Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold987
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: 13163
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Found at i:2145 original size:12 final size:12
Alignment explanation
Indices: 2128--2154 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2118 TCTTCCTCTA
2128 TCTATTTCTTTC
1 TCTATTTCTTTC
2140 TCTATTTCTTTC
1 TCTATTTCTTTC
2152 TCT
1 TCT
2155 CTATTCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTATTTCTTTC
Found at i:2455 original size:40 final size:40
Alignment explanation
Indices: 2400--2505 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
2390 CTAGAACCTT
* * *
2400 CCACATTATTCTAGAACGTTCTAGAATCTTCCAGAGCCTC
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
*
2440 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTT
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
* *
2480 CCACGATATTCTAGAACATTCCAGAA
1 CCACAATATTCTAGAACATTCTAGAA
2506 CATTCTAGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (40 bp):
CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
Found at i:2500 original size:10 final size:10
Alignment explanation
Indices: 2487--2520 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2477 CTTCCACGAT
2487 ATTCTAGAAC
1 ATTCTAGAAC
*
2497 ATTCCAGAAC
1 ATTCTAGAAC
2507 ATTCTAGAAC
1 ATTCTAGAAC
2517 ATTC
1 ATTC
2521 CAAAGTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:2522 original size:40 final size:39
Alignment explanation
Indices: 2392--2522 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
2382 ATAAAGTTCT
*
2392 AGAACCTTCCACATTATTCTAGAACGTTCTAGAATCTTCC
1 AGAACCTTCCACA-TATTCTAGAACATTCTAGAATCTTCC
* *
2432 AGAGCCTCCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCAC-ATATTCTAGAACATTCTAGAATCTTCC
* *
2472 A-AAGCCTTCCACGATATTCTAGAACATTCCAGAA-CATTCT
1 AGAA-CCTTCCAC-ATATTCTAGAACATTCTAGAATC-TTCC
*
2512 AGAACATTCCA
1 AGAACCTTCCA
2523 AAGTGTTCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
39 2 0.03
40 73 0.94
41 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (39 bp):
AGAACCTTCCACATATTCTAGAACATTCTAGAATCTTCC
Found at i:5850 original size:12 final size:12
Alignment explanation
Indices: 5802--5860 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
5792 AGGCGCAAGC
5802 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
5814 TCACCTTTCT-TA
1 TC-TCTTTCTCTA
5826 -C-CTTTCCCTCTA
1 TCTCTTT--CTCTA
5838 TCTCTTTCTCTA
1 TCTCTTTCTCTA
*
5850 TATCTTTCTCT
1 TCTCTTTCTCT
5861 CTATTCCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 4 0.10
11 3 0.08
12 21 0.54
13 7 0.18
14 4 0.10
ACGTcount: A:0.10, C:0.36, G:0.00, T:0.54
Consensus pattern (12 bp):
TCTCTTTCTCTA
Found at i:5876 original size:36 final size:35
Alignment explanation
Indices: 5802--5878 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 35
5792 AGGCGCAAGC
*
5802 TCTCTTTCTCTATCACCTTTCTTACCTTTCCCTCTA
1 TCTCTTTCTCTATCACCTTTCTTA-CTTTCCCTATA
*
5838 TCTCTTTCTCTAT-ATCTTTCTCT-CTATTCCTCTATA
1 TCTCTTTCTCTATCACCTTTCT-TACT-TTCC-CTATA
5874 TCTCT
1 TCTCT
5879 CTCAAATGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
34 2 0.06
35 11 0.31
36 23 0.64
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (35 bp):
TCTCTTTCTCTATCACCTTTCTTACTTTCCCTATA
Found at i:6161 original size:40 final size:40
Alignment explanation
Indices: 6106--6211 Score: 158
Period size: 40 Copynumber: 2.6 Consensus size: 40
6096 CTAGAACCTT
* * *
6106 CCACATTATTCTAGAACGTTCTAGAATCTTCCAGAGCCTC
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
*
6146 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTT
1 CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
* *
6186 CCACGATATTCTAGAACATTCCAGAA
1 CCACAATATTCTAGAACATTCTAGAA
6212 CATTCTAGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (40 bp):
CCACAATATTCTAGAACATTCTAGAATCTTCCAAAGCCTC
Found at i:6206 original size:10 final size:10
Alignment explanation
Indices: 6193--6226 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
6183 CTTCCACGAT
6193 ATTCTAGAAC
1 ATTCTAGAAC
*
6203 ATTCCAGAAC
1 ATTCTAGAAC
6213 ATTCTAGAAC
1 ATTCTAGAAC
6223 ATTC
1 ATTC
6227 CAAAGTGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:6228 original size:40 final size:39
Alignment explanation
Indices: 6098--6228 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
6088 ATAAAGTTCT
*
6098 AGAACCTTCCACATTATTCTAGAACGTTCTAGAATCTTCC
1 AGAACCTTCCACA-TATTCTAGAACATTCTAGAATCTTCC
* *
6138 AGAGCCTCCCACAATATTCTAGAACATTCTAGAATCTTCC
1 AGAACCTTCCAC-ATATTCTAGAACATTCTAGAATCTTCC
* *
6178 A-AAGCCTTCCACGATATTCTAGAACATTCCAGAA-CATTCT
1 AGAA-CCTTCCAC-ATATTCTAGAACATTCTAGAATC-TTCC
*
6218 AGAACATTCCA
1 AGAACCTTCCA
6229 AAGTGTTCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
39 2 0.03
40 73 0.94
41 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (39 bp):
AGAACCTTCCACATATTCTAGAACATTCTAGAATCTTCC
Done.