: 39 Copynumber: 7.0 Consensus size: 39
15310 AAGACACTGA
15320 AAATGTATCCGGGCTAAAGTCCCG-AGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15358 AAATGTATCCGGGCTAAAGT---ACAGGCTTCGTGCT-G
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
15393 AAA--TATACGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
15430 AAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15468 AAATGTAT-C-GGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
15505 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
15544 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
15582 ATAATATATT
Statistics
Matches: 205, Mismatches: 10, Indels: 17
0.88 0.04 0.07
Matches are distributed among these distances:
33 13 0.06
35 4 0.02
36 25 0.12
37 40 0.20
38 56 0.27
39 67 0.33
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Done.