Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold783
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: 6633
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.32
Warning! 131 characters in sequence are not A, C, G, or T
Found at i:1539 original size:132 final size:132
Alignment explanation
Indices: 1390--1736 Score: 517
Period size: 132 Copynumber: 2.7 Consensus size: 132
1380 AGATAGGGTA
* * ** *
1390 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCATTATCTTTGATCTACTCCA
1 ACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
* * *
1455 CTACTGCTTAGAGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGG-AGATAGA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGA
1519 ATT
130 ATT
* **
1522 ACTGGCTTCAATATACTCCACTATAACCACAATGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
* *
1587 CTACTGCTTAGGGAGACAAGATCTGAAATCTTTAATCTATTTCACTGCTGCCCAGGGAAGTAGAA
66 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
1652 TT
131 TT
*
1654 ACTGGCTTC-A-AT-GT--ACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1714 CTACTGCTTAGGGAGACAAGATC
66 CTACTGCTTAGGGAGACAAGATC
1737 NNNNNNNNNN
Statistics
Matches: 197, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
127 66 0.34
129 1 0.01
130 2 0.01
131 1 0.01
132 125 0.63
133 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
ACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
TT
Found at i:2243 original size:132 final size:132
Alignment explanation
Indices: 2098--2523 Score: 635
Period size: 132 Copynumber: 3.2 Consensus size: 132
2088 CAACTTCAGA
2098 GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTCC
1 GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTCC
*
2163 AATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGGAACCACA
66 AATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
2228 GG
131 GG
* *
2230 GAGGTAAAATCTGCCATCTTTGGTCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTCC
1 GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTCC
* *
2295 AATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCCATGTACTCCACTGTAACCTCA
66 AATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
2360 GG
131 GG
* * * * * *
2362 GAGGTAAAATCCGCCATCTTCGATCTGCTTCATTGTCGATGC--AAGAAGGCAAGATCTGAAATC
1 GAGGTAAAATCTGCCATCTTCGATCTGCTCCACT-AC--TGCTTAGGGAGGCAAGATCTGAAATC
* * *
2425 TTCAATCTATTCCACTG-CTGCCCAGGGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAA
63 TCCAATCTATTCCATTGTC-GCCCAAGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAA
2488 CCACAGG
126 CCACAGG
* *
2495 GAGGTAAAATCTGTCATCTTTGATCTGCT
1 GAGGTAAAATCTGCCATCTTCGATCTGCT
2524 TCGCTGTCTA
Statistics
Matches: 268, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
132 158 0.59
133 107 0.40
135 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (132 bp):
GAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAGATCTGAAATCTCC
AATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
GG
Found at i:2572 original size:133 final size:132
Alignment explanation
Indices: 2098--2576 Score: 569
Period size: 132 Copynumber: 3.6 Consensus size: 132
2088 CAACTTCAGA
* * * *
2098 GAGGTAAAATCTGCCATCTTCGATCTGC-TCC--ACTACTGCTTAGGGAGGCAAGATCTGAAATC
1 GAGGTAAAATCTGCCATCTTTGATCTGCTTCCTGTCTA-TGC--AAGAAGGCAAGATCTGAAATC
* * *
2160 TCCAATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGGAACC
63 TTCAATCTATTCCACTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACC
2225 ACAGG
128 ACAGG
* * * *
2230 GAGGTAAAATCTGCCATCTTTGGTCTGC-TCC--ACTACTGCTTAGGGAGGCAAGATCTGAAATC
1 GAGGTAAAATCTGCCATCTTTGATCTGCTTCCTGTCTA-TGC--AAGAAGGCAAGATCTGAAATC
* * *
2292 TCCAATCTATTCCATTGTCGCCCAAGGAGATAGAATTACTGGCTTCCATGTACTCCACTGTAACC
63 TTCAATCTATTCCACTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACC
*
2357 TCAGG
128 ACAGG
* * * *
2362 GAGGTAAAATCCGCCATCTTCGATCTGCTTCATTGTCGATGCAAGAAGGCAAGATCTGAAATCTT
1 GAGGTAAAATCTGCCATCTTTGATCTGCTTC-CTGTCTATGCAAGAAGGCAAGATCTGAAATCTT
*
2427 CAATCTATTCCACTG-CTGCCCAGGGA-AGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC
65 CAATCTATTCCACTGTC-GCCCAAGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACC
2490 ACAGG
128 ACAGG
* * **
2495 GAGGTAAAATCTGTCATCTTTGATCTGCTTCGCTGTCTATGCATGAAGGCAAGATCTGCTATCTT
1 GAGGTAAAATCTGCCATCTTTGATCTGCTTC-CTGTCTATGCAAGAAGGCAAGATCTGAAATCTT
* **
2560 CAACCTGCTCCACTGTC
65 CAATCTATTCCACTGTC
2577 TCTGAGGGAG
Statistics
Matches: 310, Mismatches: 30, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
132 154 0.50
133 150 0.48
134 1 0.00
135 3 0.01
136 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (132 bp):
GAGGTAAAATCTGCCATCTTTGATCTGCTTCCTGTCTATGCAAGAAGGCAAGATCTGAAATCTTC
AATCTATTCCACTGTCGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACA
GG
Found at i:4047 original size:8 final size:8
Alignment explanation
Indices: 4034--4062 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4024 AGCCTCTCCA
4034 TTTTTCTC
1 TTTTTCTC
4042 TTTTTCTC
1 TTTTTCTC
4050 TTTTTCTC
1 TTTTTCTC
4058 TTTTT
1 TTTTT
4063 ATTTTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTCTC
Found at i:4070 original size:16 final size:16
Alignment explanation
Indices: 4034--4069 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4024 AGCCTCTCCA
*
4034 TTTTTCTCTTTTTCTC
1 TTTTTCTCTTTTTATC
4050 TTTTTCTCTTTTTAT-
1 TTTTTCTCTTTTTATC
4065 TTTTT
1 TTTTT
4070 TGGACTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTCTTTTTATC
Done.