Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold915
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: 28867
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Found at i:1185 original size:2 final size:2
Alignment explanation
Indices: 1178--1203 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1168 TAATATGGGC
1178 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
1204 GTTTTCGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3162 original size:2 final size:2
Alignment explanation
Indices: 3155--3190 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3145 TCCTCACTTT
3155 TA TA TA TA 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 TA TA TA TA
3191 AAAGTAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8884 original size:153 final size:155
Alignment explanation
Indices: 8604--8902 Score: 379
Period size: 153 Copynumber: 1.9 Consensus size: 155
8594 GTTGAGGGAA
* *
8604 GCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * * *
8669 TTCCTTAGCCTACCAACTAGGCTTGTTGATAGCTCGCTGTCCTAGTCATCCTTTCTGTAACCTTT
66 TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
*
8734 ATTTTCACTCATTTCAGCGAAGGAG
131 ATTTTCACTCACTTCAGCGAAGGAG
* * * * **
8759 GCCAAGTGTCCTCTCCACATCCCTTCA-TTGTTTCT-TTTCTTTTTCATTTCTTTCCTTCACTCT
1 GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
* * * * *
8822 TTCATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCTGTAACCTT
66 TTCATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTT
*
8886 TATTTTCTCTCACTTCA
130 TATTTTCACTCACTTCA
8903 TTTCCTTCTT
Statistics
Matches: 122, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
152 2 0.02
153 88 0.72
154 7 0.06
155 25 0.20
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (155 bp):
GCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCT
TTCATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTT
ATTTTCACTCACTTCAGCGAAGGAG
Found at i:12798 original size:2 final size:2
Alignment explanation
Indices: 12791--12826 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12781 ATGTCTCACT
12791 TA TA TA TA 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 TA TA TA TA
12827 AAAGTAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15278 original size:21 final size:20
Alignment explanation
Indices: 15206--15279 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
15196 GAAAAGCTCT
*
15206 TAAATAATAAAGTAATTTAAACC
1 TAAATAA-AAA-TAATTTAAA-A
*
15229 TAAATAAAAATAA-ATAAAA
1 TAAATAAAAATAATTTAAAA
*
15248 CTAATTTAAAAATAACTTTAAAA
1 -TAA-ATAAAAATAA-TTTAAAA
15271 TAAATAAAA
1 TAAATAAAA
15280 TCTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.17
21 17 0.40
22 6 0.14
23 12 0.29
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAATAAAAATAATTTAAAA
Found at i:18524 original size:154 final size:155
Alignment explanation
Indices: 18243--18539 Score: 373
Period size: 154 Copynumber: 1.9 Consensus size: 155
18233 GAGGGAAGCT
* *
18243 AAGTGTCCTCTCCACCTCCCTACATTTTTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
1 AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
* * * * * *
18308 CTTAGCCTACCAACTAGGCTTGTTGATAGCTCGCTGTCCTAGTCATCCTTTCTGTAACCTTTATT
66 ATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTATT
*
18373 TTCACTCATTTCAGCGAAGGAGGCC
131 TTCACTCACTTCAGCGAAGGAGGCC
* * * * * **
18398 AAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCTTCACTCTTTC
1 AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
* * * * *
18462 ATTAG-CTAACCAACTAGCCTTATTGATCGTTTACTATCTTGGTCATCCTTCCTGTAACCTTTAT
66 ATTAGCCT-ACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTAT
*
18526 TTTCTCTCACTTCA
130 TTTCACTCACTTCA
18540 TTTCCTTCTT
Statistics
Matches: 119, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
153 2 0.02
154 95 0.80
155 22 0.18
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.43
Consensus pattern (155 bp):
AAGTGTCCTCTCCACATCCCTACATTTGTTTCTGTTTCTTTTCCACTTCTCTCCCCCACTCTTTC
ATTAGCCTACCAACTAGCCTTATTGATAGCTCACTATCCTAGTCATCCTTCCTGTAACCTTTATT
TTCACTCACTTCAGCGAAGGAGGCC
Found at i:20489 original size:2 final size:2
Alignment explanation
Indices: 20482--20523 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20472 TAATATGGGC
*
20482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT
20524 GTTTTCGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22481 original size:2 final size:2
Alignment explanation
Indices: 22474--22505 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22464 ATGTCTCACT
22474 TA TA 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 TA TA
22506 AAAGTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28165 original size:153 final size:153
Alignment explanation
Indices: 27861--28165 Score: 362
Period size: 153 Copynumber: 2.0 Consensus size: 153
27851 CATCATCGTT
* *
27861 GAAGGAAGCCAAGTGTCCTCTCCACCTCCCTACATTTTTTTCTATTTCTTTTCCACTTCTTTCCC
1 GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTTTCCC
* ** * * * * * *
27926 CACTCTTTCCTTAGCCTACCAACTAGGCTTGTTGATAGCTCCTGTCCTAGTCATCCTTTCTGTAA
66 CACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAGCTACTATCCTAGTCATCCTTCCTGTAA
* *
27991 CCTTTATTTTCACTCATTTCATC
131 CCTTTAGTTTCACTCACTTCATC
* * * * *
28014 GAAGGAGGCCAAGTGTCCTCTCCACATCCCTTCA-TTGTTTCTTTTTCTTTTTCATTTCTTTCCG
1 GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTTTCC-
* * * * *
28078 TCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATCGTTTACTATCTTGGTCATCCTTCCTGT
65 CCACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAG-CTACTATCCTAGTCATCCTTCCTGT
*
28143 AACCTTT-GTTTCTCTCACTTCAT
129 AACCTTTAGTTTCACTCACTTCAT
28166 TCCCTTTTTT
Statistics
Matches: 126, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
152 25 0.20
153 75 0.60
154 26 0.21
ACGTcount: A:0.18, C:0.30, G:0.10, T:0.41
Consensus pattern (153 bp):
GAAGGAAGCCAAGTGTCCTCTCCACATCCCTACATTTGTTTCTATTTCTTTTCCACTTCTTTCCC
CACTCTTTCATTAGCAAACCAACTAGCCTTATCGATAGCTACTATCCTAGTCATCCTTCCTGTAA
CCTTTAGTTTCACTCACTTCATC
Done.